diff --git "a/data/dataset_Bioengineering.csv" "b/data/dataset_Bioengineering.csv" new file mode 100644--- /dev/null +++ "b/data/dataset_Bioengineering.csv" @@ -0,0 +1,10792 @@ +"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language" +"Bioengineering","telatin/seqfu2","screenshots.md",".md","2336","97","# Seqfu splash screens + +## count + +![`seqfu count --help`](docs/img/screenshot-count.png ""SeqFu count"") + +## stats + +![`seqfu stats --help`](docs/img/screenshot-stats.png ""SeqFu stats"") + +## derep + +![`seqfu derep --help`](docs/img/screenshot-derep.png ""SeqFu derep"") + +## interleave + +![`seqfu interleave --help`](docs/img/screenshot-interleave.png ""SeqFu interleave"") + +## deinterleave + +![`seqfu deinterleave --help`](docs/img/screenshot-deinterleave.png ""SeqFu deinterleave"") + +## metadata + +![`seqfu metadata --help`](docs/img/screenshot-metadata.png ""SeqFu metadata"") + +## cat + +![`seqfu cat --help`](docs/img/screenshot-cat.png ""SeqFu cat"") + +## grep + +![`seqfu grep --help`](docs/img/screenshot-grep.png ""SeqFu grep"") + +## head + +![`seqfu head --help`](docs/img/screenshot-head.png ""SeqFu head"") + +## tail + +![`seqfu tail --help`](docs/img/screenshot-tail.png ""SeqFu tail"") + +## view + +![`seqfu view --help`](docs/img/screenshot-view.png ""SeqFu view"") +![`seqfu view data/primers/small.fq -o CCTACGGGAG -r ATGAGCGTCTCG`](docs/img/screenshot-view-example.png ""SeqFu view example"") + +seqfu view data/qualities.fq + +![`seqfu view data/qualities.fq`](docs/img/screenshot-view-qual.png ""SeqFu view qualities"") + +seqfu view --ascii data/qualities.fq + +![`seqfu view --ascii data/qualities.fq`](docs/img/screenshot-view-qual-ascii.png ""SeqFu view qualities"") + +seqfu view --qual-chars data/qualities.fq +![`seqfu view --qual-chars data/qualities.fq`](docs/img/screenshot-view-raw.png ""SeqFu view encoded quality"") + +## rc + +![`seqfu rc --help`](docs/img/screenshot-rc.png ""SeqFu rc"") + +## tab + +![`seqfu tab --help`](docs/img/screenshot-tab.png ""SeqFu tab"") + +## lanes + +![`seqfu lanes --help`](docs/img/screenshot-lanes.png ""SeqFu lanes"") + +## rotate + +![`seqfu rotate --help`](docs/img/screenshot-rotate.png ""SeqFu rotate"") + +## fu-orf + +![`fu-orf --help`](docs/img/screenshot-fu-orf.png ""SeqFu fu-orf"") + +## fu-nanotags + +![`fu-nanotags --help`](docs/img/screenshot-fu-nanotags.png ""SeqFu fu-nanotags"") + + +## fu-split + +![`pwd && find .. -name ""msa.*""`](docs/img/screenshot-ls.png ""Find MSA"") + +## fu-split + +![`fu-split --help`](docs/img/screenshot-fu-split.png ""SeqFu split"") + +## fu-msa + +![`fu-msa ./data/msa.fa --screenshot`](docs/img/screenshot-fu-msa-1.png ""SeqFu MSA viewer"") + +![`fu-msa ./data/msa.faa --screenshot`](docs/img/screenshot-fu-msa-2.png ""SeqFu MSA viewer"") +","Markdown" +"Bioengineering","telatin/seqfu2","re/gettable.R",".R","654","30","#!/usr/bin/env RScript + +url = ""https://en.wikipedia.org/wiki/List_of_restriction_enzyme_cutting_sites:_Ba-Bc#Whole_list_navigation"" + +args <- commandArgs(TRUE) +if (length(args) != 2) { + stop(""Missing argument: URL OutputFile\n"") +} +url <- args[[1]] +output <- args[[2]] + +library(tidyverse) +library(rvest) + +html = read_html(url) + + +tables = html %>% + html_nodes(css = ""table"") + +filt = tables %>% + html_nodes(css = ""sortable"") %>% + html_table(fill = TRUE) + +View(tables) +table <- tables[ -c(2:3) ] +colnames(table) <- c(""enzyme"", ""source"", ""seq"", ""cut"", ""isoschizomers"") +table$enzyme <- sub(""\\[.+\\]"", """", table$enzyme) +write.csv(table, output) +","R" +"Bioengineering","telatin/seqfu2","re/Ba-Bc.md",".md","10857","59","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:---------|:--------------------------------|:-----------------------|------:|:------------------------------------------------------------------------------------------------------| +| Bac36I | Bacillus alcalophilus 36 | GGNCC | 1 | AspS9I, AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV | +| BalI | Brevibacterium albidum | TGGCCA | 3 | | +| Bal228I | Bacillus alcalophilus 228 | GGNCC | 1 | AspS9I, AvcI, BavAII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | +| BamHI | Bacillus amyloliquefaciens H | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, Bce751I, Bsp98I, Bsp4009I, BspAAIII, CelI, Nsp29132II, NspSAIV, SolI, SurI | +| BamNII | Bacillus amyloliquefaciens N | GGWCC | 1 | BcuAI, BsrAI, CauI, EagMI, FdiI, HgiCII, HgiJI, SinI | +| BanI | Bacillus aneurinolyticus | GGYRCC | 1 | AccB1I, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BanII | Bacillus aneurinolyticus | GRGCYC | 5 | | +| BanIII | Bacillus aneurinolyticus | ATCGAT | 2 | AagI, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | +| BanAI | Bacillus anthracis | GGCC | 2 | | +| BauI | Bacillus aquaemaris RFL1 | CACGAG | 1 | | +| BavI | Bacillus alvei | CAGCTG | 3 | | +| BavAI | Bacillus alvei A | CAGCTG | 3 | | +| BavAII | Bacillus alvei A | GGNCC | 1 | AspS9I, AvcI, BavBII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | +| BavBI | Bacillus alvei B | CAGCTG | 3 | | +| BavBII | Bacillus alvei B | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, Bsu54I, FmuI, Pde12I | +| BavCI | Bacillus alvei C | ATCGAT | 2 | AagI, BanIII, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | +| BbeI | Bifidobacterium breve YIT4006 | GGCGCC | 5 | | +| BbiII | Bifidobacterium bifidum YIT4007 | GRCGYC | 2 | AcyI, AhaII, BbiII, HgiHII, Hin1I, Hsp92I, Msp17I, PamII | +| Bbi24I | Bifidobacterium bifidum S-24 | ACGCGT | 1 | | +| BbrI | Bordetella bronchiseptica 4994 | AAGCTT | 1 | | +| Bbr7I | Bacillus brevis 7 | GAAGAC | 9 | | +| BbrPI | Bacillus brevis | CACGTG | 3 | AcvI, BcoAI, Eco72I, PmaCI, PmlI, PspCI | +| BbsI | Bacillus laterosporus | GAAGAC | 8 | | +| BbuI | Bacillus circulans | GCATGC | 5 | | +| BbvI | Bacillus brevis | GCAGC | 8 | AlwXI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BbvII | Bacillus brevis 80 | GAAGAC | 8 | | +| Bbv12I | Bacillus brevis 12 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | +| Bbv16II | Bacillus brevis 16 | GAAGAC | 8 | | +| BbvAII | Bacillus brevis A | ATCGAT | 2 | BavCI, Bci29I, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BbvAIII | Bacillus brevis A | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Bsu23I, Kpn2I | +| BbvBI | Bacillus brevis B | GGYRCC | 1 | BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BbvCI | Bacillus brevis | CCTCAGC | 2 | AbeI | +| Bca77I | Bacillus caldolyticus | WCCGGW | 1 | | +| BccI | Bacteroides caccae | CCATC | 9 | | +| Bce22I | Bacillus cereus 22 | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, FmuI, Pde12I | +| Bce83I | Bacillus cereus 83 | CTTGAG | 12 | | +| Bce243I | Bacillus cereus | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| Bce751I | Bacillus cereus 751 | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, Bsp4009I, BstI, NspSAIV, Pfl8I | +| BceAI | Bacillus cereus 1315 | ACGGC | 9 | | +| BceBI | Bacillus cereus 1323 | CGCG | 2 | AccII, Bsh1236I, BtkI, Csp68KVI, FalII, FauBII, FnuDII, SelI, ThaI | +| BcefI | Bacillus cereus fluorescens | ACGGC | 10 | | +| Bci29I | Bacillus circulans 29 | ATCGAT | 2 | BavCI, BciBI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BciBI | Bacillus circulans B | ATCGAT | 2 | BavCI, BcmI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BciBII | Bacillus circulans B | CCWGG | 2 | AjnI, ApyI, BptI, Bst1I, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | +| BciVI | Bacillus circulans | GTATCC | 10 | BfuI | +| BclI | Bacillus caldolyticus | TGATCA | 1 | AbaI, BsiQI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | +| BcmI | Bacillus sp. | ATCGAT | 2 | BsuTUI, Bsu15I, BavCI, Bli86I, BspZEI, Rme21I, BseCI, BdiI | +| BcnI | Bacillus centrosporus RFL1 | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, Eco1831I, HgiS22I,Kpn49kII, NciI | +| BcoI | Bacillus coagulans SM 1 | CYCGRG | 1 | Ama87I, AquI, BsoBI, BstSI, Eco88I, NspSAI, OfoI, PunAI | +| Bco5I | Bacillus coagulans 5 | CTCTTC | 7 | | +| Bco27I | Bacillus coagulans 27 | CCGG | 1 | | +| Bco116I | Bacillus coagulans 116 | CTCTTC | 7 | | +| Bco118I | Bacillus coagulans 118 | RCCGGY | 1 | | +| BcoAI | Bacillus coagulans AUCM B-732 | CACGTG | 3 | AcvI, BbrPI, Eco72I, PmaCI, PmlI, PspCI | +| BcoKI | Bacillus coagulans | CTCTTC | 7 | | +| BcuI | Bacillus coagulans Vs 29-022 | ACTAGT | 1 | AhII, AclNI, SpeI | +| BcuAI | Bacillus cereus BKM B-814 | GGWCC | 1 | BamNxI, BsrAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI |","Markdown" +"Bioengineering","telatin/seqfu2","re/E-F.md",".md","16628","109","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:---------|:-----------------------------------|:-----------------------|------:|:-------------------------------------------------------------------| +| EacI | Eubacterium acidaminophilum | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI, BstH9I,  Bst31TI, Bth617I, Ral8I | +| EaeI | Enterobacter aerogenes | YGGCCR | 1 | | +| Eae46I | Enterobacter aerogenes 46 | CCGCGG | 4 | | +| EaeAI | Enterobacter aerogenes | CCCGGG | 1 | AhyI, Cfr9I, EclRI, PaeBI, PspAI, PspALI, XcyI, XmaI, XmaCI | +| EagI | Enterobacter agglomerans | CGGCCG | 1 | AaaI, BseX3I, BstZI, EclXI, Eco52I, SenPT16I, XmaIII | +| EagBI | Enterobacter agglomerans CBNU45 | CGATCG | 4 | Afa16RI, Afa22MI, BspCI, ErhB9I, NblI, Psu161I, RshI, XorII | +| EagMI | Enterobacter agglomerans M3 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | +| Eam1104I | Enterobacter amnigenus RFL1104 | CTCTTC | 7 | | +| EarI | Enterobacter aerogenes | CTCTTC | 7 | | +| EcaI | Enterobacter cloacae | GGTNACC | 1 | AcrII, Bse64I, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | +| EciI | Escherichia coli | GGCGGA | 11 | | +| Eci125I | Escherichia coli VKM-125 | GGTNACC | 1 | AcrII, AspAI, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | +| EclI | Enterobacter cloacae | CAGCTG | 3 | | +| Ecl136II | Enterobacter cloacae RFL136 | GAGCTC | 3 | | +| EclRI | Enterobacter cloacae R | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, Pac25I, PspAI, PspALI, XcyI, XmaI, XmaCI | +| EclXI | Enterobacter cloacae 590 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, Eco52I, SenPT16I, XmaIII | +| Ecl18kI | Enterobacter cloacae 18k | CCNGG | 1 | | +| Ecl37kI | Enterobacter cloacae 37k | CTGCAG | 5 | AjoI, AliAJI, Ecl2zI, PaePI, Psp23I, PstI, Sag16I, SflI, YenI | +| Ecl2zI | Enterobacter cloacae 2z | CTGCAG | 5 | AliAJI, Bsp63I, CfrA4I, PaePI, Pfl21I, PstI, SflI, Sst12I, YenI | +| Eco24I | Escherichia coli RFL24 | GRGCYC | 5 | | +| Eco31I | Escherichia coli RFL31 | GGTCTC | 7 | | +| Eco32I | Escherichia coli RFL32 | GATATC | 3 | | +| Eco47I | Escherichia coli RFL47 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | +| Eco47III | Escherichia coli RFL47 | AGCGCT | 3 | AfeI, AitI, Aor51H, FunI | +| Eco52I | Escherichia coli RFL52 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, SenPT16I, XmaIII | +| Eco56I | Escherichia coli RFL56 | GCCGGC | 1 | | +| Eco57I | Escherichia coli RFL57 | CTGAAG | 13 | AcuI, BspKT5I | +| Eco64I | Escherichia coli RFL64 | GGYRCC | 1 | BanI, BbvBI, BspT107I, BshNI, HgiCI, HgiHI, MspB4I, PfaAI | +| Eco72I | Escherichia coli RFL72 | CACGTG | 3 | AcvI, BcoAI, BbrPI, PmaCI, PmlI, PspCI | +| Eco78I | Escherichia coli RFL78 | GGCGCC | 3 | | +| Eco81I | Escherichia coli RFL81 | CCTNAGG | 2 | AxyI, Bse21I, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Eco88I | Escherichia coli RFL88 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BstSI, Eco27kI, NspSAI, PlaAI, PunAI | +| Eco91I | Escherichia coli RFL91 | GGTNACC | 1 | Bse64I, BstEII, BstPI, BstT9I, BstT10I, EcaI, Eci125I, NspSAII | +| Eco105I | Escherichia coli RFL105 | TACGTA | 3 | | +| Eco130I | Escherichia coli RFL130 | CCWWGG | 1 | | +| Eco147I | Escherichia coli RFL147 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | +| Eco255I | Escherichia coli RFL255 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, RflFII, ScaI, ZrmI | +| Eco1831I | Escherichia coli RFL1831 | CCSGG | 1 | AhaI, AseII, AsuC2I, BcnI,  BpuMI, CauII, EcoHI, HgiS22I | +| EcoA4I | Escherichia coli A4 | GGTCTC | 7 | | +| EcoHI | Escherichia coli HI | CCSGG | 1 | AsuC2I, BcnI, BpuMI, CauII, EcoHI, HgiS22I, Kpn49kII, NciI | +| EcoHK31I | Escherichia coli HK31 | YGGCCR | 1 | | +| EcoICRI | Escherichia coli 2bT | GAGCTC | 3 | | +| Eco75KI | Escherichia coli BKM | GRGCYC | 5 | | +| Eco57MI | Escherichia coli RFL57M | CTGRAG | 13 | | +| EcoO44I | Escherichia coli O44 Hiromi | GGTCTC | 7 | | +| EcoO65I | Escherichia coli K11a | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstPI, BstT9I, EcaI, Eco91I, EcoO128I | +| EcoO109I | Escherichia coli H709c | RGGNCCY | 2 | | +| EcoO128I | Escherichia coli O128Ly3 | GGTNACC | 1 | AspAI, Bse64I, BstEII, BstT9I, EcaI, EcoO65I, NspSAII, PspEI | +| EcoP15I | Escherichia coli P15 | CAGCAG | 11 | | +| EcoRI | Escherichia coli RY13 | GAATTC | 1 | | +| EcoRII | Escherichia coli R245 | CCWGG | 1 | ApaORI, BseBI, BspNI, BstNI, BstOI, Bst2UI, MvaI, SspAI, ZanI | +| EcoRV | Escherichia coli J62 pLG74 | GATATC | 3 | | +| EcoT14I | Escherichia coli TB14 | CCWWGG | 1 | | +| EcoT22I | Escherichia coli TB22 | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SepI, SspD5II | +| EcoT38I | Escherichia coli TH38 | GRGCYC | 5 | | +| EcoVIII | Escherichia coli E1585-68 | AAGCTT | 1 | | +| Eco13kI | Escherichia coli 13k | CCNGG | 1 | | +| Eco21kI | Escherichia coli 21k | CCNGG | 1 | | +| Eco27kI | Escherichia coli 27 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, OfoI, PunAI | +| Eco29kI | Escherichia coli | CCGCGG | 4 | | +| Eco53kI | Escherichia coli 53k | GAGCTC | 3 | | +| Eco137kI | Escherichia coli 137k | CCNGG | 1 | | +| EgeI | Enterobacter gergoviae NA | GGCGCC | 3 | | +| EheI | Erwinia herbicola 9/5 | GGCGCC | 3 | | +| ErhI | Erwinia rhaponici B9 | CCWWGG | 1 | | +| ErhB9I | Erwinia rhaponici B9 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, NblI, Ple19I, Psu161I, RshI, XorII | +| ErhB9II | Erwinia rhaponici B9 | CCWWGG | 1 | | +| ErpI | Erwinia rhaponici | GGWCC | 1 | Bme18I, BthAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | +| EsaBC3I | Environmental sample BC3 | TCGA | 2 | | +| EsaBC4I | Environmental sample BC4 | GGCC | 2 | | +| EspI | Eucapsis sp. | GCTNAGC | 2 | | +| Esp3I | Erwinia sp. RFL3 | CGTCTC | 7 | | +| Esp4I | Erwinia sp. RFL4 | CTTAAG | 1 | | +| FalII | Flavobacterium aquatile Ob10 | CGCG | 2 | BepI, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, FalII, SelI, ThaI | +| FaqI | Flavobacterium aquatile RFL1 | GGGAC | 9 | | +| FatI | Flavobacterium aquatile NL3 | CATG | 1 | | +| FauI | Flavobacterium aquatile | CCCGC | 9 | | +| FauBII | Flavobacterium aureus B | CGCG | 2 | Bpu95I, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, Csp68KVI, SelI, ThaI | +| FauNDI | Flavobacterium aquatile ND | CATATG | 2 | | +| FbaI | Flavobacterium balustinum | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, Ksp22I,  ParI | +| FblI | Flavobacterium balustinum | GTMKAC | 2 | AccI, XmiI | +| FbrI | Flavobacterium breve | GCNGC | 2 | | +| FdiI | Fremyella diplosiphon | GGWCC | 1 | Bme18I, BthAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | +| FdiII | Fremyella diplosiphon | TGCGCA | 3 | Acc16I, AosI, AviII, FspI, MstI, NsbI, PamI, Pun14627I | +| FgoI | Fervidobacterium gondwanense AB39T | CTAG | 1 | | +| FmuI | Flavobacterium multivorum | GGNCC | 4 | FmuI AvcI, BavAII, Bce22I, Bsu54I, NspIV, Pde12I, UnbI | +| FnuAI | Fusobacterium nucleatum A | GANTC | 1 | | +| FnuCI | Fusobacterium nucleatum C | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuEI, MgoI, NphI, SauMI | +| FnuDI | Fusobacterium nucleatum D | GGCC | 2 | | +| FnuDII | Fusobacterium nucleatum D | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FnuDII, ThaI | +| FnuDIII | Fusobacterium nucleatum D | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, HhaI, Hin6I, HinP1I, HspAI, SciNI | +| FnuEI | Fusobacterium nucleatum E | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, Sau3AI | +| Fnu4HI | Fusobacterium nucleatum 4H | GCNGC | 2 | | +| FokI | Flavobacterium okeanokoites | GGATG | 8 | | +| FriOI | Flavobacterium sp. O9 | GRGCYC | 5 | | +| FseI | Frankia sp. Eu11b | GGCCGGCC | 6 | | +| FsiI | Frankia sp. | RAATTY | 1 | AcsI, ApoI,  CfaI, XapI | +| FspI | Fischerella sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, MstI, NsbI, PamI, Pun14627I | +| FspII | Fischerella sp. | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, Ssp1I, SviI | +| Fsp1604I | Flavobacterium sp. I 16-04 | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, SleI | +| FspAI | Flexibacter sp. TV-m21K | RTGCGCAY | 4 | | +| FspBI | Flavobacterium sp. RFLI | CTAG | 1 | | +| Fsp4HI | Flavobacterium sp. 4H | GCNGC | 2 | | +| FspMSI | Fischerella sp. | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, HgiBI, HgiEI, Kzo49I, SmuEI | +| FssI | Fibrobacter succinogenes S85 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Kzo49I, VpaK11AI | +| FunI | Fischerella uniformis | AGCGCT | 3 | AfeI, AitI, Aor51H, Eco47III | +| FunII | Fischerella uniformis | GAATTC | 1 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/T-Z.md",".md","10769","69","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:--------------|:----------------------------------|:-----------------------|------:|:-------------------------------------------------------------------| +| TaaI | Thermus aquaticus Vn 4-311 | ACNGT | 3 | | +| TaiI | Thermus aquaticus cs1-331 | ACGT | 4 | | +| TaqI | Thermus aquaticus | TCGA | 1 | | +| TaqII | Thermus aquaticus YTI | GACCGA | 11 | | +| Taq52I | Thermus aquaticus YS52 | GCWGC | 1 | AceI, ApeKI, SuiI, TseI | +| TaqXI | Thermus aquaticus | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, MvaI, SleI, SspAI | +| TasI | Thermus aquaticus Vn 4-211 | AATT | 1 | | +| TatI | Thermus aquaticus CBA1-331 | WGTACW | 1 | | +| TauI | Thermus aquaticus | GCSGC | 4 | | +| TelI | Tolypothrix elabens | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, Tth111I | +| TfiI | Thermus filiformis | GAWTC | 1 | | +| ThaI | Thermoplasma acidophilum | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FalII, FnuDII | +| TliI | Thermococcus litoralis | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, StrI, XhoI | +| Tru1I | Thermus ruber RFL1 | TTAA | 1 | | +| Tru9I | Thermus ruber 9 | TTAA | 1 | | +| Tru201I | Thermus ruber 201 | RGATCY | 1 | | +| TscI | Thermus sp. 491A | ACGT | 4 | | +| TseI | Thermus sp. 93170 | GCWGC | 1 | AceI, ApeKI, SuiI, Taq52I | +| Tsp1I | Thermus sp. 1 | ACTGG | 6 | | +| Tsp32I | Thermus sp. 32 | TCGA | 1 | | +| Tsp32II | Thermus sp. 32 | TCGA | 1 | | +| Tsp45I | Thermus sp. YS45 | GTSAC | 1 | | +| Tsp49I | Thermus sp. | ACGT | 4 | | +| Tsp509I | Thermus sp. | AATT | 1 | | +| TspBI | Thermophilic sp. | CCRYGG | 1 | | +| Tsp4CI | Thermus sp. 4C | ACNGT | 3 | | +| TspDTI | Thermus sp. DT | ATGAA | 10 | — None on May 2010 — | +| TspEI | Thermus sp. 1E | AATT | 1 | | +| TspGWI | Thermus sp. GW | ACGGA | 10 | | +| TspMI = UthSI | Unidentified thermophile | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, SmaI, XcyI, XmaI, XmaCI | +| TspRI | Thermus sp. R | CASTGNN | 7 | | +| Tth111I | Thermus thermophilus 111 | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, TelI | +| Tth111II | Thermus thermophilus 111 | CAARCA | 11 | | +| TthHB8I | Thermus thermophilus HB8 | TCGA | 1 | | +| Uba4009I | Unidentified bacterium A | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, RspLKII, SolI | +| Uba153AI | Unidentified bacterium 153A | CAGCTG | 3 | | +| UbaM39I | Unidentified bacterium M39 | CAGCTG | 3 | | +| UnbI | Unidentified bacterium #8 | GGNCC | 1 | AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV, UnbI | +| Uur960I | Ureaplasma urealyticum 960 | GCNGC | 2 | | +| Vha464I | Vibrio harveyi 464 | CTTAAG | 1 | | +| VneI | Vibrio nereis 18 | GTGCAC | 1 | Alw44I, ApaLI, SnoI | +| VpaK32I | Vibrio parahaemolyticus 4387-61 | GCTCTTC | 8 | | +| VpaK11AI | Vibrio parahaemolyticus 1743 | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11BI | +| VpaK11BI | Vibrio parahaemolyticus 1743-1 | GGWCC | 1 | BsrAI, CauI, EagMI, FdiI, HgiBI, HgiJI, SinI, VpaK11AI | +| VspI | Vibrio sp. 343 | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, Sru4DI | +| XapI | Xanthomonas ampelina Slo 51-021 | RAATTY | 1 | AcsI, ApoI,  CfaI, FsiI | +| XbaI | Xanthomonas badrii | TCTAGA | 1 | | +| XcaI | Xanthomonas campestris | GTATAC | 3 | | +| XceI | Xanthomonas campestris Ast 40-024 | RCATGY | 5 | | +| XciI | Xanthomonas citri | GTCGAC | 1 | | +| XcyI | Xanthomonas cyanopsidis 13D5 | CCCGGG | 1 | CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XmaI, XmaCI | +| XhoI | Xanthomonas holcicola | CTCGAG | 1 | AbrI, BluI, BssHI, PanI, Sau3239I, Sfr274I, TliI, XpaI | +| XhoII | Xanthomonas holcicola | RGATCY | 1 | | +| XmaI | Xanthomonas malvacearum | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, TspMI, XcyI, XmaCI | +| XmaIII | Xanthomonas malvacearum | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, SenPT16I | +| XmaCI | Xanthomonas malvacearum C | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, Pac25I, PspAI, TspMI, XcyI, XmaI | +| XmaJI | Xanthomonas maltophilia Jo 85-025 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, BspA2I | +| XmiI | Xanthomonas maltophilia Jo 21-021 | GTMKAC | 2 | AccI, FblI | +| XorII | Xanthomonas oryzae | CGATCG | 4 | Afa16RI, BspCI, EagBI, ErhB9I, MvrI, Ple19I, PvuI, RshI | +| XpaI | Xanthomonas papavericola | CTCGAG | 1 | BssHI, MavI, PanI, SauLPII, Sbi68I, Sol10179I, StrI, XhoI | +| XspI | Xanthomonas sp. YK1 | CTAG | 1 | | +| YenI | Yersinia enterocolitica 08 A2635 | CTGCAG | 5 | Asp713I, BsuBI, CfrA4I, Ecl37kI, Psp23I, PstI, SalPI, SflI, Sst12I | +| ZanI | Zymomonas anaerobia | CCWGG | 2 | ApaORI, BseBI, BspNI, BstNI, Bst2UI, CthII, EcoRII, MvaI, SspAI | +| ZhoI | Zymomonas holcicola | ATCGAT | 2 | BanIII, BbvAII, BscI, BspJI, ClaI, LcaI, PgaI, SpmI, Ssp27144I | +| ZraI | Zoogloea ramigera 11 | GACGTC | 3 | AatII, Ssp5230I | +| ZrmI | Zoogloea ramigera SCA | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ScaI | +| Zsp2I | Zoogloea sp. 2 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II |","Markdown" +"Bioengineering","telatin/seqfu2","re/enzyme_table.md",".md","256435","1301","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:--------------|:----------------------------------------|:-----------------------|------:|:------------------------------------------------------------------------------------------------------| +| Bac36I | Bacillus alcalophilus 36 | GGNCC | 1 | AspS9I, AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV | +| BalI | Brevibacterium albidum | TGGCCA | 3 | | +| Bal228I | Bacillus alcalophilus 228 | GGNCC | 1 | AspS9I, AvcI, BavAII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | +| BamHI | Bacillus amyloliquefaciens H | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, Bce751I, Bsp98I, Bsp4009I, BspAAIII, CelI, Nsp29132II, NspSAIV, SolI, SurI | +| BamNII | Bacillus amyloliquefaciens N | GGWCC | 1 | BcuAI, BsrAI, CauI, EagMI, FdiI, HgiCII, HgiJI, SinI | +| BanI | Bacillus aneurinolyticus | GGYRCC | 1 | AccB1I, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BanII | Bacillus aneurinolyticus | GRGCYC | 5 | | +| BanIII | Bacillus aneurinolyticus | ATCGAT | 2 | AagI, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | +| BanAI | Bacillus anthracis | GGCC | 2 | | +| BauI | Bacillus aquaemaris RFL1 | CACGAG | 1 | | +| BavI | Bacillus alvei | CAGCTG | 3 | | +| BavAI | Bacillus alvei A | CAGCTG | 3 | | +| BavAII | Bacillus alvei A | GGNCC | 1 | AspS9I, AvcI, BavBII, BshKI, Bsp1894I, Bsu54I, FmuI, NspIV | +| BavBI | Bacillus alvei B | CAGCTG | 3 | | +| BavBII | Bacillus alvei B | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, Bsu54I, FmuI, Pde12I | +| BavCI | Bacillus alvei C | ATCGAT | 2 | AagI, BanIII, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI, ClaI | +| BbeI | Bifidobacterium breve YIT4006 | GGCGCC | 5 | | +| BbiII | Bifidobacterium bifidum YIT4007 | GRCGYC | 2 | AcyI, AhaII, BbiII, HgiHII, Hin1I, Hsp92I, Msp17I, PamII | +| Bbi24I | Bifidobacterium bifidum S-24 | ACGCGT | 1 | | +| BbrI | Bordetella bronchiseptica 4994 | AAGCTT | 1 | | +| Bbr7I | Bacillus brevis 7 | GAAGAC | 9 | | +| BbrPI | Bacillus brevis | CACGTG | 3 | AcvI, BcoAI, Eco72I, PmaCI, PmlI, PspCI | +| BbsI | Bacillus laterosporus | GAAGAC | 8 | | +| BbuI | Bacillus circulans | GCATGC | 5 | | +| BbvI | Bacillus brevis | GCAGC | 8 | AlwXI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BbvII | Bacillus brevis 80 | GAAGAC | 8 | | +| Bbv12I | Bacillus brevis 12 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | +| Bbv16II | Bacillus brevis 16 | GAAGAC | 8 | | +| BbvAII | Bacillus brevis A | ATCGAT | 2 | BavCI, Bci29I, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BbvAIII | Bacillus brevis A | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Bsu23I, Kpn2I | +| BbvBI | Bacillus brevis B | GGYRCC | 1 | BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BbvCI | Bacillus brevis | CCTCAGC | 2 | AbeI | +| Bca77I | Bacillus caldolyticus | WCCGGW | 1 | | +| BccI | Bacteroides caccae | CCATC | 9 | | +| Bce22I | Bacillus cereus 22 | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, FmuI, Pde12I | +| Bce83I | Bacillus cereus 83 | CTTGAG | 12 | | +| Bce243I | Bacillus cereus | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| Bce751I | Bacillus cereus 751 | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, Bsp4009I, BstI, NspSAIV, Pfl8I | +| BceAI | Bacillus cereus 1315 | ACGGC | 9 | | +| BceBI | Bacillus cereus 1323 | CGCG | 2 | AccII, Bsh1236I, BtkI, Csp68KVI, FalII, FauBII, FnuDII, SelI, ThaI | +| BcefI | Bacillus cereus fluorescens | ACGGC | 10 | | +| Bci29I | Bacillus circulans 29 | ATCGAT | 2 | BavCI, BciBI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BciBI | Bacillus circulans B | ATCGAT | 2 | BavCI, BcmI, Bli86I, BseCI, BspZEI, Bsu15I, ClaI, Rme21I | +| BciBII | Bacillus circulans B | CCWGG | 2 | AjnI, ApyI, BptI, Bst1I, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | +| BciVI | Bacillus circulans | GTATCC | 10 | BfuI | +| BclI | Bacillus caldolyticus | TGATCA | 1 | AbaI, BsiQI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | +| BcmI | Bacillus sp. | ATCGAT | 2 | BsuTUI, Bsu15I, BavCI, Bli86I, BspZEI, Rme21I, BseCI, BdiI | +| BcnI | Bacillus centrosporus RFL1 | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, Eco1831I, HgiS22I,Kpn49kII, NciI | +| BcoI | Bacillus coagulans SM 1 | CYCGRG | 1 | Ama87I, AquI, BsoBI, BstSI, Eco88I, NspSAI, OfoI, PunAI | +| Bco5I | Bacillus coagulans 5 | CTCTTC | 7 | | +| Bco27I | Bacillus coagulans 27 | CCGG | 1 | | +| Bco116I | Bacillus coagulans 116 | CTCTTC | 7 | | +| Bco118I | Bacillus coagulans 118 | RCCGGY | 1 | | +| BcoAI | Bacillus coagulans AUCM B-732 | CACGTG | 3 | AcvI, BbrPI, Eco72I, PmaCI, PmlI, PspCI | +| BcoKI | Bacillus coagulans | CTCTTC | 7 | | +| BcuI | Bacillus coagulans Vs 29-022 | ACTAGT | 1 | AhII, AclNI, SpeI | +| BcuAI | Bacillus cereus BKM B-814 | GGWCC | 1 | BamNxI, BsrAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | +| BdiI | Brevibacterium divaricatum | ATCGAT | 2 | BavCI, Bci29I, Bli41I, Bli86I, BseCI, BsuTUI, Rme21I, SpmI | +| BdiSI | Bacteroides distasonis | CTRYAG | 1 | | +| BecAII | Brevibacterium sp. A | GGCC | 2 | | +| BepI | Brevibacterium epidermidis | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, BtkI, FalII, FauBII, ThaI | +| BetI | Brevibacterium acetyliticum | WCCGGW | 1 | | +| BfaI | Bacteroides fragilis | CTAG | 1 | | +| BfiI | Bacillus firmus S8120 | ACTGGG | 11 | BmrI | +| Bfi57I | Butyrivibrio fibrisolvens OB157 | GATC | 1 | Bsp105I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, SsiBI | +| Bfi89I | Butyrivibrio fibrisolvens OB189 | YGGCCR | 1 | | +| BfmI | Bacillus firmus S8-336 | CTRYAG | 1 | | +| BfrI | Bacteroides fragilis | CTTAAG | 1 | | +| BfrBI | Bacteroides fragilis BE3 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | +| BfuI | Bacillus firmus Auk 22-m21 | GTATCC | 10 | BciVI | +| BfuAI | Bacillus fusiformis | ACCTGC | 10 | Acc36I, BspMI, BveI | +| BfuCI | Bacillus fusiformis 1226 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, MkrAI, Sth368I | +| BglII | Bacillus globigii | AGATCT | 1 | | +| BimI | Brevibacterium immotum | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bim19I | Brevibacterium immotum 19 | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bim19II | Brevibacterium immotum 19 | GGCC | 2 | | +| BinI | Bifidobacterium infantis 659 | GGATC | 9 | AclWI, AlwI,  BsrWI, BspPI, BstH9I,  Bth617I, EacI | +| BlfI | Bacillus licheniformis | TCCGGA | 1 | AccIII, Aor13HI, BseAI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | +| Bli41I | Bacillus licheniformis 41 | ATCGAT | 2 | Bci29I, Bli86I, BseCI, BsiXI, BsuTUI, Rme21I, SpmI, Ssp27144I | +| Bli86I | Bacillus licheniformis 86 | ATCGAT | 2 | BliAI, Bli41I, BseDI, BsiXI, Rme21I, SpmI, Ssp27144I, ZhoI | +| Bli736I | Bacillus licheniformis 736 | GGTCTC | 7 | | +| BliAI | Bacillus licheniformis | ATCGAT | 2 | BliRI, Bli41I, BsiXI, BspDI, Rme21I, SpmI, Ssp27144I, ZhoI | +| BliHKI | Bacillus licheniformis HK | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| BliRI | Bacillus licheniformis | ATCGAT | 2 | BciBI, BdiI, Bli41I, BsiXI, BspDI, BspXI, LplI, SpmI, ZhoI | +| BlnI | Brevibacterium linens | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BspA2I, XmaJI | +| BloHI | Bifidobacterium longum E194b | RGATCY | 1 | | +| BloHII | Bifidobacterium longum E194b | CTGCAG | 5 | AjoI, Asp713I, BsuBI, CflI, CfuII, HalII, PstI, SalPI, SflI, Sst12I | +| BlpI | Bacillus lentus | GCTNAGC | 2 | | +| BluI | Brevibacterium luteum | CTCGAG | 1 | AbrI, BssHI, BstVI, PanI, Sau3239I, Sfr274I, TliI, XhoI | +| Bme12I | Bacillus megaterium 12 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, SsiBI | +| Bme18I | Bacillus megaterium 18 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | +| Bme142I | Bacillus megaterium 142 | RGCGCY | 3 | AccB2I,  BfoI, Bsp143II, BstH2I, HaeII, LpnI | +| Bme216I | Bacillus megaterium 216 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | +| Bme361I | Bacillus megaterium 361 | GGCC | 2 | | +| Bme585I | Bacillus mesentericus 585 | CCCGC | 9 | | +| Bme1390I | Bacillus megaterium RFL1390 | CCNGG | 2 | | +| Bme1580I | Bacillus megaterium 1580 | GKGCMC | 5 | | +| BmgBI | Bacillus megaterium | CACGTC | 3 | | +| BmrI | Bacillus megaterium | ACTGGG | 11 | BfiI | +| BmtI | Bacillus megaterium S2 | GCTAGC | 5 | AceII, AsuNHI,  BspOI, NheI, LlaG2I, PstNHI | +| BmyI | Bacillus mycoides | GDGCHC | 5 | AocII, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | +| BnaI | Bacillus natto B3364 | GGATCC | 1 | AccEBI, BamHI, Bce751I, BstI, CelI, OkrAI, Nsp29132II, Pfl8I, SolI | +| BpcI | Bacillus sphaericus | CTRYAG | 1 | | +| BpiI | Bacillus pumilus sw 4-3 | GAAGAC | 8 | | +| BpmI | Bacillus pumilus | CTGGAG | 12 | | +| BpoAI | Bacillus polymyxa | ATTAAT | 2 | AseI, AsnI, PshBI, Sru4DI, VspI | +| BptI | Bacillus pantothenticus | CCWGG | 2 | AjnI, BseBI, Bse16I, BstNI, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | +| BpuI | Bacillus pumilus AHU1387A | GRGCYC | 5 | | +| Bpu10I | Bacillus pumilus 10 | CCTNAGC | 2 | | +| Bpu14I | Bacillus pumilus 14 | TTCGAA | 2 | AcpI, AsuII, BsiCI, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bpu95I | Bacillus pumilus 95 | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | +| Bpu1102I | Bacillus pumilus RFL1102 | GCTNAGC | 2 | | +| BpuAI | Bacillus pumilus | GAAGAC | 8 | | +| BpuAmI | Bacillus pumilus | GAGCTC | 3 | | +| BpuB5I | Bacillus pumilus | CGTACG | 1 | | +| BpuDI | Bacillus pumilus 1117 | CCTNAGC | 2 | | +| BpuEI | Bacillus pumilus 2187a | CTTGAG | 12 | | +| BpuJI | Bacillus pumilus RFL1458 | CCCGT | 9 | — None on May 2010 — | +| BpuSI | Bacillus pumilus | GGGAC | 8 | | +| BsaI | Bacillus stearothermophilus 20241 | GGTCTC | 7 | Bso31I, BspTNI, Eco31I | +| Bsa29I | Bacillus sp. 29 | ATCGAT | 2 | AagI, BanIII, BavCI, BseCI, BspDI, Bsu15I, BsuTUI, ClaI, BbvAII | +| BsaAI | Bacillus stearothermophilus G668 | YACGTR | 3 | | +| BsaHI | Bacillus stearothermophilus CPW11 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BbiII, BstACI, HgiI, PamII | +| BsaJI | Bacillus stearothermophilus J695 | CCNNGG | 1 | | +| BsaMI | Bacillus stearothermophilus M293 | GAATGC | 7 | Asp26HI, Asp35HI, Asp36HI, Asp50HI, BsaMI, BsmI, Mva1269I | +| BsaOI | Bacillus stearothermophilus O-122 | CGRYCG | 4 | | +| BsaWI | Bacillus stearothermophilus W1718 | WCCGGW | 1 | | +| BscI | Bacillus sp. | ATCGAT | 2 | BanIII, BavCI, Bci29I, BdiI, Bli41I, BliAI, LplI, PgaI, SpmI | +| Bsc91I | Bacillus sp. | GAAGAC | 8 | | +| BscAI | Bacillus schlegelii S3 | GCATC | 9 | | +| BscBI | Bacillus sp. A11 | GGNNCC | 3 | AspNI,  BmiI, BspLI, NlaIV, PspN4I | +| BscCI | Bacillus sp. 2G | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI, Asp36HI, BsaMI, BscCI, PctI | +| BscFI | Bacillus sp. JY391 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, CviAI, Kzo9I, NlaII, SsiBI | +| Bse1I | Bacillus stearothermophilus 1 | ACTGG | 6 | | +| Bse15I | Bacillus sp. 15 | CYCGRG | 1 | Ama87I, AvaI, BcoI, BsoBI, BstSI, Eco88I, NspSAI, OfoI | +| Bse16I | Bacillus sp. 16 | CCWGG | 2 | AeuI, BseBI, BsiLI, BstNI, BstM6I, BthDI, BthEI, EcoRII, MvaI | +| Bse17I | Bacillus sp. 17 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | +| Bse21I | Bacillus sp. 21 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Bse24I | Bacillus sp. 24 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | +| Bse64I | Bacillus sp. 64 | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BstPI, EcaI, Eci125I, EcoO65I, NspSAII | +| Bse118I | Bacillus sp. 118 | RCCGGY | 1 | | +| Bse634I | Bacillus sp. 634 | RCCGGY | 1 | | +| BseAI | Bacillus sphaericus | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, Kpn2I | +| BseBI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, AorI, Bse17I, Bst1I, BstOI, Bst2UI, EcoRII, MvaI, SleI, ZanI | +| BseCI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BspDI, Bsu15I, BsuTUI, ClaI, LcaI | +| BseDI | Bacillus stearothermophilus RFL1434 | CCNNGG | 1 | | +| Bse3DI | Bacillus stearothermophilus 3D | GCAATG | 8 | | +| BseGI | Bacillus stearothermophilus Vs 34-031 | GGATG | 7 | | +| BseKI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BseMI | Bacillus stearothermophilus Isl 15-111 | GCAATG | 8 | | +| BseMII | Bacillus stearothermophilus Isl 15-111 | CTCAG | 10 | | +| BseNI | Bacillus sp. N | ACTGG | 6 | | +| BsePI | Bacillus stearothermophilus P6 | GCGCGC | 1 | | +| BseQI | Bacillus sp. Q | GGCC | 2 | | +| BseRI | Bacillus sp. R | GAGGAG | 11 | | +| BseSI | Bacillus stearothermophilus Jo-553 | GKGCMC | 5 | | +| BseT9I | Bacillus sp. T9 | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstT9I, EcaI, Eci125I, EcoO65I, NspSAII, PspEI | +| BseT10I | Bacillus sp. T10 | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT10I, BstPI, EcoO128I, EcoO65I, PspEI | +| BseXI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseKI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BseX3I | Bacillus stearothermophilus X3 | CGGCCG | 1 | AaaI, BstZI, EagI, EclXI, Eco52I, SenPT16I, XmaIII | +| BseYI | Bacillus sp. 2521 | CCCAGC | 1 | | +| BseZI | Bacillus sp. Z | CTCTTC | 7 | | +| BsgI | Bacillus sphaericus B922 | GTGCAG | 13 | | +| BshI | Bacillus sphaericus | GGCC | 2 | | +| Bsh45I | Bacillus sphaericus 45 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | +| Bsh1236I | Bacillus sphaericus RFL1236 | CGCG | 2 | AccII, BceBI, BspFNI, Bsp50I, Csp68KVI, FauBII, MvnI, SelI | +| Bsh1285I | Bacillus sphaericus RFL1285 | CGRYCG | 4 | | +| BshFI | Bacillus sphaericus | GGCC | 2 | | +| BshGI | Bacillus sphaericus | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, PspGI, SspAI | +| BshKI | Bacillus sphaericus | GGNCC | 1 | AspS9I, Bac36I, BavAII, Bsp1894I, BspBII, CcuI, MaeK81II, Pde12I | +| BshNI | Bacillus sphaericus TK-45 | GGYRCC | 1 | BanI, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BshTI | Bacillus sphaericus Jo22-024 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, CsiAI CspAI, PinAI | +| BsiI | Bacillus sphaericus | CACGAG | 1 | | +| BsiCI | Bacillus sp. | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, Csp45I, FspII, NspV, PpaAI, SfuI | +| BsiEI | Bacillus sp. | CGRYCG | 4 | | +| BsiHKAI | Bacillus stearothermophilus | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I,  Bsm6I, HgiAI, MspV281I | +| BsiHKCI | Bacillus sp. HKC | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | +| BsiKI | Bacillus sp. | GGTNACC | 1 | | +| BsiLI | Bacillus sp. | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, BstNI, Bst38I, Bst100I, EcoRII, MvaI | +| BsiMI | Bacillus sp. | TCCGGA | 1 | AccIII, BbvAIII, BlfI, Bsp13I, BspMII, Bsu23I, Kpn2I, PinBII | +| BsiQI | Bacillus sp. | TGATCA | 1 | AbaI, BclI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | +| BsiSI | Bacillus sp. | CCGG | 1 | | +| BsiWI | Bacillus sp. | CGTACG | 1 | | +| BsiXI | Bacillus sp. X | ATCGAT | 2 | BscI, BsiXI, Bsp106I, BspDI, Bsu15I, BsuTUI, ClaI, Rme21I | +| BsiZI | Bacillus sp. | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | +| BslFI | Bacillus stearothermophilus FI | GGGAC | 9 | | +| BsmI | Bacillus stearothermophilus NUB | GAATGC | 7 | Asp26HI, Asp36HI, Asp40HI, BmaHI, BscCI, Mva1269I, PctI | +| BsmAI | Bacillus stearothermophilus A664 | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsoMAI, BstMAI | +| BsmBI | Bacillus stearothermophilus B61 | CGTCTC | 7 | | +| BsmFI | Bacillus stearothermophilus F | GGGAC | 9 | | +| BsmSI | Bacillus stearothermophilus CP114 | CCWWGG | 1 | | +| Bso31I | Bacillus stearothermophilus E31 | GGTCTC | 7 | | +| BsoBI | Bacillus stearothermophilus JN2091 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | +| BsoCI | Bacillus stearothermophilus AU891 | GDGCHC | 5 | AocII, BmyI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | +| BsoFI | Bacillus stearothermophilus F66 | GCNGC | 2 | | +| BsoMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BstMAI | +| Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | +| Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | +| Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | +| Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | +| Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | +| Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | +| Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | +| Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | +| Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | +| Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | +| Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | +| Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | +| Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | +| Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | +| Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | +| Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | +| Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | +| Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | +| Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | +| Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | +| BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | +| Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | +| BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BspAAII | Bacillus sp. AA | TCTAGA | 1 | | +| BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | +| BspANI | Bacillus sp. AN | GGCC | 2 | | +| BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | +| BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | +| BspBRI | Bacillus sp. | GGCC | 2 | | +| BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | +| BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | +| BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | +| BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | +| BspD6I | Bacillus sp. D6 | GACTC | 9 | | +| BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | +| BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| BspHI | Bacillus sp. H3 | TCATGA | 1 | | +| BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | +| BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | +| BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | +| BspKI | Bacillus sp. K | GGCC | 2 | | +| BspKT5I | Bacillus sp. | CTGAAG | 13 | | +| BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | +| BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | +| BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | +| BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BspLAII | Bacillus sp. LA | TTCGAA | 2 | | +| BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | +| BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | +| BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | +| BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | +| BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | +| BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | +| BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | +| BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | +| BspM90I | Bacillus sp. M90 | GTATAC | 3 | | +| BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | +| BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | +| BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | +| BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | +| BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | +| BspRI | Bacillus sphaericus R | GGCC | 2 | | +| BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| BspST5I | Bacillus sp. ST5 | GCATC | 8 | | +| BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | +| BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | +| BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BspTNI | Bacillus sp. TN | GGTCTC | 7 | | +| BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | +| BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | +| BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | +| BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | +| BsrI | Bacillus stearothermophilus | ACTGG | 6 | | +| BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | +| BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | +| BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | +| BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | +| BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | +| BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | +| BssAI | Bacillus sp. | RCCGGY | 1 | | +| BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | +| BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | +| BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | +| BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | +| BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | +| BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | +| BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | +| BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | | +| Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | +| Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | +| Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | +| Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | +| Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | +| Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | +| Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | +| Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | +| Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | +| Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | +| Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | +| Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | +| Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | +| Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | +| Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | +| Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | +| Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | +| Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | +| Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | +| Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | +| BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | +| Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | +| BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BspAAII | Bacillus sp. AA | TCTAGA | 1 | | +| BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | +| BspANI | Bacillus sp. AN | GGCC | 2 | | +| BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | +| BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | +| BspBRI | Bacillus sp. | GGCC | 2 | | +| BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | +| BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | +| BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | +| BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | +| BspD6I | Bacillus sp. D6 | GACTC | 9 | | +| BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | +| BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| BspHI | Bacillus sp. H3 | TCATGA | 1 | | +| BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | +| BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | +| BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | +| BspKI | Bacillus sp. K | GGCC | 2 | | +| BspKT5I | Bacillus sp. | CTGAAG | 13 | | +| BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | +| BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | +| BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | +| BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BspLAII | Bacillus sp. LA | TTCGAA | 2 | | +| BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | +| BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | +| BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | +| BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | +| BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | +| BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | +| BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | +| BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | +| BspM90I | Bacillus sp. M90 | GTATAC | 3 | | +| BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | +| BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | +| BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | +| BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | +| BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | +| BspRI | Bacillus sphaericus R | GGCC | 2 | | +| BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| BspST5I | Bacillus sp. ST5 | GCATC | 8 | | +| BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | +| BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | +| BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BspTNI | Bacillus sp. TN | GGTCTC | 7 | | +| BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | +| BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | +| BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | +| BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | +| BsrI | Bacillus stearothermophilus | ACTGG | 6 | | +| BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | +| BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | +| BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | +| BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | +| BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | +| BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | +| BssAI | Bacillus sp. | RCCGGY | 1 | | +| BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | +| BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | +| BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | +| BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | +| BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | +| BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | +| BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | +| BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | | +| BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | +| Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | +| Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | +| Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | +| Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | +| Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | +| Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | +| Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | +| Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | +| Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | +| Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | +| Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | +| BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | +| BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | +| BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | +| Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | +| BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | +| BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | +| BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | +| BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | +| BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | +| Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | +| BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | +| BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | +| BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | +| BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | +| BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | +| BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | +| BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | +| BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | +| BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | +| BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | +| BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | +| BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | +| BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | +| BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | +| BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | +| BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | +| BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | +| BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | +| BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | +| BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | +| BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | +| BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | +| Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | +| BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | +| BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | +| BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | +| BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | +| BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstPZ418I | | GGATG | 8 | | +| BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | +| BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | +| BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | +| BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | +| BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | +| BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | +| BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | +| BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | +| BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | +| BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | +| Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | +| BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | +| BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | +| Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | +| BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | +| BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | +| BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | +| BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | +| BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | +| BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | +| BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | +| Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | +| Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | +| Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | +| Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | +| BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | +| BsuFI | Bacillus subtilis | CCGG | 1 | | +| BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | +| BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | +| BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | +| BteI | Brochothrix thermosphacter | GGCC | 2 | | +| BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | +| BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | +| BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | +| BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | +| BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | +| BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | +| BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | +| BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | +| BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | +| BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | +| BvuI | Bacillus vulgatis | GRGCYC | 5 | | +| BvuBI | Bacteroides vulgatus | CGTACG | 1 | | +| BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | +| Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | +| Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | +| Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | +| Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | +| Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | +| Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | +| Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | +| Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | +| Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | +| Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | +| Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | +| BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | +| BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | +| BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | +| Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | +| BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | +| BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | +| BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | +| BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | +| BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | +| Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | +| BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | +| BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | +| BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | +| BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | +| BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | +| BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | +| BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | +| BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | +| BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | +| BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | +| BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | +| BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | +| BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | +| BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | +| BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | +| BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | +| BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | +| BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | +| BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | +| BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | +| BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | +| BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | +| Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | +| BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | +| BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | +| BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | +| BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | +| BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstPZ418I | | GGATG | 8 | | +| BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | +| BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | +| BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | +| BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | +| BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | +| BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | +| BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | +| BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | +| BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | +| BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | +| Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | +| BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | +| BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | +| Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | +| BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | +| BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | +| BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | +| BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | +| BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | +| BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | +| BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | +| Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | +| Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | +| Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | +| Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | +| BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | +| BsuFI | Bacillus subtilis | CCGG | 1 | | +| BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | +| BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | +| BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | +| BteI | Brochothrix thermosphacter | GGCC | 2 | | +| BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | +| BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | +| BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | +| BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | +| BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | +| BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | +| BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | +| BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | +| BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | +| BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | +| BvuI | Bacillus vulgatis | GRGCYC | 5 | | +| BvuBI | Bacteroides vulgatus | CGTACG | 1 | | +| CacI | Clostridium acetobutylicum N1-4081 | GATC | 1 | | +| Cac8I | Clostridium acetobutylicum ABKn8 | GCNNGC | 3 | | +| CaiI | Comamonas acidovarans Iti19-021 | CAGNNNCTG | 6 | AlwNI | +| CauI | Chloroflexus aurantiacus | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | +| CauII | Chloroflexus aurantiacus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, Eco1831I, EcoHI, Kpn49kII, NciI | +| CauB3I | Chloroflexus aurantiacus B3 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BspEI, BspMII, Kpn2I, MroI, PtaI | +| CbiI | Clostridium bifermentans B-4 | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, Csp45I, LspI, NspV, SspRFI | +| CboI | Clostridium botulinum | CCGG | 1 | | +| CbrI | Citrobacter braakii 1146 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI | +| CciNI | Curtobacterium citreus | GCGGCCGC | 2 | | +| CcoI | Clostridium coccoides B-2 | GCCGGC | 3 | | +| CcrI | Caulobacter crescentus CB-13 | CTCGAG | 1 | | +| CcuI | Chroococcidiopsis cubana | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, PspPI | +| CcyI | Clostridium cylindrosporum | GATC | 1 | BfuCI, Bsp67I, Bst19II, CviAI, FnuCI, MboI, NmeCI, SauMI | +| CdiI | Citrobacter freundii RFL2 | CATCG | 4 | | +| CelI | Citrobacter freundii RFL6 | GGATCC | 1 | AliI, ApaCI, AsiI, BamHI, CelI, NspSAIV, RspLKII, SolI, Uba4009I | +| CelII | Coccochloris elabens 17a | GCTNAGC | 2 | | +| CeqI | Corynebacterium equi | GATATC | 3 | | +| CflI | Cellulomonas flavigena | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, PaePI, PstI, SalPI, Srl5DI, Sst12I | +| CfoI | Clostridium formicoaceticum | GCGC | 3 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, HinP1I, HsoI, HspAI, SciNI | +| CfrI | Citrobacter freundii RFL2 | YGGCCR | 1 | | +| Cfr6I | Citrobacter freundii RFL6 | CAGCTG | 3 | | +| Cfr9I | Citrobacter freundii | CCCGGG | 1 | AhyI, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | +| Cfr10I | Citrobacter freundii RFL10 | RCCGGY | 1 | | +| Cfr13I | Citrobacter freundii RFL13 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, FmuI, Nsp7121I, PspPI | +| Cfr42I | Citrobacter freundii RFL42 | CCGCGG | 4 | SacII, CscI, HgaI | +| CfrA4I | Citrobacter freundii A4 | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl2zI, PaePI, PstI, SalPI, Srl5DI, Sst12I | +| CfrBI | Citrobacter freundii 4111 | CCWWGG | 1 | | +| CfrJ4I | Citrobacter freundii J4 | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI | +| CfuI | Caulobacter fusiformis BC-25 | GATC | 2 | | +| CfuII | Caulobacter fusiformis BC-25 | CTGCAG | 5 | AjoI, AliAJI, CfuII, HalII, PaePI, Psp23I, PstI, SalPI, Srl5DI, YenI | +| ChaI | Corynebacterium halofytica | GATC | 4 | BfuCI, Bsp2095I, BspKT6I BtkII, FnuCI, MboI, NmeCI, SsiAI | +| ClaI | Caryophanon latum L | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI | +| CltI | Caryophanon latum | GGCC | 2 | | +| CpfI | Clostridium perfringens | GATC | 1 | AspMDI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NphI, SauMI | +| CpoI | Caseobacter polymorphus | CGGWCCG | 2 | | +| CscI | Calothrix scopulorum | CCGCGG | 4 | Cfr42I, SacII, HgaI | +| CsiAI | Corynebacterium sp. A | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CspAI, PinAI | +| CsiBI | Corynebacterium sp. B | GCGGCCGC | 2 | | +| CspI | Corynebacterium sp. | CGGWCCG | 2 | | +| Csp6I | Corynebacterium sp. RFL6 | GTAC | 1 | AfaI, CviQI, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| Csp45I | Clostridium sporogenes | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, FspII, LspI, NspV, SspRFI | +| CspAI | Corynebacterium sp. 301 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, PinAI | +| CspBI | Corynebacterium sp. B | GCGGCCGC | 2 | | +| Csp68KI | Cyanothece sp. BH68K | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, Kzo49I, SmuEI | +| Csp68KII | Cyanothece sp. BH68K | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, SviI | +| Csp68KIII | Cyanothece sp. BH68K | ATGCAT | 5 | BfrBI, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | +| Csp68KVI | Cyanothece sp. BH68K | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | +| CspKVI | Cyanothece sp. BH68K | CGCG | 2 | | +| CstI | Clostridium sticklandii | CTGCAG | 5 | AjoI, AliAJI, CfrA4I, HalII, MhaAI, Pfl21I, PstI, SflI, Srl5DI, YenI | +| CstMI | Corynebacterium striatum M82B | AAGGAG | 12 | — None on May 2010 — | +| CthII | Clostridium thermocellum | CCWGG | 2 | ApaORI, BseBI, Bse24I, Bst2UI, BstNI, BstM6I, EcoRII, MvaI | +| CviAI | Chlorella NC64A (PBCV-1) | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, SauMI | +| CviAII | Chlorella NC64A (PBCV-1) | CATG | 1 | | +| CviBI | Chlorella NC64A (NC-1A) | GANTC | 1 | | +| CviJI | Chlorella NC64A (IL-3A) | RGCY | 2 | | +| CviQI | Chlorella NC64A (NY-2A) | GTAC | 1 | AfaI, Csp6I, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| CviRI | Chlorella NC64A (XZ-6E) | TGCA | 2 | | +| CviRII | Chlorella NC64A (XZ-6E) | GTAC | 1 | AfaI, Csp6I, CviQI, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| CviTI | Chlorella NC64A (CA-1A) | RGCY | 2 | | +| CvnI | Chromatium vinosum | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| DdeI | Desulfovibrio desulfuricans | CTNAG | 1 | | +| DmaI | Deleya marina | CAGCTG | 3 | | +| DpaI | Deleya pacifica | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, Eco255I, RflFII, ScaI, ZrmI | +| DpnI | Diplococcus pneumoniae G41 | GATC | 2 | | +| DpnII | Diplococcus pneumoniae G41 | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CpfI, Kzo9I, NdeII, Sth368I | +| DraI | Deinococcus radiophilus | TTTAAA | 3 | AhaIII, PauAII, SruI | +| DraII | Deinococcus radiophilus | RGGNCCY | 2 | | +| DraIII | Deinococcus radiophilus | CACNNNGTG | 6 | AdeI, BstIZ316I | +| DsaI | Dactylococcopsis salina | CCRYGG | 1 | | +| DsaII | Dactylococcopsis salina | GGCC | 2 | | +| DsaIII | Dactylococcopsis salina | RGATCY | 1 | | +| DsaIV | Dactylococcopsis salina | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiEI, Kzo49I, SmuEI | +| DsaV | Dactylococcopsis salina | CCNGG | 1 | | +| EacI | Eubacterium acidaminophilum | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI, BstH9I,  Bst31TI, Bth617I, Ral8I | +| EaeI | Enterobacter aerogenes | YGGCCR | 1 | | +| Eae46I | Enterobacter aerogenes 46 | CCGCGG | 4 | | +| EaeAI | Enterobacter aerogenes | CCCGGG | 1 | AhyI, Cfr9I, EclRI, PaeBI, PspAI, PspALI, XcyI, XmaI, XmaCI | +| EagI | Enterobacter agglomerans | CGGCCG | 1 | AaaI, BseX3I, BstZI, EclXI, Eco52I, SenPT16I, XmaIII | +| EagBI | Enterobacter agglomerans CBNU45 | CGATCG | 4 | Afa16RI, Afa22MI, BspCI, ErhB9I, NblI, Psu161I, RshI, XorII | +| EagMI | Enterobacter agglomerans M3 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | +| Eam1104I | Enterobacter amnigenus RFL1104 | CTCTTC | 7 | | +| EarI | Enterobacter aerogenes | CTCTTC | 7 | | +| EcaI | Enterobacter cloacae | GGTNACC | 1 | AcrII, Bse64I, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | +| EciI | Escherichia coli | GGCGGA | 11 | | +| Eci125I | Escherichia coli VKM-125 | GGTNACC | 1 | AcrII, AspAI, BseT10I, BstEII, Eco91I, EcoO65I, EcoO128I | +| EclI | Enterobacter cloacae | CAGCTG | 3 | | +| Ecl136II | Enterobacter cloacae RFL136 | GAGCTC | 3 | | +| EclRI | Enterobacter cloacae R | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, Pac25I, PspAI, PspALI, XcyI, XmaI, XmaCI | +| EclXI | Enterobacter cloacae 590 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, Eco52I, SenPT16I, XmaIII | +| Ecl18kI | Enterobacter cloacae 18k | CCNGG | 1 | | +| Ecl37kI | Enterobacter cloacae 37k | CTGCAG | 5 | AjoI, AliAJI, Ecl2zI, PaePI, Psp23I, PstI, Sag16I, SflI, YenI | +| Ecl2zI | Enterobacter cloacae 2z | CTGCAG | 5 | AliAJI, Bsp63I, CfrA4I, PaePI, Pfl21I, PstI, SflI, Sst12I, YenI | +| Eco24I | Escherichia coli RFL24 | GRGCYC | 5 | | +| Eco31I | Escherichia coli RFL31 | GGTCTC | 7 | | +| Eco32I | Escherichia coli RFL32 | GATATC | 3 | | +| Eco47I | Escherichia coli RFL47 | GGWCC | 1 | Bme18I, BsrAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | +| Eco47III | Escherichia coli RFL47 | AGCGCT | 3 | AfeI, AitI, Aor51H, FunI | +| Eco52I | Escherichia coli RFL52 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, SenPT16I, XmaIII | +| Eco56I | Escherichia coli RFL56 | GCCGGC | 1 | | +| Eco57I | Escherichia coli RFL57 | CTGAAG | 13 | AcuI, BspKT5I | +| Eco64I | Escherichia coli RFL64 | GGYRCC | 1 | BanI, BbvBI, BspT107I, BshNI, HgiCI, HgiHI, MspB4I, PfaAI | +| Eco72I | Escherichia coli RFL72 | CACGTG | 3 | AcvI, BcoAI, BbrPI, PmaCI, PmlI, PspCI | +| Eco78I | Escherichia coli RFL78 | GGCGCC | 3 | | +| Eco81I | Escherichia coli RFL81 | CCTNAGG | 2 | AxyI, Bse21I, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Eco88I | Escherichia coli RFL88 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BstSI, Eco27kI, NspSAI, PlaAI, PunAI | +| Eco91I | Escherichia coli RFL91 | GGTNACC | 1 | Bse64I, BstEII, BstPI, BstT9I, BstT10I, EcaI, Eci125I, NspSAII | +| Eco105I | Escherichia coli RFL105 | TACGTA | 3 | | +| Eco130I | Escherichia coli RFL130 | CCWWGG | 1 | | +| Eco147I | Escherichia coli RFL147 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | +| Eco255I | Escherichia coli RFL255 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, RflFII, ScaI, ZrmI | +| Eco1831I | Escherichia coli RFL1831 | CCSGG | 1 | AhaI, AseII, AsuC2I, BcnI,  BpuMI, CauII, EcoHI, HgiS22I | +| EcoA4I | Escherichia coli A4 | GGTCTC | 7 | | +| EcoHI | Escherichia coli HI | CCSGG | 1 | AsuC2I, BcnI, BpuMI, CauII, EcoHI, HgiS22I, Kpn49kII, NciI | +| EcoHK31I | Escherichia coli HK31 | YGGCCR | 1 | | +| EcoICRI | Escherichia coli 2bT | GAGCTC | 3 | | +| Eco75KI | Escherichia coli BKM | GRGCYC | 5 | | +| Eco57MI | Escherichia coli RFL57M | CTGRAG | 13 | | +| EcoO44I | Escherichia coli O44 Hiromi | GGTCTC | 7 | | +| EcoO65I | Escherichia coli K11a | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstPI, BstT9I, EcaI, Eco91I, EcoO128I | +| EcoO109I | Escherichia coli H709c | RGGNCCY | 2 | | +| EcoO128I | Escherichia coli O128Ly3 | GGTNACC | 1 | AspAI, Bse64I, BstEII, BstT9I, EcaI, EcoO65I, NspSAII, PspEI | +| EcoP15I | Escherichia coli P15 | CAGCAG | 11 | | +| EcoRI | Escherichia coli RY13 | GAATTC | 1 | | +| EcoRII | Escherichia coli R245 | CCWGG | 1 | ApaORI, BseBI, BspNI, BstNI, BstOI, Bst2UI, MvaI, SspAI, ZanI | +| EcoRV | Escherichia coli J62 pLG74 | GATATC | 3 | | +| EcoT14I | Escherichia coli TB14 | CCWWGG | 1 | | +| EcoT22I | Escherichia coli TB22 | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SepI, SspD5II | +| EcoT38I | Escherichia coli TH38 | GRGCYC | 5 | | +| EcoVIII | Escherichia coli E1585-68 | AAGCTT | 1 | | +| Eco13kI | Escherichia coli 13k | CCNGG | 1 | | +| Eco21kI | Escherichia coli 21k | CCNGG | 1 | | +| Eco27kI | Escherichia coli 27 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, OfoI, PunAI | +| Eco29kI | Escherichia coli | CCGCGG | 4 | | +| Eco53kI | Escherichia coli 53k | GAGCTC | 3 | | +| Eco137kI | Escherichia coli 137k | CCNGG | 1 | | +| EgeI | Enterobacter gergoviae NA | GGCGCC | 3 | | +| EheI | Erwinia herbicola 9/5 | GGCGCC | 3 | | +| ErhI | Erwinia rhaponici B9 | CCWWGG | 1 | | +| ErhB9I | Erwinia rhaponici B9 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, NblI, Ple19I, Psu161I, RshI, XorII | +| ErhB9II | Erwinia rhaponici B9 | CCWWGG | 1 | | +| ErpI | Erwinia rhaponici | GGWCC | 1 | Bme18I, BthAI, Csp68KI, Eco47I, FssI, HgiEI, Kzo49I, SmuEI | +| EsaBC3I | Environmental sample BC3 | TCGA | 2 | | +| EsaBC4I | Environmental sample BC4 | GGCC | 2 | | +| EspI | Eucapsis sp. | GCTNAGC | 2 | | +| Esp3I | Erwinia sp. RFL3 | CGTCTC | 7 | | +| Esp4I | Erwinia sp. RFL4 | CTTAAG | 1 | | +| FalII | Flavobacterium aquatile Ob10 | CGCG | 2 | BepI, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, FalII, SelI, ThaI | +| FaqI | Flavobacterium aquatile RFL1 | GGGAC | 9 | | +| FatI | Flavobacterium aquatile NL3 | CATG | 1 | | +| FauI | Flavobacterium aquatile | CCCGC | 9 | | +| FauBII | Flavobacterium aureus B | CGCG | 2 | Bpu95I, BspFNI, Bsp123I, BspFNI, BstUI, BtkI, Csp68KVI, SelI, ThaI | +| FauNDI | Flavobacterium aquatile ND | CATATG | 2 | | +| FbaI | Flavobacterium balustinum | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, Ksp22I,  ParI | +| FblI | Flavobacterium balustinum | GTMKAC | 2 | AccI, XmiI | +| FbrI | Flavobacterium breve | GCNGC | 2 | | +| FdiI | Fremyella diplosiphon | GGWCC | 1 | Bme18I, BthAI, Csp68KI, ErpI, FssI, HgiEI, Kzo49I, SmuEI | +| FdiII | Fremyella diplosiphon | TGCGCA | 3 | Acc16I, AosI, AviII, FspI, MstI, NsbI, PamI, Pun14627I | +| FgoI | Fervidobacterium gondwanense AB39T | CTAG | 1 | | +| FmuI | Flavobacterium multivorum | GGNCC | 4 | FmuI AvcI, BavAII, Bce22I, Bsu54I, NspIV, Pde12I, UnbI | +| FnuAI | Fusobacterium nucleatum A | GANTC | 1 | | +| FnuCI | Fusobacterium nucleatum C | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuEI, MgoI, NphI, SauMI | +| FnuDI | Fusobacterium nucleatum D | GGCC | 2 | | +| FnuDII | Fusobacterium nucleatum D | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FnuDII, ThaI | +| FnuDIII | Fusobacterium nucleatum D | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, HhaI, Hin6I, HinP1I, HspAI, SciNI | +| FnuEI | Fusobacterium nucleatum E | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, Sau3AI | +| Fnu4HI | Fusobacterium nucleatum 4H | GCNGC | 2 | | +| FokI | Flavobacterium okeanokoites | GGATG | 8 | | +| FriOI | Flavobacterium sp. O9 | GRGCYC | 5 | | +| FseI | Frankia sp. Eu11b | GGCCGGCC | 6 | | +| FsiI | Frankia sp. | RAATTY | 1 | AcsI, ApoI,  CfaI, XapI | +| FspI | Fischerella sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, MstI, NsbI, PamI, Pun14627I | +| FspII | Fischerella sp. | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, Ssp1I, SviI | +| Fsp1604I | Flavobacterium sp. I 16-04 | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, SleI | +| FspAI | Flexibacter sp. TV-m21K | RTGCGCAY | 4 | | +| FspBI | Flavobacterium sp. RFLI | CTAG | 1 | | +| Fsp4HI | Flavobacterium sp. 4H | GCNGC | 2 | | +| FspMSI | Fischerella sp. | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, HgiBI, HgiEI, Kzo49I, SmuEI | +| FssI | Fibrobacter succinogenes S85 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Kzo49I, VpaK11AI | +| FunI | Fischerella uniformis | AGCGCT | 3 | AfeI, AitI, Aor51H, Eco47III | +| FunII | Fischerella uniformis | GAATTC | 1 | | +| GalI | Gluconobacter albidus | CCGCGG | 4 | | +| GceI | Gluconobacter cerinus | CCGCGG | 4 | | +| GceGLI | Gluconobacter cerinus | CCGCGG | 4 | | +| GdiI | Gluconobacter dioxyacetonicus | AGGCCT | 3 | AatI, AspMI, Eco147I, PceI, SarI, Sru30DI, SseBI, SteI, StuI | +| GdiII | Gluconobacter dioxyacetonicus | CGGCCR | 1 | | +| GstI | Geobacillus stearothermophilus | GGATCC | 1 | | +| GsuI | Gluconobacter suboxydans H-15T | CTGGAG | 13 | | +| HacI | Halococcus acetoinfaciens | GATC | 1 | Bme12I, Bsp67I, BstENII, CcyI, FnuEI, MgoI, NphI, Sau3AI | +| HaeI | Haemophilus aegyptius | WGGCCW | 3 | | +| HaeII | Haemophilus aegypticus | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, LpnI | +| HaeIII | Haemophilus aegypticus | GGCC | 2 | BsuRI | +| HalI | Hafnia alvei B6 | GAATTC | 1 | | +| HalII | Hafnia alvei B6 | CTGCAG | 5 | AjoI, AliAJI, Bsp63I, CfrA4I, CfuII, CstI, PstI, SflI, Srl5DI, Sst12I | +| HapII | Haemophilus aphrophilus | CCGG | 1 | | +| HgaI | Haemophilus gallinarum | GACGC | 8 | | +| HgiI | Herpetosiphon giganteus 3303 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiHII, Hin1I, PamII | +| HgiAI | Herpetosiphon giganteus HP1023 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI,  Bsm6I, HpyF46II, MspV281I | +| HgiBI | Herpetosiphon giganteus Hpg5 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Psp03I, VpaK11AI | +| HgiCI | Herpetosiphon giganteus Hpg9 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiHI, MspB4I, PfaAI | +| HgiCII | Herpetosiphon giganteus Hpg9 | GGWCC | 1 | Bme18I, BthAI, DsaIV, FspMSI, HgiHIII, Psp03I, VpaK11AI | +| HgiCIII | Herpetosiphon giganteus Hpg9 | GTCGAC | 1 | | +| HgiDI | Herpetosiphon giganteus Hpa2 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiI, Hin1I, PamII | +| HgiDII | Herpetosiphon giganteus Hpa2 | GTCGAC | 1 | | +| HgiEI | Herpetosiphon giganteus Hpg24 | GGWCC | 1 | Bme216I, BthAI, DsaIV, ErpI, FspMSI, HgiHIII, VpaK11AI | +| HgiGI | Herpetosiphon giganteus Hpa1 | GRCGYC | 2 | AcyI, AosII, BbiII, BstACI, HgiI, HgiGI, Msp17I, PamII | +| HgiHI | Herpetosiphon giganteus HP1049 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiCI, MspB4I, PfaAI | +| HgiHII | Herpetosiphon giganteus HP1049 | GRCGYC | 2 | AosII, AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Msp17I, PamII | +| HgiHIII | Herpetosiphon giganteus HP1049 | GGWCC | 1 | Bme216I, DsaIV, ErpI, HgiBI, Psp03I, VpaK11AI, VpaK11BI | +| HgiJI | Herpetosiphon giganteus HFS101 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | +| HgiJII | Herpetosiphon giganteus HFS101 | GRGCYC | 5 | | +| HgiS22I | Herpetosiphon giganteus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, CauII, Eco1831I, EcoHI, Kpn49kII | +| HhaI | Haemophilus haemolyticus | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, SciNI | +| HhaII | Haemophilus haemolyticus | GANTC | 1 | | +| Hin1I | Haemophilus influenzae RFL1 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, HgiI, HgiDI, HgiDI, Hsp92I | +| Hin1II | Haemophilus influenzae RFL1 | CATG | 4 | | +| Hin2I | Haemophilus influenzae RFL2 | CCGG | 1 | | +| Hin6I | Haemophilus influenzae RFL6 | GCGC | 1 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, HhaI, HsoI, HspAI, SciNI | +| HinJCI | Haemophilus influenzae JC9 | GTYRAC | 3 | | +| HinP1I | Haemophilus influenzae P1 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HsoI, HspAI, SciNI | +| HincII | Haemophilus influenzae Rc | GTYRAC | 3 | | +| HindII | Haemophilus influenzae Rd | GTYRAC | 3 | | +| HindIII | Haemophilus influenzae Rd | AAGCTT | 1 | | +| HinfI | Haemophilus influenzae Rf | GANTC | 1 | | +| HjaI | Hyphomonas jannaschiana | GATATC | 3 | | +| HpaI | Haemophilus parainfluenzae | GTTAAC | 3 | | +| HpaII | Haemophilus parainfluenzae | CCGG | 1 | | +| HphI | Haemophilus parahaemolyticus | GGTGA | 9 | AsuHPI, SspD5I | +| Hpy8I | Helicobacter pylori A 8-5 | GTNNAC | 3 | | +| Hpy51I | Helicobacter pylori 51 | GTSAC | 1 | | +| Hpy99I | Helicobacter pylori J99 | CGWCG | 5 | | +| Hpy178III | Helicobacter pylori J178 | TCNNGA | 2 | | +| Hpy188I | Helicobacter pylori J188 | TCNGA | 3 | | +| Hpy188III | Helicobacter pylori J188 | TCNNGA | 2 | | +| HpyAV | Helicobacter pylori 26695 | CCTTC | 9 | | +| HpyBI | Helicobacter pylori Roberts | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, PabI, PlaAII, RsaI, RsaNI | +| HpyBII | Helicobacter pylori Roberts | GTNNAC | 3 | | +| HpyCI | Helicobacter pylori | GATATC | 3 | | +| HpyC1I | Helicobacter pylori | CCATC | 9 | | +| HpyCH4I | Helicobacter pylori CH4 | CATG | 4 | | +| HpyCH4III | Helicobacter pylori CH4 | ACNGT | 3 | | +| HpyCH4IV | Helicobacter pylori CH4 | ACGT | 1 | | +| HpyCH4V | Helicobacter pylori CH4 | TGCA | 2 | | +| HpyF44III | Helicobacter pylori RFL44 | TGCA | 2 | | +| HsoI | Haemophilus somnus 2336 | GCGC | 1 | AspLEI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, HspAI, SciNI | +| Hsp92I | Haemophilus sp. 92 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, HgiI, HgiDI, HgiHII, Hin1I, Hsp92I | +| Hsp92II | Haemophilus sp. 92 | CATG | 4 | | +| HspAI | Haemophilus sp. A | GCGC | 1 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, SciNI | +| HsuI | Haemophilus suis | AAGCTT | 1 | | +| ItaI | Ilyobcater tartaricus | GCNGC | 2 | | +| KasI | Kluyvera ascorbata | GGCGCC | 1 | | +| Kaz48kI | Klebsiella azeanae | RGGNCCY | 5 | | +| KoxII | Klebsiella oxytoca | GRGCYC | 5 | | +| KpnI | Klebsiella pneumoniae OK8 | GGTACC | 5 | Acc65I, AhaB8I, Asp718I, SthI | +| Kpn2I | Klebsiella pneumoniae RFL2 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | +| Kpn378I | Klebsiella pneumoniae 378 | CCGCGG | 4 | | +| Kpn2kI | Klebsiella pneumoniae 2k | CCNGG | 1 | | +| Kpn49kI | Klebsiella pneumoniae 49k | GAATTC | 1 | | +| Kpn49kII | Klebsiella pneumoniae 49k | CCSGG | 1 | AhaI, AsuC2I, BcnI, CauII, EcoHI, HgiS22I, Mgl14481I, NciI, | +| KspI | Kluyvera sp. | CCGCGG | 4 | | +| Ksp22I | Kurthia sp. 22 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, FbaI,  ParI | +| Ksp632I | Kluyvera sp. 632 | CTCTTC | 7 | | +| KspAI | Kurthia sp. N88 | GTTAAC | 3 | | +| Kzo9I | Kurthia zopfii 9 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstMBI, CpfI, LlaAI, NdeII, Sth368I | +| Kzo49I | Kurthia zopfii 49 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | +| LcaI | Lactobacillus casei | ATCGAT | 2 | BdiI, Bli41I, Bsa29I, BscI, Bsp106I, BspDI, Bst28I, LplI, PgaI, ZhoI | +| LlaAI | Lactococcus lactis cremoris W9 | GATC | 1 | Bme12I, Bsp67I, BstENII, ChaI, FnuEI, MgoI, NphI, RalF40I | +| LlaBI | Lactococcus lactis cremoris W56 | CTRYAG | 1 | | +| LlaCI | Lactococcus lactis W15 | AAGCTT | 1 | | +| LlaG2I | Lactococcus lactis cremoris | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, PstNHI | +| Lmu60I | Listeria murrayi 60 | CCTNAGG | 2 | AocI, AxyI, BspR7I, CvnI, Lmu60I, MstII, SauI, SshAI | +| LplI | Lactobacillus plantarum | ATCGAT | 2 | BanIII, BbvAII, BdiI, Bsa29I, BscI, BstNZ169I, ClaI, LcaI, PgaI | +| LpnI | Legionella pneumophila | RGCGCY | 3 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, HaeII | +| LspI | Lactobacillus sp. | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp45I, PlaII, PpaAI, Ssp1I | +| LweI | Listeria welshimeri RFL131 | GCATC | 8 | | +| MabI | Microbacterium arborescens SE | ACCWGGT | 1 | | +| MaeI | Methanococcus aeolicus PL-15/H | CTAG | 1 | | +| MaeII | Methanococcus aeolicus | ACGT | 1 | | +| MaeIII | Methanococcus aeolicus | GTNAC | 1 | | +| MaeK81I | Microcystis aeruginosa K-81 | CGTACG | 1 | | +| MaeK81II | Microcystis aeruginosa | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | +| MavI | Mycobacterium avium | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SciI, SlaI, Sol10179I, XhoI | +| MbiI | Moraxella bovis Fr1-022 | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, Bst31NI | +| MboI | Moraxella bovis | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| MboII | Moraxella bovis | GAAGA | 9 | | +| MchI | Micromonospora chalcea | GGCGCC | 2 | | +| MchAI | Mycobacterium chelonei | GCGGCCGC | 2 | | +| MchAII | Mycobacterium chelonei | GGCC | 2 | | +| McrI | Micrococcus cryophilus | CGRYCG | 4 | | +| MfeI | Mycoplasma fermentans | CAATTG | 1 | | +| MflI | Microbacterium flavum | RGATCY | 1 | | +| MfoAI | Mycobacterium fortuitum TMC 1529 | GGCC | 2 | | +| Mgl14481I | Merismopedia glauca 1448-1 | CCSGG | 2 | AseII, AsuC2I, BcnI, BpuMI, CauII, Eco1831I, EcoHI, HgiS22I, NciI | +| MgoI | Mycobacterium gordonae | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, NphI, Sau3AI | +| MhaAI | Mycobacterium habana 206 | CTGCAG | 5 | AliAJI, Asp713I, Bsp63I, CstI, Ecl37kI, HalII, PaePI, PstI, YenI | +| MhlI | Micrococcus halobius SD | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, SduI | +| MkrAI | Micrococcus kristinae | GATC | 1 | Bme12I, BspAI, BstENII, ChaI, FnuEI, MgoI, NphI, Sau3AI | +| MlaI | Mastigocladus laminosus | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp68KII, LspI, PlaII, Ssp1I | +| MlaAI | Micromonospora lacustris | CTCGAG | 1 | BspAAI, BstVI, PanI, SauLPII, Sbi68I, Sfr274I, SlaI, XhoI | +| MlsI | Micrococcus luteus Ng 16-122 | TGGCCA | 3 | | +| MltI | Micrococcus luteus | AGCT | 2 | AluBI, AluI | +| MluI | Micrococcus luteus | ACGCGT | 1 | | +| Mlu23I | Micrococcus luteus 23 | GGATCC | 1 | | +| Mlu31I | Micrococcus luteus 31 | TGGCCA | 3 | | +| MluB2I | Micrococcus luteus B2 | TCGCGA | 3 | | +| MluNI | Micrococcus luteus N | TGGCCA | 3 | | +| MlyI | Micrococcus lylae | GAGTC | 8 | | +| Mly113I | Micrococcus lylae 113 | GGCGCC | 2 | | +| MmeI | Methylophilus methylotrophus | TCCRAC | 12 | | +| MnlI | Moraxella nonliquefaciens | CCTC | 9 | | +| MnoI | Moraxella nonliquefaciens | CCGG | 1 | | +| Mph1103I | Moraxella phenylpyruvica RFL1103 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II | +| MroI | Micrococcus roseus | TCCGGA | 1 | BbvAIII, BseAI, Bsp13I, BspEI, Bsu23I, CauB3I, PinBII, PtaI | +| MroNI | Micrococcus roseus N | GCCGGC | 1 | | +| MscI | Micrococcus sp. | TGGCCA | 3 | | +| MseI | Micrococcus sp. | TTAA | 1 | | +| MspI | Moraxella sp. | CCGG | 1 | | +| Msp17I | Micrococcus sp. 17 | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Hin1I, Msp17I, PamII | +| Msp20I | Micrococcus sp. | TGGCCA | 3 | | +| Msp67I | Micrococcus sp. MS67 | CCNGG | 2 | | +| MspA1I | Moraxella sp. A1 | CMGCKG | 3 | | +| MspB4I | Moraxella sp. B4 | GGYRCC | 1 | AccB1I, BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, PfaAI | +| MspCI | Micrococcus sp. | CTTAAG | 1 | | +| MspR9I | Micrococcus sp. R9 | CCNGG | 2 | | +| MspSWI | Moraxella sp. SW | ATTTAAAT | 4 | | +| MspV281I | Myxosarcinia sp. V/281 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I, BsiHKAI,  Bsm6I, HgiAI,  HpyF46II, | +| MspYI | Microcystis sp. J2 | YACGTR | 3 | | +| MssI | Methylobacterium sp. Dd 5-732 | GTTTAAAC | 4 | PmeI | +| MstI | Microcoleus sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, NsbI, PamI, Pun14627I | +| MstII | Microcoleus sp. | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| MthZI | Methanobacterium thermoformicicum Z-245 | CTAG | 1 | | +| MunI | Mycoplasma sp. | CAATTG | 1 | | +| MvaI | Micrococcus varians RFL19 | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, Bst2UI, SslI, TaqXI, ZanI | +| Mva1269I | Micrococcus varians RFL1269 | GAATGC | 7 | Asp26HI, Asp40HI, Asp50HI, BscCI, BsmI, Mva1269I, PctI | +| MvnI | Methanococcus vannielii | CGCG | 2 | AccII, Bsh1236I, BstFNI, BtkI, Csp68KVI, FalII, FauBII, ThaI | +| MvrI | Micrococcus varians | CGATCG | 4 | Afa22MI, BspCI, EagBI, ErhB9I, Ple19I, PvuI, RshI, XorII | +| MxaI | Myxococcus xanthus F18E | GAGCTC | 3 | | +| NaeI | Nocardia aerocolonigenes | GCCGGC | 3 | | +| NarI | Nocardia argentinensis | GGCGCC | 2 | | +| NblI | Nocardia blackwellii | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, MvrI, Ple19I, Psu161I, RshI, XorII | +| NciI | Neisseria cinerea | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, EcoHI, HgiS22I, Mgl14481I | +| NcoI | Nocardia corallina | CCATGG | 1 | | +| NcrI | Nocardia carnea C-212 | AGATCT | 1 | | +| NcuI | Neisseria cuniculi | GAAGA | 9 | | +| NdaI | Nocardia dassonvillei | GGCGCC | 2 | | +| NdeI | Neisseria denitrificans | CATATG | 2 | | +| NdeII | Neisseria denitrificans | GATC | 1 | Bce243I, Bsp105I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, Sth368I | +| NgoAIII | Neisseria gonorrhoeae FA1090 | CCGCGG | 4 | | +| NgoAIV | Neisseria gonorrhoeae FA1090 | GCCGGC | 1 | | +| NgoMIV | Neisseria gonorrhoeae MS11 | GCCGGC | 1 | | +| NgoPII | Neisseria gonorrhoeae P9-2 | GGCC | 2 | | +| NgoPIII | Neisseria gonorrhoeae P9-2 | CCGCGG | 4 | | +| NheI | Neisseria mucosa heidelbergensis | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, LlaG2I, PstNHI | +| NlaII | Neisseria lactamica | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | +| NlaIII | Neisseria lactamica | CATG | 4 | | +| NlaIV | Neisseria lactamica | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, PspN4I | +| Nli3877I | Nostoc linckia | CYCGRG | 5 | Ama87I, AvaI, BcoI, BsiHKCI, Eco27kI, Eco88I, NspSAI, OfoI | +| NmeCI | Neisseria meningitidis C114 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | +| NmeRI | Neisseria meningitidis | CAGCTG | 3 | | +| NmuCI | Neisseria mucosa C9-2 | GTSAC | 1 | | +| NopI | Nocardia opaca | GTCGAC | 1 | | +| NotI | Nocardia otitidis-caviarum | GCGGCCGC | 2 | | +| NphI | Neisseria pharyngis C245 | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, RalF40I, Sau3AI | +| NruI | Nocardia rubra | TCGCGA | 3 | | +| NsbI | Neisseria subflava Va-1 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, PamI, Pun14627I | +| NsiI | Neisseria sicca | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | +| NsiCI | Neisseria sicca C351 | GATATC | 3 | | +| NspI | Nostoc sp. C | RCATGY | 5 | | +| NspII | Nostoc sp. C | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, MhlI, NspII, SduI | +| NspIII | Nostoc sp. C | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, Eco88I, OfoI, PunAI | +| NspIV | Nostoc sp. C | GGNCC | 1 | AvcI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | +| NspV | Nostoc sp. C | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, PlaII, SspRFI | +| Nsp7121I | Nostoc sp. 7121 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | +| Nsp29132II | Nostoc sp. | GGATCC | 1 | AliI, ApaCI, BamHI, Bce751I, Nsp29132II, Pfl8I, SolI, Uba4009I | +| NspBII | Nostoc sp. | CMGCKG | 3 | | +| NspHI | Nostoc sp. | RCATGY | 5 | | +| NspLKI | Nocardia sp. LK | GGCC | 2 | | +| NspMACI | Nostoc sp. | AGATCT | 1 | | +| NspSAI | Nostoc sp. SA | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | +| NspSAII | Nostoc sp. SA | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BseT10I, BstPI, Eco91I, NspSAII, PspEI | +| NspSAIV | Nostoc sp. SA | GGATCC | 1 | AliI, BamHI, Bsp98I, Bsp4009I, NspSAIV, Pfl8I, SolI, Uba4009I | +| NunII | Nocardia uniformis | GGCGCC | 2 | | +| OfoI | Oscillatoria foreaui A-1340 | CYCGRG | 1 | AquI, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, PlaAI, PunAI | +| OkrAI | Oceanospirillum kriegii | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, BstI, OkrAI, SolI, Uba4009I | +| OxaNI | Oerskovia xanthineolytica N | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| PabI | Pyrococcus abyssi | GTAC | 3 | AfaI, Csp6I, CviQI, HpyBI, HpyBI, PlaAII, RsaI,  RsaNI, | +| PacI | Pseudomonas alcaligenes | TTAATTAA | 5 | | +| Pac25I | Pseudomonas alcaligenes | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PspAI, PspALI, XcyI, XmaI, XmaCI | +| PaeI | Pseudomonas aeruginosa | GCATGC | 5 | | +| PaeAI | Pseudomonas aeruginosa | CCGCGG | 4 | | +| PaeBI | Pseudomonas aeruginosa - 18 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | +| PaeHI | Pseudomonas aeruginosa 4148 | GRGCYC | 5 | | +| PaeHII | Pseudomonas aeruginosa 4148 | CTGCAG | 5 | AliAJI, BspBI, BspMAI, CfuII, Ecl2zI, HalII, Srl5DI, Sst12I, XcpI | +| PaeQI | Pseudomonas aeruginosa Q2 | CCGCGG | 4 | | +| PaeR7I | Pseudomonas aeruginosa PA0303 pMG7 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | +| Pae2kI | Pseudomonas aeruginosa 2k | AGATCT | 1 | | +| Pae5kI | Pseudomonas aeruginosa 5k | CCGCGG | 4 | | +| Pae14kI | Pseudomonas aeruginosa 14k | CCGCGG | 4 | | +| Pae17kI | Pseudomonas aeruginosa 17k | CAGCTG | 3 | | +| Pae18kI | Pseudomonas aeruginosa 18k | AGATCT | 1 | | +| PagI | Pseudomonas alcaligenes Sau 14-027 | TCATGA | 1 | | +| PalI | Providencia alcalifaciens | GGCC | 2 | | +| PamI | Phormidium ambiguum | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, Pun14627I | +| PamII | Phormidium ambiguum | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiDI, HgiGI, HgiHII, Hin1I, Hsp92I, Msp17I | +| PanI | Pseudomonas alkanolytica | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| PasI | Pseudomonas anguilliseptica RFL1 | CCCWGGG | 2 | — None on May 2010 — | +| PauI | Paracoccus alcaliphilus ZVK3-3 | GCGCGC | 1 | | +| PauAI | Phormidium autumnale | RCATGY | 5 | | +| PauAII | Phormidium autumnale | TTTAAA | 3 | AhaIII, DraI, SruI | +| PceI | Planococcus citreus 55 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | +| PciI | Planococcus citreus SE-F45 | ACATGT | 1 | | +| PctI | Planococcus citreus SM | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI BmaHI, BsaMI, BscCI, Mva1269I | +| Pde12I | Paracoccus denitrificans 12 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | +| Pde133I | Paracoccus denitrificans 133 | GGCC | 2 | | +| Pde137I | Paracoccus denitrificans 137 | CCGG | 1 | | +| PdiI | Pseudomonas diminuta Mck 33-321 | GCCGGC | 3 | | +| PfaAI | Phormidium favosum | GGYRCC | 1 | AccB1I, BanI, BbvBI, BshNI, Eco64I, HgiCI, HgiHI, MspB4I | +| PfaAII | Phormidium favosum | CATATG | 2 | | +| PfaAIII | Phormidium favosum | GCATGC | 5 | | +| PfeI | Psychrobacter faecalis RFL1 | GAWTC | 1 | | +| Pfl8I | Pseudomonas fluorescens 8 | GGATCC | 1 | AliAJI, BspBI, BsuBI, CflI, CfrA4I, PaePI, Pfl21I, PstI, SflII, Sst12I | +| Pfl21I | Pseudomonas sp. 21 | CTGCAG | 5 | | +| Pfl23II | Pseudomonas fluorescens RFL23 | CGTACG | 1 | | +| Pfl27I | Pseudomonas fluorescens RFL27 | RGGWCCY | 2 | | +| PflFI | Pseudomonas fluorescens biotype F | GACNNNGTC | 4 | AspI, AtsI, PsyI, TelI, Tth111I | +| PflKI | Pseudomonas fluorescens | GGCC | 2 | | +| PfoI | Pseudomonas fluorescens biovar 126 | TCCNGGA | 1 | | +| PgaI | Pseudomonas gladioli B4 | ATCGAT | 2 | BanIII, BbvAII, BliAI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | +| PhaI | Pasteurella haemolytica | GCATC | 8 | | +| PhoI | Pyrococcus horikoshii OT3 | GGCC | 2 | | +| PinAI | Pseudomonas inequalis | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, CspAI | +| PinBI | Phormidium inundatum | ATGCAT | 5 | EcoT22I, BfrBI, Mph1103I, NsiI, Ppu10I, SepI, SspD5II, Zsp2I | +| PinBII | Phormidium inundatum | TCCGGA | 1 | Aor13HI, BlfI, Bsp13I, BspEI, Bsu23I, Kpn2I, PinBII, PtaI | +| PlaI | Phormidium lapideum | GGCC | 2 | | +| PlaII | Phormidium lapideum | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, SfuI, SspRFI | +| PlaAI | Phormidium laminosum | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | +| PlaAII | Phormidium laminosum | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, RsaI,  RsaNI, | +| PleI | Pseudomonas lemoignei | GAGTC | 9 | | +| Ple19I | Pseudomonas lemoignei 19 | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, MvrI, Psu161I, PvuI, RshI, XorII | +| PmaCI | Pseudomonas maltophilia CB50P | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmlI, PspCI | +| PmeI | Pseudomonas mendocina | GTTTAAAC | 4 | MssI | +| Pme55I | Pseudomonas mendocina 55 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI, StuI | +| PmlI | Pseudomonas maltophilia | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PspCI | +| PovII | Proteus vulgaris | CAGCTG | 3 | | +| PpaAI | Phormidium papyraceum | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, SfuI, SspRFI, SviI | +| PpaAII | Phormidium papyraceum | TCGA | 1 | | +| PpeI | Phormidium persicinum | GGGCCC | 5 | ApaI, Bsp120I, PspOMI | +| PpsI | Pseudomonas pseudoalcaligenes PL | GAGTC | 9 | | +| Ppu10I | Pseudomonas putida RFL10 | ATGCAT | 1 | BfrBI, Csp68KII, EcoT22I, Mph1103I, NsiI, SepI, SspD5II | +| Ppu111I | Pseudomonas putida P111 | GAATTC | 1 | | +| PpuAI | Pseudomonas putida A1 | CGTACG | 1 | | +| PpuMI | Pseudomonas putida M | RGGWCCY | 2 | | +| PpuXI | Pseudomonas putida X | RGGWCCY | 2 | | +| PshBI | Plesiomonas shigelloides TPS970 | ATTAAT | 2 | AseI, AsnI, BpoAI, Sru4DI, VspI | +| PsiI | Pseudomonas sp. SE-G49 | TTATAA | 3 | | +| Psp03I | Phormidium sp. | GGWCC | 4 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11AI | +| Psp5II | Pseudomonas sp. RFL5 | RGGWCCY | 2 | | +| Psp6I | Pseudomonas sp. B6 | CCWGG | 1 | AeuI, AglI, ApaORI, Bse17I, EcoRII, Fsp1604I, SspAI, Sth117I | +| Psp23I | Pseudomonas sp. 23 | CTGCAG | 5 | ApiI, BspBI, CflI, MhaAI, Pfl21I, PstI, SalPI, Sst12I, YenI | +| Psp1406I | Pseudomonas pseudoalcaligenes RFL1406 | AACGTT | 2 | AclI | +| PspAI | Pseudomonas sp. | CCCGGG | 1 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI, XmaCI | +| PspALI | Pseudomonas sp. AL1637 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | +| Psp124BI | Pseudomonas sp. 124B | GAGCTC | 5 | | +| PspCI | Pseudomonas sp. C | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PmlI | +| PspEI | Pseudomonas sp. E | GGTNACC | 1 | AcrII, AspAI, BstEII, BstPI, Eci125I, Eco91I, EcoO65I, EcoO128I | +| PspGI | Pyrococcus sp. GI-H | CCWGG | 1 | AeuI, AjnI, AorI, Bse17I, EcoRII, Fsp1604I, Psp6I, SspAI, Sth117I | +| PspLI | Pseudomonas sp. L | CGTACG | 1 | | +| PspN4I | Pseudomonas sp. N4 | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, NlaIV | +| PspOMI | Pseudomonas sp. OM2164 | GGGCCC | 1 | ApaI, Bsp120I, PpeI | +| PspPI | Psychrobacter immobilis TA137 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | +| PspPPI | Pseudomonas sp. PP | RGGWCCY | 2 | | +| PspXI | Pseudomonas sp. A1-1 | VCTCGAGB | 2 | | +| PssI | Pseudomonas sp. | RGGNCCY | 5 | | +| PstI | Providencia stuartii 164 | CTGCAG | 5 | AliAJI, BspBI, CfuII, Ecl2zI, HalII, PstI, Sag16I, Sag23I, Sst12I, XcpI | +| PstNHI | Pseudomonas stutzeri NH | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, LlaG2I | +| PsuI | Pseudomonas stutzeri Mck 28-pH52 | RGATCY | 1 | | +| Psu161I | Pseudomonas stutzeri 161 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, PvuI, RshI, XorII | +| PsuAI | Phormidium subfuscum | YACGTR | 3 | | +| PsyI | Pseudomonas syringae Lki 1-pH124 | GACNNNGTC | 4 | AspI, AtsI, PflFI, TelI, Tth111I | +| PtaI | Phormidium tadzschicicum | TCCGGA | 1 | Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Kpn2I, PinBII, PtaI | +| Pun14627I | Phormidium uncinatum 1462/7 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, PamI | +| Pun14627II | Phormidium uncinatum 1462/7 | CAGCTG | 3 | | +| PunAI | Phormidium uncinatum | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco27kI, Nli3877I, PlaAI | +| PunAII | Phormidium uncinatum | RCATGY | 5 | | +| PvuI | Proteus vulgaris | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, NblI, Ple19I, Psu161I, RshI, XorII | +| PvuII | Proteus vulgaris | CAGCTG | 3 | | +| Pvu84II | Proteus vulgaris 84 | CAGCTG | 3 | | +| RalF40I | Ruminococcus albus F-40 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, HacI, MkrAI, Sau3AI, SsiAI | +| RcaI | Rhodococcus capsulatum | TCATGA | 1 | | +| RflFI | Ruminococcus flavefaciens FD-1 | GTCGAC | 1 | | +| RflFII | Ruminococcus flavefaciens FD-1 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, ScaI, ZrmI | +| RleAI | Rhizobium leguminosarum | CCCACA | 12 | | +| RmaI | Rhodothermus marinus | CTAG | 1 | | +| Rme21I | Rhizobium meliloti | ATCGAT | 2 | BanIII, BbvAII, BliRI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | +| RsaI | Rhodopseudomonas sphaeroides | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, PlaAII,  RsaNI, | +| RshI | Rhodopseudomonas sphaeroides 2.4.1 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, Psu161I, PvuI, XorII | +| RspLKI | Rhodococcus sp. LK2 | GCATGC | 5 | | +| RspLKII | Rhodococcus sp. LK2 | GGATCC | 1 | AliI, AsiI, BamHI, Bce751I, Nsp29132II, OkrAI, RspLKII, SolI | +| RspXI | Rhodococcus sp. | TCATGA | 1 | | +| RsrI | Rhodopseudomonas sphaeroides | GAATTC | 1 | | +| RsrII | Rhodopseudomonas sphaeroides | CGGWCCG | 2 | | +| Rsr2I | Rhodobacter sphaeroides SE-I2 | CGGWCCG | 2 | | +| RtrI | Rhizobium trifolii | GTCGAC | 1 | | +| Rtr63I | Rhizobium trifolii 63 | GTCGAC | 1 | | +| SacI | Streptomyces achromogenes | GAGCTC | 5 | | +| SacII | Streptomyces achromogenes | CCGCGG | 4 | Cfr42I | +| SacNI | Streptomyces achromogenes N-J-H | GRGCYC | 5 | | +| SalI | Streptomyces albus | GTCGAC | 1 | | +| SalPI | Streptomyces albus | CTGCAG | 5 | ApiI, BspMAI, CstI, Ecl37kI, Ecl2zI, Psp23I, PstI, Srl5DI, YenI | +| SanDI | Streptomyces sp. | GGGWCCC | 2 | | +| SapI | Saccharopolyspora sp. | GCTCTTC | 8 | | +| SarI | Streptomyces aureomonopodiales | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, Sru30DI, SseBI, SteI, StuI | +| SatI | Staphylococcus arlettae RFL832 | GCNGC | 2 | | +| SauI | Streptomyces aureofaciens IKA 18/4 | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| Sau96I | Staphylococcus aureus PS96 | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | +| Sau3239I | Streptomyces aureofaciens | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| Sau3AI | Staphylococcus aureus 3A | GATC | 1 | Bce243I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| SauBMKI | Streptomyces aureofaciens BM-K | GCCGGC | 3 | | +| SauHPI | Streptomyces aureofaciens R8/26 | GCCGGC | 3 | | +| SauLPI | Streptomyces aureofaciens B-96 | GCCGGC | 3 | | +| SauLPII | Streptomyces aureofaciens B-96 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| SauMI | Staphylococcus aureus M | GATC | 1 | BscFI, BspAI, BstKTI, ChaI, HacI, MkrAI, RalF40I, SsiAI | +| SauNI | Streptomyces aureofaciens NMU | GCCGGC | 3 | | +| SauSI | Streptomyces aureofaciens 16 | GCCGGC | 3 | | +| SbfI | Streptomyces sp. BF-61 | CCTGCAGG | 6 | | +| Sbi68I | Streptomyces bikiniensis JAM68 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | +| Sbo13I | Shigella boydii 13 | TCGCGA | 3 | | +| SbvI | Streptococcus bovis II/1 | GGCC | 2 | | +| ScaI | Streptomyces caespitosus | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ZrmI | +| SceIII | Saccharomyces cerevisiae | GCCGGC | 1 | | +| SchI | Staphylococcus cohnii Lki 19-320 | GAGTC | 8 | | +| SchZI | Streptomyces chusanensis ZS-2 | CCGCGG | 4 | | +| SciI | Streptoverticillium cinnamoneum | CTCGAG | 3 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SlaI, Sol10179I, XhoI | +| SciNI | Spiroplasma citri ASP2 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI | +| ScrFI | Streptococcus cremoris F | CCNGG | 2 | | +| SdaI | Streptomyces diastaticus Ng7-324 | CCTGCAGG | 6 | | +| SduI | Streptococcus durans RFL3 | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII | +| SecI | Synechocystis sp. 6701 | CCNNGG | 1 | | +| SelI | Synechococcus elongatus | CGCG | 1 | AccII, Bsh1236I, Bsp123I, Bsp50I, BstFNI, BstUI, BtkI, Csp68KVI | +| SenPT16I | Salmonella enteritidis PT16 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, XmaIII | +| SenPT14bI | Salmonella enteritidis PT14b | CCGCGG | 4 | | +| SepI | Staphylococcus epidermidis | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | +| SexAI | Streptomyces exfoliatus | ACCWGGT | 1 | | +| SexBI | Streptomyces exfoliatus | CCGCGG | 4 | | +| SexCI | Streptomyces exfoliatus | CCGCGG | 4 | | +| SfaI | Streptococcus faecalis zymogenes | GGCC | 2 | | +| SfaNI | Streptococcus faecalis ND547 | GCATC | 8 | | +| SfcI | Streptococcus faecium | CTRYAG | 1 | | +| SfeI | Streptococcus faecalis | CTRYAG | 1 | | +| SflI | Streptoverticillium flavopersicum | CTGCAG | 5 | ApiI, BspMAI, BsuBI, CfrA4I, Psp23I, PstI, Sag23I, Srl5DI, YenI | +| SfoI | Serratia fonticola | GGCGCC | 3 | | +| Sfr274I | Streptomyces fradiae 274 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | +| Sfr303I | Streptomyces fradiae 303 | CCGCGG | 4 | | +| SfuI | Streptomyces fulvissimus | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, PlaII, Ssp1I, SviI | +| SgfI | Streptomyces griseoruber | GCGATCGC | 5 | AsiSI,  RgaI, SfaAI | +| SgrAI | Streptomyces griseus | CRCCGGYG | 2 | | +| SgrBI | Streptomyces griseus | CCGCGG | 4 | | +| SimI | Staphylococcus intermedius 6H | GGGTC | 2 | | +| SinI | Salmonella infantis | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | +| SlaI | Streptomyces lavendulae | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | +| SleI | Synechococcus leopoliensis | CCWGG | 1 | AeuI, AglI, ApaORI, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | +| Slu1777I | Streptomyces lusitanus 1777 | GCCGGC | 3 | | +| SmaI | Serratia marcescens Sb | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | +| SmiI | Streptococcus milleri S | ATTTAAAT | 4 | | +| SmlI | Stenotrophomonas maltophilia | CTYRAG | 1 | | +| SmuI | Sphingobacterium multivorum RFL21 | CCCGC | 9 | | +| SmuEI | Streptococcus mutans E | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | +| SnaBI | Sphaerotilus natans | TACGTA | 3 | | +| SniI | Streptomyces niveus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, MvaI, SspAI | +| SnoI | Streptomyces novocastria | GTGCAC | 1 | Alw44I, ApaLI, VneI | +| SolI | Streptoverticillium olivoverticillatum | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, Bce751I, CelI, OkrAI, SolI, SurI | +| Sol10179I | Streptomyces olivochromogenes ST10179 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | +| SpaHI | Synechococus parietina | GCATGC | 5 | | +| SpeI | Sphaerotilus natans | ACTAGT | 1 | AhII, AclNI, BcuI | +| SphI | Streptomyces phaeochromogenes | GCATGC | 5 | | +| SplI | Spirulina platensis | CGTACG | 1 | | +| SpmI | Sphingobacterium multivorum RFL21 | ATCGAT | 2 | BanIII, BbvAII, BdiI, BscI, Bsa29I, BspJI, ClaI, LcaI, PgaI, Ssp27144I | +| SpoI | Salmonella potsdam | TCGCGA | 3 | | +| SpuI | Streptomyces pulveraceus | CCGCGG | 4 | | +| SrfI | Streptomyces sp. | GCCCGGGC | 4 | | +| SrlI | Selenomonas ruminantium lactilytica 84 | GCCGGC | 1 | | +| Srl5DI | Selenomonas ruminantium 5 | CTGCAG | 5 | AliAJI, Asp713I, BspMAI, BsuBI, CfrA4I, Pfl21I, PstI, SflI, Srl5DI | +| Srl32DII | Selenomonas ruminantium 32 | GAATTC | 1 | | +| Srl55DI | Selenomonas ruminantium lactilytica 55 | GAATTC | 1 | | +| Srl56DI | Selenomonas ruminantium 56 | CTRYAG | 1 | | +| SruI | Selenomonas ruminantium 18D | TTTAAA | 3 | AhaIII, DraI, PauAII | +| Sru4DI | Selenomonas ruminantium | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, VspI | +| Sru30DI | Selenomonas ruminantium 30 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, SseBI, SteI, StuI | +| SsbI | Streptomyces scabies | AAGCTT | 1 | | +| SscL1I | Staphylococcus sp. L1 | GANTC | 1 | | +| Sse9I | Sporosarcina sp. 9 | AATT | 1 | | +| Sse232I | Streptomyces sp. RH232 | CGCCGGCG | 2 | | +| Sse1825I | Streptomyces sp. | GGGWCCC | 2 | | +| Sse8387I | Streptomyces sp. 8387 | CCTGCAGG | 6 | | +| Sse8647I | Streptomyces sp. | AGGWCCT | 2 | | +| SseAI | Streptomyces sp. | GGCGCC | 2 | | +| SseBI | Streptomyces sp. | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SteI, StuI | +| SshAI | Salmonella shikmonah | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| SsiI | Staphylococcus sciuri RFL1 | CCGC | 1 | AciI | +| SsiAI | Staphylococcus sp. A | GATC | 1 | BscFI, BspAI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| SsiBI | Staphylococcus sp. B | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| SslI | Streptococcus salivarius thermophilus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, MvaI | +| SsoI | Shigella sonnei 47 | GAATTC | 1 | | +| SsoII | Shigella sonnei 47 | CCNGG | 1 | | +| SspI | Sphaerotilus sp. | AATATT | 3 | | +| Ssp1I | Streptomyces sp. RFL1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PlaII, SfuI, SspRFI, SviI | +| Ssp4800I | Streptomyces sp. BMTU 4800 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, SspBI | +| Ssp5230I | Streptomyces sp. 5230 | GACGTC | 5 | AatII, ZraI | +| Ssp27144I | Synechococcus sp. | ATCGAT | 2 | BanIII, BavCI, BbvAII, BscI, BspJI, BspOVII, BstNZ169I, ClaI, LcaI | +| SspAI | Synechococcus sp. | CCWGG | 1 | AeuI, AorI, Bse17I, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | +| SspBI | Streptomyces sp. | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, Ssp4800I | +| SspCI | Streptomyces sp. | GCCGGC | 3 | | +| SspD5I | Staphylococcus sp. D5 | GGTGA | 8 | AsuHPI, HphI | +| SspD5II | Staphylococcus sp. D5 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SepI, Zsp2I | +| SspRFI | Synechococcus sp. RF-1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I, SviI | +| SsrI | Staphylococcus saprophyticus B6 | GTTAAC | 3 | | +| SstI | Streptomyces stanford | GAGCTC | 5 | | +| SstII | Streptomyces stanford | CCGCGG | 4 | | +| Sst12I | Streptomyces sp. ST-12 | CTGCAG | 5 | Asp713I, BloHII, BspMAI, BsuBI, CfuII, Psp23I, PstI, SflI, Srl5DI | +| SteI | Streptomyces tendae | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, StuI | +| SthI | Salmonella thompson YY356 | GGTACC | 1 | Acc65I, AhaB8I, Asp718I, KpnI, | +| Sth117I | Streptococcus thermophilus ST117 | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, EcoRII, MvaI, SspAI | +| Sth132I | Streptococcus thermophilus | CCCG | 8 | | +| Sth134I | Streptococcus thermophilus 134 | CCGG | 1 | | +| Sth368I | Streptococcus thermophilus CNRZ368 | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| StrI | Streptomyces thermodiastaticus | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | +| StsI | Streptococcus sanguis 54 | GGATG | 9 | | +| StuI | Streptomyces tubercidicus | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI | +| StyI | Salmonella typhi | CCWWGG | 1 | | +| StyD4I | Salmonella typhi D4 | CCNGG | 1 | | +| SuaI | Sulfolobus acidocaldarius | GGCC | 2 | | +| SuiI | Sulfolobus islandicus REN2HI | GCWGC | 1 | AceI, ApeKI, Taq52I, TseI | +| SunI | Synechococcus uniformis | CGTACG | 1 | | +| SurI | Sporosarcina ureae 2 | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, OkrAI, RspLKII, SolI | +| SviI | Streptomyces violochromogenes | TTCGAA | 2 | AsuII, Bpu14I, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I | +| SwaI | Staphylococcus warneri | ATTTAAAT | 4 | | +| TaaI | Thermus aquaticus Vn 4-311 | ACNGT | 3 | | +| TaiI | Thermus aquaticus cs1-331 | ACGT | 4 | | +| TaqI | Thermus aquaticus | TCGA | 1 | | +| TaqII | Thermus aquaticus YTI | GACCGA | 11 | | +| Taq52I | Thermus aquaticus YS52 | GCWGC | 1 | AceI, ApeKI, SuiI, TseI | +| TaqXI | Thermus aquaticus | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, MvaI, SleI, SspAI | +| TasI | Thermus aquaticus Vn 4-211 | AATT | 1 | | +| TatI | Thermus aquaticus CBA1-331 | WGTACW | 1 | | +| TauI | Thermus aquaticus | GCSGC | 4 | | +| TelI | Tolypothrix elabens | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, Tth111I | +| TfiI | Thermus filiformis | GAWTC | 1 | | +| ThaI | Thermoplasma acidophilum | CGCG | 2 | Bpu95I, Bsh1236I, Bsp50I, BstFNI, BstUI, Csp68KVI, FalII, FnuDII | +| TliI | Thermococcus litoralis | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, StrI, XhoI | +| Tru1I | Thermus ruber RFL1 | TTAA | 1 | | +| Tru9I | Thermus ruber 9 | TTAA | 1 | | +| Tru201I | Thermus ruber 201 | RGATCY | 1 | | +| TscI | Thermus sp. 491A | ACGT | 4 | | +| TseI | Thermus sp. 93170 | GCWGC | 1 | AceI, ApeKI, SuiI, Taq52I | +| Tsp1I | Thermus sp. 1 | ACTGG | 6 | | +| Tsp32I | Thermus sp. 32 | TCGA | 1 | | +| Tsp32II | Thermus sp. 32 | TCGA | 1 | | +| Tsp45I | Thermus sp. YS45 | GTSAC | 1 | | +| Tsp49I | Thermus sp. | ACGT | 4 | | +| Tsp509I | Thermus sp. | AATT | 1 | | +| TspBI | Thermophilic sp. | CCRYGG | 1 | | +| Tsp4CI | Thermus sp. 4C | ACNGT | 3 | | +| TspDTI | Thermus sp. DT | ATGAA | 10 | — None on May 2010 — | +| TspEI | Thermus sp. 1E | AATT | 1 | | +| TspGWI | Thermus sp. GW | ACGGA | 10 | | +| TspMI = UthSI | Unidentified thermophile | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, SmaI, XcyI, XmaI, XmaCI | +| TspRI | Thermus sp. R | CASTGNN | 7 | | +| Tth111I | Thermus thermophilus 111 | GACNNNGTC | 4 | AspI, AtsI, PflFI, PsyI, TelI | +| Tth111II | Thermus thermophilus 111 | CAARCA | 11 | | +| TthHB8I | Thermus thermophilus HB8 | TCGA | 1 | | +| Uba4009I | Unidentified bacterium A | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, RspLKII, SolI | +| Uba153AI | Unidentified bacterium 153A | CAGCTG | 3 | | +| UbaM39I | Unidentified bacterium M39 | CAGCTG | 3 | | +| UnbI | Unidentified bacterium #8 | GGNCC | 1 | AvcI, BavAII, Bce22I, Bsp1894I, Bsu54I, FmuI, NspIV, UnbI | +| Uur960I | Ureaplasma urealyticum 960 | GCNGC | 2 | | +| Vha464I | Vibrio harveyi 464 | CTTAAG | 1 | | +| VneI | Vibrio nereis 18 | GTGCAC | 1 | Alw44I, ApaLI, SnoI | +| VpaK32I | Vibrio parahaemolyticus 4387-61 | GCTCTTC | 8 | | +| VpaK11AI | Vibrio parahaemolyticus 1743 | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11BI | +| VpaK11BI | Vibrio parahaemolyticus 1743-1 | GGWCC | 1 | BsrAI, CauI, EagMI, FdiI, HgiBI, HgiJI, SinI, VpaK11AI | +| VspI | Vibrio sp. 343 | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, Sru4DI | +| XapI | Xanthomonas ampelina Slo 51-021 | RAATTY | 1 | AcsI, ApoI,  CfaI, FsiI | +| XbaI | Xanthomonas badrii | TCTAGA | 1 | | +| XcaI | Xanthomonas campestris | GTATAC | 3 | | +| XceI | Xanthomonas campestris Ast 40-024 | RCATGY | 5 | | +| XciI | Xanthomonas citri | GTCGAC | 1 | | +| XcyI | Xanthomonas cyanopsidis 13D5 | CCCGGG | 1 | CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XmaI, XmaCI | +| XhoI | Xanthomonas holcicola | CTCGAG | 1 | AbrI, BluI, BssHI, PanI, Sau3239I, Sfr274I, TliI, XpaI | +| XhoII | Xanthomonas holcicola | RGATCY | 1 | | +| XmaI | Xanthomonas malvacearum | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, PspAI, TspMI, XcyI, XmaCI | +| XmaIII | Xanthomonas malvacearum | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, SenPT16I | +| XmaCI | Xanthomonas malvacearum C | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PaeBI, Pac25I, PspAI, TspMI, XcyI, XmaI | +| XmaJI | Xanthomonas maltophilia Jo 85-025 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, BspA2I | +| XmiI | Xanthomonas maltophilia Jo 21-021 | GTMKAC | 2 | AccI, FblI | +| XorII | Xanthomonas oryzae | CGATCG | 4 | Afa16RI, BspCI, EagBI, ErhB9I, MvrI, Ple19I, PvuI, RshI | +| XpaI | Xanthomonas papavericola | CTCGAG | 1 | BssHI, MavI, PanI, SauLPII, Sbi68I, Sol10179I, StrI, XhoI | +| XspI | Xanthomonas sp. YK1 | CTAG | 1 | | +| YenI | Yersinia enterocolitica 08 A2635 | CTGCAG | 5 | Asp713I, BsuBI, CfrA4I, Ecl37kI, Psp23I, PstI, SalPI, SflI, Sst12I | +| ZanI | Zymomonas anaerobia | CCWGG | 2 | ApaORI, BseBI, BspNI, BstNI, Bst2UI, CthII, EcoRII, MvaI, SspAI | +| ZhoI | Zymomonas holcicola | ATCGAT | 2 | BanIII, BbvAII, BscI, BspJI, ClaI, LcaI, PgaI, SpmI, Ssp27144I | +| ZraI | Zoogloea ramigera 11 | GACGTC | 3 | AatII, Ssp5230I | +| ZrmI | Zoogloea ramigera SCA | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ScaI | +| Zsp2I | Zoogloea sp. 2 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II |","Markdown" +"Bioengineering","telatin/seqfu2","re/C-D.md",".md","11862","76","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:----------|:-----------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| +| CacI | Clostridium acetobutylicum N1-4081 | GATC | 1 | | +| Cac8I | Clostridium acetobutylicum ABKn8 | GCNNGC | 3 | | +| CaiI | Comamonas acidovarans Iti19-021 | CAGNNNCTG | 6 | AlwNI | +| CauI | Chloroflexus aurantiacus | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | +| CauII | Chloroflexus aurantiacus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, Eco1831I, EcoHI, Kpn49kII, NciI | +| CauB3I | Chloroflexus aurantiacus B3 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BspEI, BspMII, Kpn2I, MroI, PtaI | +| CbiI | Clostridium bifermentans B-4 | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, Csp45I, LspI, NspV, SspRFI | +| CboI | Clostridium botulinum | CCGG | 1 | | +| CbrI | Citrobacter braakii 1146 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI | +| CciNI | Curtobacterium citreus | GCGGCCGC | 2 | | +| CcoI | Clostridium coccoides B-2 | GCCGGC | 3 | | +| CcrI | Caulobacter crescentus CB-13 | CTCGAG | 1 | | +| CcuI | Chroococcidiopsis cubana | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, PspPI | +| CcyI | Clostridium cylindrosporum | GATC | 1 | BfuCI, Bsp67I, Bst19II, CviAI, FnuCI, MboI, NmeCI, SauMI | +| CdiI | Citrobacter freundii RFL2 | CATCG | 4 | | +| CelI | Citrobacter freundii RFL6 | GGATCC | 1 | AliI, ApaCI, AsiI, BamHI, CelI, NspSAIV, RspLKII, SolI, Uba4009I | +| CelII | Coccochloris elabens 17a | GCTNAGC | 2 | | +| CeqI | Corynebacterium equi | GATATC | 3 | | +| CflI | Cellulomonas flavigena | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, PaePI, PstI, SalPI, Srl5DI, Sst12I | +| CfoI | Clostridium formicoaceticum | GCGC | 3 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, HinP1I, HsoI, HspAI, SciNI | +| CfrI | Citrobacter freundii RFL2 | YGGCCR | 1 | | +| Cfr6I | Citrobacter freundii RFL6 | CAGCTG | 3 | | +| Cfr9I | Citrobacter freundii | CCCGGG | 1 | AhyI, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | +| Cfr10I | Citrobacter freundii RFL10 | RCCGGY | 1 | | +| Cfr13I | Citrobacter freundii RFL13 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, FmuI, Nsp7121I, PspPI | +| Cfr42I | Citrobacter freundii RFL42 | CCGCGG | 4 | SacII, CscI, HgaI | +| CfrA4I | Citrobacter freundii A4 | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl2zI, PaePI, PstI, SalPI, Srl5DI, Sst12I | +| CfrBI | Citrobacter freundii 4111 | CCWWGG | 1 | | +| CfrJ4I | Citrobacter freundii J4 | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI | +| CfuI | Caulobacter fusiformis BC-25 | GATC | 2 | | +| CfuII | Caulobacter fusiformis BC-25 | CTGCAG | 5 | AjoI, AliAJI, CfuII, HalII, PaePI, Psp23I, PstI, SalPI, Srl5DI, YenI | +| ChaI | Corynebacterium halofytica | GATC | 4 | BfuCI, Bsp2095I, BspKT6I BtkII, FnuCI, MboI, NmeCI, SsiAI | +| ClaI | Caryophanon latum L | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI | +| CltI | Caryophanon latum | GGCC | 2 | | +| CpfI | Clostridium perfringens | GATC | 1 | AspMDI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NphI, SauMI | +| CpoI | Caseobacter polymorphus | CGGWCCG | 2 | | +| CscI | Calothrix scopulorum | CCGCGG | 4 | Cfr42I, SacII, HgaI | +| CsiAI | Corynebacterium sp. A | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CspAI, PinAI | +| CsiBI | Corynebacterium sp. B | GCGGCCGC | 2 | | +| CspI | Corynebacterium sp. | CGGWCCG | 2 | | +| Csp6I | Corynebacterium sp. RFL6 | GTAC | 1 | AfaI, CviQI, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| Csp45I | Clostridium sporogenes | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BspT104I, FspII, LspI, NspV, SspRFI | +| CspAI | Corynebacterium sp. 301 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, PinAI | +| CspBI | Corynebacterium sp. B | GCGGCCGC | 2 | | +| Csp68KI | Cyanothece sp. BH68K | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, Kzo49I, SmuEI | +| Csp68KII | Cyanothece sp. BH68K | TTCGAA | 2 | Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, SviI | +| Csp68KIII | Cyanothece sp. BH68K | ATGCAT | 5 | BfrBI, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | +| Csp68KVI | Cyanothece sp. BH68K | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | +| CspKVI | Cyanothece sp. BH68K | CGCG | 2 | | +| CstI | Clostridium sticklandii | CTGCAG | 5 | AjoI, AliAJI, CfrA4I, HalII, MhaAI, Pfl21I, PstI, SflI, Srl5DI, YenI | +| CstMI | Corynebacterium striatum M82B | AAGGAG | 12 | — None on May 2010 — | +| CthII | Clostridium thermocellum | CCWGG | 2 | ApaORI, BseBI, Bse24I, Bst2UI, BstNI, BstM6I, EcoRII, MvaI | +| CviAI | Chlorella NC64A (PBCV-1) | GATC | 1 | Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, SauMI | +| CviAII | Chlorella NC64A (PBCV-1) | CATG | 1 | | +| CviBI | Chlorella NC64A (NC-1A) | GANTC | 1 | | +| CviJI | Chlorella NC64A (IL-3A) | RGCY | 2 | | +| CviQI | Chlorella NC64A (NY-2A) | GTAC | 1 | AfaI, Csp6I, CviRII, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| CviRI | Chlorella NC64A (XZ-6E) | TGCA | 2 | | +| CviRII | Chlorella NC64A (XZ-6E) | GTAC | 1 | AfaI, Csp6I, CviQI, HpyBI, PabI, PlaAII, RsaI, RsaNI, | +| CviTI | Chlorella NC64A (CA-1A) | RGCY | 2 | | +| CvnI | Chromatium vinosum | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| DdeI | Desulfovibrio desulfuricans | CTNAG | 1 | | +| DmaI | Deleya marina | CAGCTG | 3 | | +| DpaI | Deleya pacifica | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, Eco255I, RflFII, ScaI, ZrmI | +| DpnI | Diplococcus pneumoniae G41 | GATC | 2 | | +| DpnII | Diplococcus pneumoniae G41 | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CpfI, Kzo9I, NdeII, Sth368I | +| DraI | Deinococcus radiophilus | TTTAAA | 3 | AhaIII, PauAII, SruI | +| DraII | Deinococcus radiophilus | RGGNCCY | 2 | | +| DraIII | Deinococcus radiophilus | CACNNNGTG | 6 | AdeI, BstIZ316I | +| DsaI | Dactylococcopsis salina | CCRYGG | 1 | | +| DsaII | Dactylococcopsis salina | GGCC | 2 | | +| DsaIII | Dactylococcopsis salina | RGATCY | 1 | | +| DsaIV | Dactylococcopsis salina | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiEI, Kzo49I, SmuEI | +| DsaV | Dactylococcopsis salina | CCNGG | 1 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/S.md",".md","21577","134","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:----------|:---------------------------------------|:-----------------------|------:|:-----------------------------------------------------------------------| +| SacI | Streptomyces achromogenes | GAGCTC | 5 | | +| SacII | Streptomyces achromogenes | CCGCGG | 4 | Cfr42I | +| SacNI | Streptomyces achromogenes N-J-H | GRGCYC | 5 | | +| SalI | Streptomyces albus | GTCGAC | 1 | | +| SalPI | Streptomyces albus | CTGCAG | 5 | ApiI, BspMAI, CstI, Ecl37kI, Ecl2zI, Psp23I, PstI, Srl5DI, YenI | +| SanDI | Streptomyces sp. | GGGWCCC | 2 | | +| SapI | Saccharopolyspora sp. | GCTCTTC | 8 | | +| SarI | Streptomyces aureomonopodiales | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, Sru30DI, SseBI, SteI, StuI | +| SatI | Staphylococcus arlettae RFL832 | GCNGC | 2 | | +| SauI | Streptomyces aureofaciens IKA 18/4 | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| Sau96I | Staphylococcus aureus PS96 | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | +| Sau3239I | Streptomyces aureofaciens | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| Sau3AI | Staphylococcus aureus 3A | GATC | 1 | Bce243I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| SauBMKI | Streptomyces aureofaciens BM-K | GCCGGC | 3 | | +| SauHPI | Streptomyces aureofaciens R8/26 | GCCGGC | 3 | | +| SauLPI | Streptomyces aureofaciens B-96 | GCCGGC | 3 | | +| SauLPII | Streptomyces aureofaciens B-96 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| SauMI | Staphylococcus aureus M | GATC | 1 | BscFI, BspAI, BstKTI, ChaI, HacI, MkrAI, RalF40I, SsiAI | +| SauNI | Streptomyces aureofaciens NMU | GCCGGC | 3 | | +| SauSI | Streptomyces aureofaciens 16 | GCCGGC | 3 | | +| SbfI | Streptomyces sp. BF-61 | CCTGCAGG | 6 | | +| Sbi68I | Streptomyces bikiniensis JAM68 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | +| Sbo13I | Shigella boydii 13 | TCGCGA | 3 | | +| SbvI | Streptococcus bovis II/1 | GGCC | 2 | | +| ScaI | Streptomyces caespitosus | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, RflFII, ZrmI | +| SceIII | Saccharomyces cerevisiae | GCCGGC | 1 | | +| SchI | Staphylococcus cohnii Lki 19-320 | GAGTC | 8 | | +| SchZI | Streptomyces chusanensis ZS-2 | CCGCGG | 4 | | +| SciI | Streptoverticillium cinnamoneum | CTCGAG | 3 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SlaI, Sol10179I, XhoI | +| SciNI | Spiroplasma citri ASP2 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI | +| ScrFI | Streptococcus cremoris F | CCNGG | 2 | | +| SdaI | Streptomyces diastaticus Ng7-324 | CCTGCAGG | 6 | | +| SduI | Streptococcus durans RFL3 | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII | +| SecI | Synechocystis sp. 6701 | CCNNGG | 1 | | +| SelI | Synechococcus elongatus | CGCG | 1 | AccII, Bsh1236I, Bsp123I, Bsp50I, BstFNI, BstUI, BtkI, Csp68KVI | +| SenPT16I | Salmonella enteritidis PT16 | CGGCCG | 1 | AaaI, BseX3I, BstZI, EagI, EclXI, Eco52I, XmaIII | +| SenPT14bI | Salmonella enteritidis PT14b | CCGCGG | 4 | | +| SepI | Staphylococcus epidermidis | ATGCAT | 5 | BfrBI, Csp68KIII, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I | +| SexAI | Streptomyces exfoliatus | ACCWGGT | 1 | | +| SexBI | Streptomyces exfoliatus | CCGCGG | 4 | | +| SexCI | Streptomyces exfoliatus | CCGCGG | 4 | | +| SfaI | Streptococcus faecalis zymogenes | GGCC | 2 | | +| SfaNI | Streptococcus faecalis ND547 | GCATC | 8 | | +| SfcI | Streptococcus faecium | CTRYAG | 1 | | +| SfeI | Streptococcus faecalis | CTRYAG | 1 | | +| SflI | Streptoverticillium flavopersicum | CTGCAG | 5 | ApiI, BspMAI, BsuBI, CfrA4I, Psp23I, PstI, Sag23I, Srl5DI, YenI | +| SfoI | Serratia fonticola | GGCGCC | 3 | | +| Sfr274I | Streptomyces fradiae 274 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | +| Sfr303I | Streptomyces fradiae 303 | CCGCGG | 4 | | +| SfuI | Streptomyces fulvissimus | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, PlaII, Ssp1I, SviI | +| SgfI | Streptomyces griseoruber | GCGATCGC | 5 | AsiSI,  RgaI, SfaAI | +| SgrAI | Streptomyces griseus | CRCCGGYG | 2 | | +| SgrBI | Streptomyces griseus | CCGCGG | 4 | | +| SimI | Staphylococcus intermedius 6H | GGGTC | 2 | | +| SinI | Salmonella infantis | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | +| SlaI | Streptomyces lavendulae | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | +| SleI | Synechococcus leopoliensis | CCWGG | 1 | AeuI, AglI, ApaORI, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | +| Slu1777I | Streptomyces lusitanus 1777 | GCCGGC | 3 | | +| SmaI | Serratia marcescens Sb | CCCGGG | 3 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI | +| SmiI | Streptococcus milleri S | ATTTAAAT | 4 | | +| SmlI | Stenotrophomonas maltophilia | CTYRAG | 1 | | +| SmuI | Sphingobacterium multivorum RFL21 | CCCGC | 9 | | +| SmuEI | Streptococcus mutans E | GGWCC | 1 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11BI | +| SnaBI | Sphaerotilus natans | TACGTA | 3 | | +| SniI | Streptomyces niveus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, MvaI, SspAI | +| SnoI | Streptomyces novocastria | GTGCAC | 1 | Alw44I, ApaLI, VneI | +| SolI | Streptoverticillium olivoverticillatum | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, Bce751I, CelI, OkrAI, SolI, SurI | +| Sol10179I | Streptomyces olivochromogenes ST10179 | CTCGAG | 1 | BspAAI, MavI, MlaAI, PaeR7I, Sbi68I, Sol10179I, StrI, XpaI | +| SpaHI | Synechococus parietina | GCATGC | 5 | | +| SpeI | Sphaerotilus natans | ACTAGT | 1 | AhII, AclNI, BcuI | +| SphI | Streptomyces phaeochromogenes | GCATGC | 5 | | +| SplI | Spirulina platensis | CGTACG | 1 | | +| SpmI | Sphingobacterium multivorum RFL21 | ATCGAT | 2 | BanIII, BbvAII, BdiI, BscI, Bsa29I, BspJI, ClaI, LcaI, PgaI, Ssp27144I | +| SpoI | Salmonella potsdam | TCGCGA | 3 | | +| SpuI | Streptomyces pulveraceus | CCGCGG | 4 | | +| SrfI | Streptomyces sp. | GCCCGGGC | 4 | | +| SrlI | Selenomonas ruminantium lactilytica 84 | GCCGGC | 1 | | +| Srl5DI | Selenomonas ruminantium 5 | CTGCAG | 5 | AliAJI, Asp713I, BspMAI, BsuBI, CfrA4I, Pfl21I, PstI, SflI, Srl5DI | +| Srl32DII | Selenomonas ruminantium 32 | GAATTC | 1 | | +| Srl55DI | Selenomonas ruminantium lactilytica 55 | GAATTC | 1 | | +| Srl56DI | Selenomonas ruminantium 56 | CTRYAG | 1 | | +| SruI | Selenomonas ruminantium 18D | TTTAAA | 3 | AhaIII, DraI, PauAII | +| Sru4DI | Selenomonas ruminantium | ATTAAT | 2 | AseI, AsnI, BpoAI, PshBI, VspI | +| Sru30DI | Selenomonas ruminantium 30 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, SseBI, SteI, StuI | +| SsbI | Streptomyces scabies | AAGCTT | 1 | | +| SscL1I | Staphylococcus sp. L1 | GANTC | 1 | | +| Sse9I | Sporosarcina sp. 9 | AATT | 1 | | +| Sse232I | Streptomyces sp. RH232 | CGCCGGCG | 2 | | +| Sse1825I | Streptomyces sp. | GGGWCCC | 2 | | +| Sse8387I | Streptomyces sp. 8387 | CCTGCAGG | 6 | | +| Sse8647I | Streptomyces sp. | AGGWCCT | 2 | | +| SseAI | Streptomyces sp. | GGCGCC | 2 | | +| SseBI | Streptomyces sp. | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SteI, StuI | +| SshAI | Salmonella shikmonah | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| SsiI | Staphylococcus sciuri RFL1 | CCGC | 1 | AciI | +| SsiAI | Staphylococcus sp. A | GATC | 1 | BscFI, BspAI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| SsiBI | Staphylococcus sp. B | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| SslI | Streptococcus salivarius thermophilus | CCWGG | 2 | ApaORI, BseBI, BshGI, BstNI, BstOI, Bst2UI, BthEI, EcoRII, MvaI | +| SsoI | Shigella sonnei 47 | GAATTC | 1 | | +| SsoII | Shigella sonnei 47 | CCNGG | 1 | | +| SspI | Sphaerotilus sp. | AATATT | 3 | | +| Ssp1I | Streptomyces sp. RFL1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PlaII, SfuI, SspRFI, SviI | +| Ssp4800I | Streptomyces sp. BMTU 4800 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, SspBI | +| Ssp5230I | Streptomyces sp. 5230 | GACGTC | 5 | AatII, ZraI | +| Ssp27144I | Synechococcus sp. | ATCGAT | 2 | BanIII, BavCI, BbvAII, BscI, BspJI, BspOVII, BstNZ169I, ClaI, LcaI | +| SspAI | Synechococcus sp. | CCWGG | 1 | AeuI, AorI, Bse17I, BspNI, Bst2I, EcoRII, SniI, SslI, SspAI, ZanI | +| SspBI | Streptomyces sp. | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, BstAUI, Ssp4800I | +| SspCI | Streptomyces sp. | GCCGGC | 3 | | +| SspD5I | Staphylococcus sp. D5 | GGTGA | 8 | AsuHPI, HphI | +| SspD5II | Staphylococcus sp. D5 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SepI, Zsp2I | +| SspRFI | Synechococcus sp. RF-1 | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I, SviI | +| SsrI | Staphylococcus saprophyticus B6 | GTTAAC | 3 | | +| SstI | Streptomyces stanford | GAGCTC | 5 | | +| SstII | Streptomyces stanford | CCGCGG | 4 | | +| Sst12I | Streptomyces sp. ST-12 | CTGCAG | 5 | Asp713I, BloHII, BspMAI, BsuBI, CfuII, Psp23I, PstI, SflI, Srl5DI | +| SteI | Streptomyces tendae | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, StuI | +| SthI | Salmonella thompson YY356 | GGTACC | 1 | Acc65I, AhaB8I, Asp718I, KpnI, | +| Sth117I | Streptococcus thermophilus ST117 | CCWGG | 2 | ApaORI, BseBI, BsiLI, BstNI, BstOI, Bst2UI, EcoRII, MvaI, SspAI | +| Sth132I | Streptococcus thermophilus | CCCG | 8 | | +| Sth134I | Streptococcus thermophilus 134 | CCGG | 1 | | +| Sth368I | Streptococcus thermophilus CNRZ368 | GATC | 1 | BscFI, BspFI, BstKTI, CpfI, HacI, MkrAI, RalF40I, SauMI | +| StrI | Streptomyces thermodiastaticus | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sfr274I, TliI, XhoI | +| StsI | Streptococcus sanguis 54 | GGATG | 9 | | +| StuI | Streptomyces tubercidicus | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI | +| StyI | Salmonella typhi | CCWWGG | 1 | | +| StyD4I | Salmonella typhi D4 | CCNGG | 1 | | +| SuaI | Sulfolobus acidocaldarius | GGCC | 2 | | +| SuiI | Sulfolobus islandicus REN2HI | GCWGC | 1 | AceI, ApeKI, Taq52I, TseI | +| SunI | Synechococcus uniformis | CGTACG | 1 | | +| SurI | Sporosarcina ureae 2 | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, OkrAI, RspLKII, SolI | +| SviI | Streptomyces violochromogenes | TTCGAA | 2 | AsuII, Bpu14I, Bsp119I, CbiI, MlaI, PpaAI, SfuI, Ssp1I | +| SwaI | Staphylococcus warneri | ATTTAAAT | 4 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/Bst-Bv.md",".md","17071","106","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:----------|:------------------------------------|:-----------------------|------:|:--------------------------------------------------------------------------| +| BstI | Bacillus stearothermophilus 1503-4R | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, BnaI, BspAAIII, Nsp29132II | +| Bst1I | Bacillus stearothermophilus 1 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| Bst2I | Bacillus stearothermophilus 2 | CCWGG | 2 | AglI, BseBI, Bse17I, BstNI, BstOI, Bst2UI, CthII, EcoRII, MvaI | +| Bst6I | Bacillus stearothermophilus 6 | CTCTTC | 7 | | +| Bst11I | Bacillus stearothermophilus 11 | ACTGG | 6 | | +| Bst12I | Bacillus stearothermophilus 12 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst71I, BstV1I | +| Bst19I | Bacillus stearothermophilus 19 | GCATC | 9 | | +| Bst19II | Bacillus stearothermophilus 19 | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| Bst28I | Bacillus stearothermophilus 28 | ATCGAT | 2 | BciBI, BdiI, Bli41I, Bsa29I, Bsp106I, BspDI, LplI, SpmI, ZhoI | +| Bst38I | Bacillus stearothermophilus 38 | CCWGG | 2 | AorI, BseBI, Bse17I, BsiLI, BspNI, BstOI, Bst2UI, EcoRII, MvaI | +| Bst40I | Bacillus stearothermophilus 40 | CCGG | 1 | | +| Bst71I | Bacillus stearothermophilus 71 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, BstV1I | +| Bst98I | Bacillus stearothermophilus C98 | CTTAAG | 1 | | +| Bst100I | Bacillus stearothermophilus 100 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| Bst1107I | Bacillus stearothermophilus RFL1107 | GTATAC | 3 | | +| BstACI | Bacillus stearothermophilus AC | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, HgiDI, Hsp92I | +| BstAUI | Bacillus stearothermophilus AU | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BsrGI, Ssp4800I, SspBI | +| BstBI | Bacillus stearothermophilus B225 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, LspI, NspV, SspRFI | +| Bst2BI | Bacillus stearothermophilus 2B | CACGAG | 1 | | +| BstBAI | Bacillus stearothermophilus BA | YACGTR | 3 | | +| BstBSI | Bacillus stearothermophilus BS | GTATAC | 3 | | +| BstB7SI | Bacillus stearothermophilus B7S | RCCGGY | 1 | | +| BstBS32I | Bacillus stearothermophilus BS32 | GAAGAC | 8 | | +| BstBZ153I | Bacillus stearothermophilus BZ153 | GCGCGC | 1 | | +| Bst4CI | Bacillus stearothermophilus 4C | ACNGT | 3 | | +| BstC8I | Bacillus stearothermophilus C8 | GCNNGC | 3 | | +| BstD102I | Bacillus stearothermophilus D102 | CCGCTC | 3 | AccBSI, BsrBI, Bst31NI, MbiI | +| BstDEI | Bacillus stearothermophilus DE | CTNAG | 1 | | +| BstDSI | Bacillus stearothermophilus DS | CCRYGG | 1 | | +| BstEII | Bacillus stearothermophilus ET | GGTNACC | 1 | AcrII, BstPI, BstT9I, BstT10I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstENII | Bacillus stearothermophilus EN | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, CcyI, FnuCI, MboI, NmeCI, SsiAI | +| BstEZ359I | Bacillus stearothermophilus EZ359 | GTTAAC | 3 | | +| BstFI | Bacillus stearothermophilus FH58 | AAGCTT | 1 | | +| BstF5I | Bacillus stearothermophilus F5 | GGATG | 7 | | +| BstFNI | Bacillus stearothermophilus | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BstUI, Csp68KVI, FauBII, MvnI, SelI | +| BstFZ438I | Bacillus stearothermophilus FZ438 | CCCGC | 9 | | +| BstGZ53I | Bacillus stearothermophilus GZ53 | CGTCTC | 7 | | +| BstH2I | Bacillus stearothermophilus H2 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, HaeII, LpnI | +| BstH9I | Bacillus stearothermophilus H9 | GGATC | 9 | AclWI, AlwI, BinI,  BpuFI, BspPI,  Bst31TI, BthII, Bth617I, EacI | +| BstHHI | Bacillus stearothermophilus HH | GCGC | 3 | AspLEI, BspLAI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BstHPI | Bacillus stearothermophilus HP | GTTAAC | 3 | | +| BstIZ316I | Bacillus stearothermophilus IZ316 | CACNNNGTG | 6 | AdeI, DraIII | +| BstJZ301I | Bacillus stearothermophilus JZ301 | CTNAG | 1 | | +| BstKTI | Bacillus stearothermophilus KT | GATC | 3 | AspMDI, Bsp2095I, Bst19II, BspKT6I, DpnII, MboI, NmeCI, SsiAI | +| BstM6I | Bacillus stearothermophilus M6 | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, Fsp1604I, MvaI | +| BstMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BsoMAI | +| BstMBI | Bacillus stearothermophilus MB | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I | +| BstMCI | Bacillus stearothermophilus MC | CGRYCG | 4 | | +| BstMZ611I | Bacillus stearothermophilus MZ611 | CCNGG | 1 | | +| BstNI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, Bst2UI, Fsp1604I, SniI, Sth117I | +| Bst31NI | Bacillus stearothermophilus 31N | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, MbiI | +| BstNSI | Bacillus stearothermophilus 1161NS | RCATGY | 5 | | +| BstNZ169I | Bacillus stearothermophilus NZ169 | ATCGAT | 2 | BanIII, BciBI, BdiI, Bli41I, Bsa29I, BspDI, LplI, Rme21I, SpmI, ZhoI | +| BstOI | Bacillus stearothermophilus O22 | CCWGG | 2 | AjnI, ApyI, BciBII, BptI, Bst1I, Bst2UI, Fsp1604I, SniI, Sth117I | +| BstOZ616I | Bacillus stearothermophilus OZ616 | GGGAC | 9 | | +| BstPI | Bacillus stearothermophilus | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT9I, EcaI, Eco91I, EcoO65I, NspSAII, PspEI | +| BstPZ418I | | GGATG | 8 | | +| BstPZ740I | Bacillus stearothermophilus PZ740 | CTTAAG | 1 | | +| BstRZ246I | Bacillus stearothermophilus RZ246 | ATTTAAAT | 4 | | +| BstSI | Bacillus stearothermophilus S183 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, NspIII, OfoI, PunAI | +| BstSCI | Bacillus stearothermophilus SC | CCNGG | 1 | | +| BstSFI | Bacillus stearothermophilus SF | CTRYAG | 1 | | +| BstSNI | Bacillus stearothermophilus SN | TACGTA | 3 | | +| BstSWI | Bacillus stearothermophilus SW | ATTTAAAT | 4 | | +| BstT7I | Bacillus stearothermophilus T7 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, FbaI, Ksp22I,  ParI | +| BstT9I | Bacillus stearothermophilus T9 | GGTNACC | 1 | AspAI, Bse64I, BstT10I, BstPI, Eco91I, EcoO128I, NspSAII, PspEI | +| BstT10I | Bacillus stearothermophilus T10 | GGTNACC | 1 | AspAI, BseT10I, BstEII, BstT10I, Eco91I, EcoO128I, NspSAII, PspEI | +| Bst31TI | Bacillus stearothermophilus 31T | GGATC | 9 | | +| BstTS5I | Bacillus stearothermophilus TS5 | GAAGAC | 8 | | +| BstUI | Bacillus stearothermophilus U458 | CGCG | 2 | AccII, BceBI, BepI, Bpu95I, BtkI, Csp68KVI, FauBII, MvnI, SelI | +| Bst2UI | Bacillus stearothermophilus 2U | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, SniI, SslI, TaqXI, ZanI | +| BstVI | Bacillus stearothermophilus V | CTCGAG | 1 | BluI, BssHI, MlaAI, PanI, SauLPII, SciI, SlaI, StrI, XhoI | +| BstV1I | Bacillus stearothermophilus V1 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bsp423I, Bst12I, Bst71I | +| BstV2I | Bacillus stearothermophilus V2 | GAAGAC | 8 | | +| BstX2I | Bacillus stearothermophilus X2 | RGATCY | 1 | | +| BstYI | Bacillus stearothermophilus Y406 | RGATCY | 1 | | +| BstZI | Bacillus stearothermophilus Z130 | CGGCCG | 1 | AaaI, BseX3I, EagI, EclXI, Eco52I, SenPT16I, XmaIII | +| BstZ17I | Bacillus stearothermophilus 38M | GTATAC | 3 | | +| Bsu6I | Bacillus subtilis 6v1 | CTCTTC | 7 | | +| Bsu15I | Bacillus subtilis 15 | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, BsuTUI, ClaI | +| Bsu23I | Bacillus subtilis 23 | TCCGGA | 1 | AccIII, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | +| Bsu36I | Bacillus subtilis 36 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Bsu54I | Bacillus subtilis 54 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| Bsu1532I | Bacillus subtilis 1532 | CGCG | 2 | BceBI, Bpu95I, Bsp123I, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsu1854I | Bacillus subtilis 1854 | GRGCYC | 5 | | +| BsuBI | Bacillus subtilis | CTGCAG | 5 | AjoI, BloHII, CflI, CstI, Ecl37kI, HalII, Psp23I, PstI, SalPI, SflI, YenI | +| BsuFI | Bacillus subtilis | CCGG | 1 | | +| BsuMI | Bacillus subtilis 168 | CTCGAG | 1 | XhoI, BssHI, TliI, PaeR7I, Sfr274I, SlaI, StrI | +| BsuRI | Bacillus subtilis R | GGCC | 2 | HaeIII | +| BsuTUI | Bacillus subtilis TU | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, ClaI | +| BteI | Brochothrix thermosphacter | GGCC | 2 | | +| BtgI | Bacillus thermoglucosidasius | CCRYGG | 1 | | +| BtgZI | Bacillus thermoglucosidasius | GCGATG | 10 | | +| BthAI | Bacillus thuringiensis AII | GGWCC | 1 | BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI | +| BthCI | Bacillus thuringiensis 2294 | GCNGC | 4 | | +| BthDI | Bacillus thuringiensis D4 | CCWGG | 2 | AorI, ApyI, Bse24I, BstNI, BstOI, Bst2UI, CbrI, EcoRII, MvaI, SleI | +| BthEI | Bacillus thuringiensis E | CCWGG | 2 | AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII, MvaI, SleI | +| BtkI | Bacillus thuringiensis Kumantoensis | CGCG | 2 | BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI, ThaI | +| BtkII | Bacillus thuringiensis Kumantoensis | GATC | 1 | BfuCI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NmeCI, SauMI | +| BtrI | Bacillus stearothermophilus SE-U62 | CACGTC | 3 | | +| BtsI | Bacillus thermoglucosidasius | GCAGTG | 8 | | +| BveI | Brevundimonas vesicularis RFL1 | ACCTGC | 10 | Acc36I, BfuAI, BspMI | +| BvuI | Bacillus vulgatis | GRGCYC | 5 | | +| BvuBI | Bacteroides vulgatus | CGTACG | 1 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/O-R.md",".md","20097","124","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:-----------|:--------------------------------------|:-----------------------|------:|:------------------------------------------------------------------------| +| OfoI | Oscillatoria foreaui A-1340 | CYCGRG | 1 | AquI, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, PlaAI, PunAI | +| OkrAI | Oceanospirillum kriegii | GGATCC | 1 | BamHI, Bce751I, BnaI, Bsp98I, BstI, OkrAI, SolI, Uba4009I | +| OxaNI | Oerskovia xanthineolytica N | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| PabI | Pyrococcus abyssi | GTAC | 3 | AfaI, Csp6I, CviQI, HpyBI, HpyBI, PlaAII, RsaI,  RsaNI, | +| PacI | Pseudomonas alcaligenes | TTAATTAA | 5 | | +| Pac25I | Pseudomonas alcaligenes | CCCGGG | 1 | AhyI, Cfr9I, EaeAI, EclRI, PspAI, PspALI, XcyI, XmaI, XmaCI | +| PaeI | Pseudomonas aeruginosa | GCATGC | 5 | | +| PaeAI | Pseudomonas aeruginosa | CCGCGG | 4 | | +| PaeBI | Pseudomonas aeruginosa - 18 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | +| PaeHI | Pseudomonas aeruginosa 4148 | GRGCYC | 5 | | +| PaeHII | Pseudomonas aeruginosa 4148 | CTGCAG | 5 | AliAJI, BspBI, BspMAI, CfuII, Ecl2zI, HalII, Srl5DI, Sst12I, XcpI | +| PaeQI | Pseudomonas aeruginosa Q2 | CCGCGG | 4 | | +| PaeR7I | Pseudomonas aeruginosa PA0303 pMG7 | CTCGAG | 1 | AbrI, BluI, BssHI, MavI, Sau3239I, Sol10179I, StrI, TliI | +| Pae2kI | Pseudomonas aeruginosa 2k | AGATCT | 1 | | +| Pae5kI | Pseudomonas aeruginosa 5k | CCGCGG | 4 | | +| Pae14kI | Pseudomonas aeruginosa 14k | CCGCGG | 4 | | +| Pae17kI | Pseudomonas aeruginosa 17k | CAGCTG | 3 | | +| Pae18kI | Pseudomonas aeruginosa 18k | AGATCT | 1 | | +| PagI | Pseudomonas alcaligenes Sau 14-027 | TCATGA | 1 | | +| PalI | Providencia alcalifaciens | GGCC | 2 | | +| PamI | Phormidium ambiguum | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, Pun14627I | +| PamII | Phormidium ambiguum | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiDI, HgiGI, HgiHII, Hin1I, Hsp92I, Msp17I | +| PanI | Pseudomonas alkanolytica | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, Sbi68I, Sfr274I, SlaI, XpaI | +| PasI | Pseudomonas anguilliseptica RFL1 | CCCWGGG | 2 | — None on May 2010 — | +| PauI | Paracoccus alcaliphilus ZVK3-3 | GCGCGC | 1 | | +| PauAI | Phormidium autumnale | RCATGY | 5 | | +| PauAII | Phormidium autumnale | TTTAAA | 3 | AhaIII, DraI, SruI | +| PceI | Planococcus citreus 55 | AGGCCT | 3 | AatI, AspMI, GdiI, PceI, Pme55I, SarI, Sru30DI, SseBI, SteI, StuI | +| PciI | Planococcus citreus SE-F45 | ACATGT | 1 | | +| PctI | Planococcus citreus SM | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI BmaHI, BsaMI, BscCI, Mva1269I | +| Pde12I | Paracoccus denitrificans 12 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | +| Pde133I | Paracoccus denitrificans 133 | GGCC | 2 | | +| Pde137I | Paracoccus denitrificans 137 | CCGG | 1 | | +| PdiI | Pseudomonas diminuta Mck 33-321 | GCCGGC | 3 | | +| PfaAI | Phormidium favosum | GGYRCC | 1 | AccB1I, BanI, BbvBI, BshNI, Eco64I, HgiCI, HgiHI, MspB4I | +| PfaAII | Phormidium favosum | CATATG | 2 | | +| PfaAIII | Phormidium favosum | GCATGC | 5 | | +| PfeI | Psychrobacter faecalis RFL1 | GAWTC | 1 | | +| Pfl8I | Pseudomonas fluorescens 8 | GGATCC | 1 | AliAJI, BspBI, BsuBI, CflI, CfrA4I, PaePI, Pfl21I, PstI, SflII, Sst12I | +| Pfl21I | Pseudomonas sp. 21 | CTGCAG | 5 | | +| Pfl23II | Pseudomonas fluorescens RFL23 | CGTACG | 1 | | +| Pfl27I | Pseudomonas fluorescens RFL27 | RGGWCCY | 2 | | +| PflFI | Pseudomonas fluorescens biotype F | GACNNNGTC | 4 | AspI, AtsI, PsyI, TelI, Tth111I | +| PflKI | Pseudomonas fluorescens | GGCC | 2 | | +| PfoI | Pseudomonas fluorescens biovar 126 | TCCNGGA | 1 | | +| PgaI | Pseudomonas gladioli B4 | ATCGAT | 2 | BanIII, BbvAII, BliAI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | +| PhaI | Pasteurella haemolytica | GCATC | 8 | | +| PhoI | Pyrococcus horikoshii OT3 | GGCC | 2 | | +| PinAI | Pseudomonas inequalis | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, BshTI CsiAI, CspAI | +| PinBI | Phormidium inundatum | ATGCAT | 5 | EcoT22I, BfrBI, Mph1103I, NsiI, Ppu10I, SepI, SspD5II, Zsp2I | +| PinBII | Phormidium inundatum | TCCGGA | 1 | Aor13HI, BlfI, Bsp13I, BspEI, Bsu23I, Kpn2I, PinBII, PtaI | +| PlaI | Phormidium lapideum | GGCC | 2 | | +| PlaII | Phormidium lapideum | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, SfuI, SspRFI | +| PlaAI | Phormidium laminosum | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | +| PlaAII | Phormidium laminosum | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, RsaI,  RsaNI, | +| PleI | Pseudomonas lemoignei | GAGTC | 9 | | +| Ple19I | Pseudomonas lemoignei 19 | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, MvrI, Psu161I, PvuI, RshI, XorII | +| PmaCI | Pseudomonas maltophilia CB50P | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmlI, PspCI | +| PmeI | Pseudomonas mendocina | GTTTAAAC | 4 | MssI | +| Pme55I | Pseudomonas mendocina 55 | AGGCCT | 3 | AatI, AspMI, Eco147I, GdiI, PceI, SarI, Sru30DI, SseBI, SteI, StuI | +| PmlI | Pseudomonas maltophilia | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PspCI | +| PovII | Proteus vulgaris | CAGCTG | 3 | | +| PpaAI | Phormidium papyraceum | TTCGAA | 2 | AsuII, BimI, Bsp119I, CbiI, Csp68KII, SfuI, SspRFI, SviI | +| PpaAII | Phormidium papyraceum | TCGA | 1 | | +| PpeI | Phormidium persicinum | GGGCCC | 5 | ApaI, Bsp120I, PspOMI | +| PpsI | Pseudomonas pseudoalcaligenes PL | GAGTC | 9 | | +| Ppu10I | Pseudomonas putida RFL10 | ATGCAT | 1 | BfrBI, Csp68KII, EcoT22I, Mph1103I, NsiI, SepI, SspD5II | +| Ppu111I | Pseudomonas putida P111 | GAATTC | 1 | | +| PpuAI | Pseudomonas putida A1 | CGTACG | 1 | | +| PpuMI | Pseudomonas putida M | RGGWCCY | 2 | | +| PpuXI | Pseudomonas putida X | RGGWCCY | 2 | | +| PshBI | Plesiomonas shigelloides TPS970 | ATTAAT | 2 | AseI, AsnI, BpoAI, Sru4DI, VspI | +| PsiI | Pseudomonas sp. SE-G49 | TTATAA | 3 | | +| Psp03I | Phormidium sp. | GGWCC | 4 | Bme216I, CauI, EagMI, FdiI, HgiBI, HgiHIII, SinI, VpaK11AI | +| Psp5II | Pseudomonas sp. RFL5 | RGGWCCY | 2 | | +| Psp6I | Pseudomonas sp. B6 | CCWGG | 1 | AeuI, AglI, ApaORI, Bse17I, EcoRII, Fsp1604I, SspAI, Sth117I | +| Psp23I | Pseudomonas sp. 23 | CTGCAG | 5 | ApiI, BspBI, CflI, MhaAI, Pfl21I, PstI, SalPI, Sst12I, YenI | +| Psp1406I | Pseudomonas pseudoalcaligenes RFL1406 | AACGTT | 2 | AclI | +| PspAI | Pseudomonas sp. | CCCGGG | 1 | AhyI, CfrJ4I, EaeAI, EclRI, Pac25I, SmaI, TspMI, XcyI, XmaI, XmaCI | +| PspALI | Pseudomonas sp. AL1637 | CCCGGG | 3 | AhyI, Cfr9I, EaeAI, EclRI, PspALI, SmaI, TspMI, XcyI, XmaI, XmaCI | +| Psp124BI | Pseudomonas sp. 124B | GAGCTC | 5 | | +| PspCI | Pseudomonas sp. C | CACGTG | 3 | AcvI, BcoAI, BbrPI, Eco72I, PmaCI, PmlI | +| PspEI | Pseudomonas sp. E | GGTNACC | 1 | AcrII, AspAI, BstEII, BstPI, Eci125I, Eco91I, EcoO65I, EcoO128I | +| PspGI | Pyrococcus sp. GI-H | CCWGG | 1 | AeuI, AjnI, AorI, Bse17I, EcoRII, Fsp1604I, Psp6I, SspAI, Sth117I | +| PspLI | Pseudomonas sp. L | CGTACG | 1 | | +| PspN4I | Pseudomonas sp. N4 | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, NlaIV | +| PspOMI | Pseudomonas sp. OM2164 | GGGCCC | 1 | ApaI, Bsp120I, PpeI | +| PspPI | Psychrobacter immobilis TA137 | GGNCC | 1 | AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | +| PspPPI | Pseudomonas sp. PP | RGGWCCY | 2 | | +| PspXI | Pseudomonas sp. A1-1 | VCTCGAGB | 2 | | +| PssI | Pseudomonas sp. | RGGNCCY | 5 | | +| PstI | Providencia stuartii 164 | CTGCAG | 5 | AliAJI, BspBI, CfuII, Ecl2zI, HalII, PstI, Sag16I, Sag23I, Sst12I, XcpI | +| PstNHI | Pseudomonas stutzeri NH | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, LlaG2I | +| PsuI | Pseudomonas stutzeri Mck 28-pH52 | RGATCY | 1 | | +| Psu161I | Pseudomonas stutzeri 161 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, PvuI, RshI, XorII | +| PsuAI | Phormidium subfuscum | YACGTR | 3 | | +| PsyI | Pseudomonas syringae Lki 1-pH124 | GACNNNGTC | 4 | AspI, AtsI, PflFI, TelI, Tth111I | +| PtaI | Phormidium tadzschicicum | TCCGGA | 1 | Aor13HI, BlfI, BseAI, Bsp13I, BspEI, Kpn2I, PinBII, PtaI | +| Pun14627I | Phormidium uncinatum 1462/7 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, NsbI, PamI | +| Pun14627II | Phormidium uncinatum 1462/7 | CAGCTG | 3 | | +| PunAI | Phormidium uncinatum | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco27kI, Nli3877I, PlaAI | +| PunAII | Phormidium uncinatum | RCATGY | 5 | | +| PvuI | Proteus vulgaris | CGATCG | 4 | Afa22MI, BspCI, ErhB9I, NblI, Ple19I, Psu161I, RshI, XorII | +| PvuII | Proteus vulgaris | CAGCTG | 3 | | +| Pvu84II | Proteus vulgaris 84 | CAGCTG | 3 | | +| RalF40I | Ruminococcus albus F-40 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, HacI, MkrAI, Sau3AI, SsiAI | +| RcaI | Rhodococcus capsulatum | TCATGA | 1 | | +| RflFI | Ruminococcus flavefaciens FD-1 | GTCGAC | 1 | | +| RflFII | Ruminococcus flavefaciens FD-1 | AGTACT | 3 | Acc113I, AssI,  BmcAI, Bpa34I, DpaI, Eco255I, ScaI, ZrmI | +| RleAI | Rhizobium leguminosarum | CCCACA | 12 | | +| RmaI | Rhodothermus marinus | CTAG | 1 | | +| Rme21I | Rhizobium meliloti | ATCGAT | 2 | BanIII, BbvAII, BliRI, BscI, BspJI, BstNZ169I, ClaI, LcaI, Ssp27144I | +| RsaI | Rhodopseudomonas sphaeroides | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, HpyBI, PabI, PlaAII,  RsaNI, | +| RshI | Rhodopseudomonas sphaeroides 2.4.1 | CGATCG | 4 | Afa16RI, BspCI, EagBI, MvrI, Ple19I, Psu161I, PvuI, XorII | +| RspLKI | Rhodococcus sp. LK2 | GCATGC | 5 | | +| RspLKII | Rhodococcus sp. LK2 | GGATCC | 1 | AliI, AsiI, BamHI, Bce751I, Nsp29132II, OkrAI, RspLKII, SolI | +| RspXI | Rhodococcus sp. | TCATGA | 1 | | +| RsrI | Rhodopseudomonas sphaeroides | GAATTC | 1 | | +| RsrII | Rhodopseudomonas sphaeroides | CGGWCCG | 2 | | +| Rsr2I | Rhodobacter sphaeroides SE-I2 | CGGWCCG | 2 | | +| RtrI | Rhizobium trifolii | GTCGAC | 1 | | +| Rtr63I | Rhizobium trifolii 63 | GTCGAC | 1 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/G-K.md",".md","13074","86","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:----------|:-------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| +| GalI | Gluconobacter albidus | CCGCGG | 4 | | +| GceI | Gluconobacter cerinus | CCGCGG | 4 | | +| GceGLI | Gluconobacter cerinus | CCGCGG | 4 | | +| GdiI | Gluconobacter dioxyacetonicus | AGGCCT | 3 | AatI, AspMI, Eco147I, PceI, SarI, Sru30DI, SseBI, SteI, StuI | +| GdiII | Gluconobacter dioxyacetonicus | CGGCCR | 1 | | +| GstI | Geobacillus stearothermophilus | GGATCC | 1 | | +| GsuI | Gluconobacter suboxydans H-15T | CTGGAG | 13 | | +| HacI | Halococcus acetoinfaciens | GATC | 1 | Bme12I, Bsp67I, BstENII, CcyI, FnuEI, MgoI, NphI, Sau3AI | +| HaeI | Haemophilus aegyptius | WGGCCW | 3 | | +| HaeII | Haemophilus aegypticus | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, LpnI | +| HaeIII | Haemophilus aegypticus | GGCC | 2 | BsuRI | +| HalI | Hafnia alvei B6 | GAATTC | 1 | | +| HalII | Hafnia alvei B6 | CTGCAG | 5 | AjoI, AliAJI, Bsp63I, CfrA4I, CfuII, CstI, PstI, SflI, Srl5DI, Sst12I | +| HapII | Haemophilus aphrophilus | CCGG | 1 | | +| HgaI | Haemophilus gallinarum | GACGC | 8 | | +| HgiI | Herpetosiphon giganteus 3303 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiHII, Hin1I, PamII | +| HgiAI | Herpetosiphon giganteus HP1023 | GWGCWC | 5 | Alw21I, AspHI, Bsh45I, BsiHKAI,  Bsm6I, HpyF46II, MspV281I | +| HgiBI | Herpetosiphon giganteus Hpg5 | GGWCC | 1 | Bme18I, BthAI, DsaIV, ErpI, FspMSI, HgiEI, Psp03I, VpaK11AI | +| HgiCI | Herpetosiphon giganteus Hpg9 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiHI, MspB4I, PfaAI | +| HgiCII | Herpetosiphon giganteus Hpg9 | GGWCC | 1 | Bme18I, BthAI, DsaIV, FspMSI, HgiHIII, Psp03I, VpaK11AI | +| HgiCIII | Herpetosiphon giganteus Hpg9 | GTCGAC | 1 | | +| HgiDI | Herpetosiphon giganteus Hpa2 | GRCGYC | 2 | AcyI, AsuIII, BbiII, BstACI, HgiGI, HgiI, Hin1I, PamII | +| HgiDII | Herpetosiphon giganteus Hpa2 | GTCGAC | 1 | | +| HgiEI | Herpetosiphon giganteus Hpg24 | GGWCC | 1 | Bme216I, BthAI, DsaIV, ErpI, FspMSI, HgiHIII, VpaK11AI | +| HgiGI | Herpetosiphon giganteus Hpa1 | GRCGYC | 2 | AcyI, AosII, BbiII, BstACI, HgiI, HgiGI, Msp17I, PamII | +| HgiHI | Herpetosiphon giganteus HP1049 | GGYRCC | 1 | AccB1I, BanI, BspT107I, BshNI, Eco64I, HgiCI, MspB4I, PfaAI | +| HgiHII | Herpetosiphon giganteus HP1049 | GRCGYC | 2 | AosII, AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Msp17I, PamII | +| HgiHIII | Herpetosiphon giganteus HP1049 | GGWCC | 1 | Bme216I, DsaIV, ErpI, HgiBI, Psp03I, VpaK11AI, VpaK11BI | +| HgiJI | Herpetosiphon giganteus HFS101 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI | +| HgiJII | Herpetosiphon giganteus HFS101 | GRGCYC | 5 | | +| HgiS22I | Herpetosiphon giganteus | CCSGG | 2 | AhaI, AseII, AsuC2I, BcnI, CauII, Eco1831I, EcoHI, Kpn49kII | +| HhaI | Haemophilus haemolyticus | GCGC | 3 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, SciNI | +| HhaII | Haemophilus haemolyticus | GANTC | 1 | | +| Hin1I | Haemophilus influenzae RFL1 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, HgiI, HgiDI, HgiDI, Hsp92I | +| Hin1II | Haemophilus influenzae RFL1 | CATG | 4 | | +| Hin2I | Haemophilus influenzae RFL2 | CCGG | 1 | | +| Hin6I | Haemophilus influenzae RFL6 | GCGC | 1 | AspLEI, BspLAI, BstHHI, CfoI, FnuDIII, HhaI, HsoI, HspAI, SciNI | +| HinJCI | Haemophilus influenzae JC9 | GTYRAC | 3 | | +| HinP1I | Haemophilus influenzae P1 | GCGC | 1 | BspLAI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HsoI, HspAI, SciNI | +| HincII | Haemophilus influenzae Rc | GTYRAC | 3 | | +| HindII | Haemophilus influenzae Rd | GTYRAC | 3 | | +| HindIII | Haemophilus influenzae Rd | AAGCTT | 1 | | +| HinfI | Haemophilus influenzae Rf | GANTC | 1 | | +| HjaI | Hyphomonas jannaschiana | GATATC | 3 | | +| HpaI | Haemophilus parainfluenzae | GTTAAC | 3 | | +| HpaII | Haemophilus parainfluenzae | CCGG | 1 | | +| HphI | Haemophilus parahaemolyticus | GGTGA | 9 | AsuHPI, SspD5I | +| Hpy8I | Helicobacter pylori A 8-5 | GTNNAC | 3 | | +| Hpy51I | Helicobacter pylori 51 | GTSAC | 1 | | +| Hpy99I | Helicobacter pylori J99 | CGWCG | 5 | | +| Hpy178III | Helicobacter pylori J178 | TCNNGA | 2 | | +| Hpy188I | Helicobacter pylori J188 | TCNGA | 3 | | +| Hpy188III | Helicobacter pylori J188 | TCNNGA | 2 | | +| HpyAV | Helicobacter pylori 26695 | CCTTC | 9 | | +| HpyBI | Helicobacter pylori Roberts | GTAC | 2 | AfaI, Csp6I, CviQI, CviRII, PabI, PlaAII, RsaI, RsaNI | +| HpyBII | Helicobacter pylori Roberts | GTNNAC | 3 | | +| HpyCI | Helicobacter pylori | GATATC | 3 | | +| HpyC1I | Helicobacter pylori | CCATC | 9 | | +| HpyCH4I | Helicobacter pylori CH4 | CATG | 4 | | +| HpyCH4III | Helicobacter pylori CH4 | ACNGT | 3 | | +| HpyCH4IV | Helicobacter pylori CH4 | ACGT | 1 | | +| HpyCH4V | Helicobacter pylori CH4 | TGCA | 2 | | +| HpyF44III | Helicobacter pylori RFL44 | TGCA | 2 | | +| HsoI | Haemophilus somnus 2336 | GCGC | 1 | AspLEI, BstHHI, CfoI, FnuDIII, Hin6I, HinP1I, HspAI, SciNI | +| Hsp92I | Haemophilus sp. 92 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, HgiI, HgiDI, HgiHII, Hin1I, Hsp92I | +| Hsp92II | Haemophilus sp. 92 | CATG | 4 | | +| HspAI | Haemophilus sp. A | GCGC | 1 | AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, SciNI | +| HsuI | Haemophilus suis | AAGCTT | 1 | | +| ItaI | Ilyobcater tartaricus | GCNGC | 2 | | +| KasI | Kluyvera ascorbata | GGCGCC | 1 | | +| Kaz48kI | Klebsiella azeanae | RGGNCCY | 5 | | +| KoxII | Klebsiella oxytoca | GRGCYC | 5 | | +| KpnI | Klebsiella pneumoniae OK8 | GGTACC | 5 | Acc65I, AhaB8I, Asp718I, SthI | +| Kpn2I | Klebsiella pneumoniae RFL2 | TCCGGA | 1 | Aor13HI, BbvAIII, BseAI, BsiMI, BspEI, BspMII, CauB3I, MroI | +| Kpn378I | Klebsiella pneumoniae 378 | CCGCGG | 4 | | +| Kpn2kI | Klebsiella pneumoniae 2k | CCNGG | 1 | | +| Kpn49kI | Klebsiella pneumoniae 49k | GAATTC | 1 | | +| Kpn49kII | Klebsiella pneumoniae 49k | CCSGG | 1 | AhaI, AsuC2I, BcnI, CauII, EcoHI, HgiS22I, Mgl14481I, NciI, | +| KspI | Kluyvera sp. | CCGCGG | 4 | | +| Ksp22I | Kurthia sp. 22 | TGATCA | 1 | AbaI, BclI, BsiQI, BspXII, BstT7I, FbaI,  ParI | +| Ksp632I | Kluyvera sp. 632 | CTCTTC | 7 | | +| KspAI | Kurthia sp. N88 | GTTAAC | 3 | | +| Kzo9I | Kurthia zopfii 9 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstMBI, CpfI, LlaAI, NdeII, Sth368I | +| Kzo49I | Kurthia zopfii 49 | GGWCC | 1 | Bme216I, CauI, DsaIV, FdiI, HgiBI, HgiHIII, Psp03I, VpaK11AI |","Markdown" +"Bioengineering","telatin/seqfu2","re/Bsp-Bss.md",".md","15588","98","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:-----------|:------------------------------------|:-----------------------|------:|:-----------------------------------------------------------------------| +| Bsp6I | Bacillus sp. RFL6 | GCNGC | 2 | | +| Bsp13I | Bacillus sp. 13 | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | +| Bsp19I | Bacillus sp. 19 | CCATGG | 1 | | +| Bsp50I | Bacillus sp. RFL50 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | +| Bsp63I | Bacillus sphaericus 63 | CTGCAG | 5 | AjoI, Asp713I, BloHII, MhaAI, Pfl21I, PstI, SalPI, SflI, Sst12I, YenI | +| Bsp67I | Bacillus sphaericus 67 | GATC | 1 | AspMDI, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp68I | Bacillus sp. RFL68 | TCGCGA | 3 | NruI | +| Bsp98I | Bacillus sp. RFL98 | GGATCC | 1 | AccEBI, AliI, BamHI, BnaI, BstI, CelI, OkrAI, NspSAIV, Pfl8I, SurI | +| Bsp105I | Bacillus sphaericus 105 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp106I | Bacillus sphaericus 106 | ATCGAT | 2 | BbvAII, Bci29I, BciBI, BcmI, BspOVII, BstNZ169I, Rme21I | +| Bsp119I | Bacillus sp. RFL119 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BspT104I, Csp45I, FspII, NspV, SspRFI | +| Bsp120I | Bacillus sp. RFL120 | GGGCCC | 1 | ApaI, PpeI, PspOMI | +| Bsp123I | Bacillus sp. 123 | CGCG | 2 | BceBI, Bsh1236I, BstFNI, BstUI, BtkI, Csp68KVI, FnuDII, MvnI, ThaI | +| Bsp143I | Bacillus sp. RFL143 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, NdeII, Sth368I, Sau3AI | +| Bsp143II | Bacillus sp. RFL143 | RGCGCY | 5 | AccB2I,  BfoI, Bme142I, BstH2I, HaeII, LpnI | +| Bsp211I | Bacillus sphaericus 211 | GGCC | 2 | | +| Bsp423I | Bacillus sp. 423 | GCAGC | 8 | AlwXI, BbvI, BseKI, BseXI, Bst12I, Bst71I, BstV1I | +| Bsp519I | Bacillus sp. 519 | GRGCYC | 5 | | +| Bsp1286I | Bacillus sphaericus | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, NspII, SduI | +| Bsp1407I | Bacillus stearothermophilus RFL1407 | TGTACA | 1 | AauI,  BsmRI, BsrGI, BstAUI, Ssp4800I, SspBI | +| Bsp1720I | Bacillus sp. 1720 | GCTNAGC | 2 | | +| Bsp1894I | Bacillus sphaericus 1894 | GGNCC | 1 | AspS9I, Bac36I, BavBII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | +| Bsp2095I | Bacillus sphaericus 2095 | GATC | 1 | Bfi57I, Bsp143I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| Bsp4009I | Bacillus sp. 4009 | GGATCC | 1 | AccEBI, AliI, ApaCI, BamHI, BstI, CelI, OkrAI, Pfl8I, RspLKII, SurI | +| BspAI | Bacillus sphaericus JL4B | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspA2I | Bacillus sp. A2 | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BlnI, XmaJI | +| Bsp153AI | Bacillus sp. 153A | CAGCTG | 3 | | +| BspAAI | Bacillus sp. AA | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BspAAII | Bacillus sp. AA | TCTAGA | 1 | | +| BspAAIII | Bacillus sp. AA | GGATCC | 1 | AccEBI, AliI, ApaCI, AsiI, BamHI, Bce751I, Pfl8I, RspLKII, SolI | +| BspANI | Bacillus sp. AN | GGCC | 2 | | +| BspBI | Bacillus sphaericus JL14 | CTGCAG | 5 | AjoI, ApiI, Asp713I, BloHII, CfrA4I, Pfl21I, PstI, SalPI, Sst12I, YenI | +| BspBII | Bacillus sphaericus JL14 | GGNCC | 1 | AsuI, Bac36I, BavBII, BshKI, BspF4I, CcuI, MaeK81II, PspPI | +| BspBRI | Bacillus sp. | GGCC | 2 | | +| BspBS31I | Bacillus sp. BS31 | GAAGAC | 8 | | +| BspCI | Bacillus sp. C1 | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, ErhB9I, NblI, Psu161I, RshI, XorII | +| BspCNI | Bacillus sp. 1310 | CTCAG | 10 | | +| BspDI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BseCI, Bsu15I, BsuTUI, ClaI, ZhoI | +| BspD6I | Bacillus sp. D6 | GACTC | 9 | | +| BspEI | Bacillus sp. | TCCGGA | 1 | AccIII, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, MroI, PinBII | +| BspFI | Bacillus sp. | GATC | 1 | Bfi57I, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NlaII, SsiBI | +| BspF4I | Bacillus sp. F4 | GGNCC | 1 | AsuI, Bac36I, BavBII, BsiZI, BspBII, CcuI, MaeK81II, PspPI | +| BspHI | Bacillus sp. H3 | TCATGA | 1 | | +| BspIS4I | Bacillus sp. IS4 | GAAGAC | 8 | | +| BspJI | Bacillus sp. | GATC | 1 | BfuCI, Bsp2095I, BspKT6I, BtkII, DpnII, LlaAI, NmeCI, SsiAI | +| BspJII | Bacillus sp. | ATCGAT | 2 | Bsa29I, BseCI, Bsp106I, BspDI, BspOVII, BspXI, BspZEI | +| BspKI | Bacillus sp. K | GGCC | 2 | | +| BspKT5I | Bacillus sp. | CTGAAG | 13 | | +| BspKT6I | Bacillus sp. KT6 | GATC | 3 | BfuCI, Bsp2095I, Bst19II, BstKTI, DpnII, LlaAI, NmeCI, SsiAI | +| BspKT8I | Bacillus sp. KT8 | AAGCTT | 1 | | +| BspLI | Bacillus sp. RJ3-212 | GGNNCC | 3 | AspNI, BscBI,  BmiI, NlaIV, PspN4I | +| BspLAI | Bacillus sp. LA | GCGC | 3 | AspLEI, BstHHI, CfoI, FnuDIII, HhaI, Hin6I, HinP1I, HsoI, HspAI, SciNI | +| BspLAII | Bacillus sp. LA | TTCGAA | 2 | | +| BspLAIII | Bacillus sp. LA | AAGCTT | 1 | | +| BspLS2I | Bacillus sp. LS2 | GDGCHC | 5 | AocII, BmyI, BsoCI, BspLS2I, MhlI, NspII, SduI | +| BspLU4I | Bacillus sp. LU4 | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, BstSI, NspIII, NspSAI, OfoI | +| BspLU11I | Bacillus sp. LU11 | ACATGT | 1 | | +| BspLU11III | Bacillus sp. LU11 | GGGAC | 9 | | +| BspMI | Bacillus sp. M | ACCTGC | 10 | Acc36I, BfuAI, BveI | +| BspMII | Bacillus sp. M | TCCGGA | 1 | AccIII, BbvAIII, BlfI, BsiMI, BspEI, Bsu23I, CauB3I, MroI | +| BspM39I | Bacillus sp. M39 | CAGCTG | 3 | | +| BspM90I | Bacillus sp. M90 | GTATAC | 3 | | +| BspMAI | Bacillus stearothermophilus MA | CTGCAG | 5 | AjoI, Asp713I, BloHII, PaePI, Psp23I, PstI, SalPI, Sst12I, YenI | +| BspMKI | Bacillus sp. MKI | GTCGAC | 1 | | +| BspNI | Bacillus sp. N | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, CbrI, CthII, EcoRII, MvaI, SspAI, TaqXI | +| BspO4I | Bacillus sp. O-4 | CAGCTG | 3 | | +| BspOVII | Bacillus sp. OV | ATCGAT | 2 | BanIII, BavCI, BciBI, BcmI, Bli86I, BliRI, BspJII, BstNZ169I, SpmI | +| BspPI | Bacillus sp. d 1-34 | GGATC | 9 | AclWI, AlwI, BinI,  BsrWI, BstH9I,  Bst31TI, Bth617I, EacI | +| BspRI | Bacillus sphaericus R | GGCC | 2 | | +| BspR7I | Bacillus sp. R7 | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| BspST5I | Bacillus sp. ST5 | GCATC | 8 | | +| BspTI | Bacillus sp. RFL1265 | CTTAAG | 1 | AflII | +| BspT104I | Bacillus sp. T104 | TTCGAA | 2 | AcpI, Bim19I, Bpu14I, BstBI, Csp45I, LspI, NspV, SspRFI | +| BspT107I | Bacillus sp. T107 | GGYRCC | 1 | AccB1I, BanI, BbvBI, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BspTNI | Bacillus sp. TN | GGTCTC | 7 | | +| BspTS514I | Bacillus sp. TS514 | GAAGAC | 8 | | +| BspXI | Bacillus sphaericus X | ATCGAT | 2 | BliAI, BliRI, BscI, Bst28I, Bsu15I, LcaI, PgaI, Ssp27144I, ZhoI | +| BspXII | Bacillus sphaericus X | TGATCA | 1 | AbaI, BclI, BsiQI, BstT7I, FbaI, Ksp22I,  ParI | +| BspZEI | Bacillus sp. ZE | ATCGAT | 2 | Bsa29I, BseCI, BspDI, BspXI, Bst28I, BstNZ169I, BsuTUI, LplI | +| BsrI | Bacillus stearothermophilus | ACTGG | 6 | | +| BsrAI | Bacillus stearothermophilus CPW7 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | +| BsrBI | Bacillus stearothermophilus CPW193 | CCGCTC | 3 | AccBSI, BstD102I, Bst31NI, MbiI | +| BsrDI | Bacillus stearothermophilus D70 | GCAATG | 8 | | +| BsrFI | Bacillus stearothermophilus CPW16 | RCCGGY | 1 | | +| BsrGI | Bacillus stearothermophilus GR75 | TGTACA | 1 | AauI,  BsmRI, Bsp1407I, BstAUI, Ssp4800I, SspBI | +| BsrSI | Bacillus stearothermophilus CPW19 | ACTGG | 6 | | +| BssAI | Bacillus sp. | RCCGGY | 1 | | +| BssECI | Bacillus stearothermophilus EC | CCNNGG | 1 | | +| BssHI | Bacillus stearothermophilus H3 | CTCGAG | 1 | AbrI, BluI, BstVI, PanI, SauLPII, SciI, SlaI, StrI, TliI | +| BssHII | Bacillus stearothermophilus H3 | GCGCGC | 1 | | +| BssIMI | Bacillus stearothermophilus IM | GGGTC | 2 | | +| BssKI | Bacillus stearothermophilus TBI | CCNGG | 1 | | +| BssNAI | Bacillus stearothermophilus NA | GTATAC | 3 | | +| BssNI | Bacillus sphaericus KTN | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BsaHI, HgiI, Hsp92I, Msp17I | +| BssSI | Bacillus stearothermophilus S719 | CACGAG | 1 | | +| BssT1I | Bacillus stearothermophilus T1 | CCWWGG | 1 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/Bsa-Bso.md",".md","12567","79","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:---------|:---------------------------------------|:-----------------------|------:|:----------------------------------------------------------------------| +| BsaI | Bacillus stearothermophilus 20241 | GGTCTC | 7 | Bso31I, BspTNI, Eco31I | +| Bsa29I | Bacillus sp. 29 | ATCGAT | 2 | AagI, BanIII, BavCI, BseCI, BspDI, Bsu15I, BsuTUI, ClaI, BbvAII | +| BsaAI | Bacillus stearothermophilus G668 | YACGTR | 3 | | +| BsaHI | Bacillus stearothermophilus CPW11 | GRCGYC | 2 | AcyI, AhaII, AosII, AstWI, AsuIII, BbiII, BstACI, HgiI, PamII | +| BsaJI | Bacillus stearothermophilus J695 | CCNNGG | 1 | | +| BsaMI | Bacillus stearothermophilus M293 | GAATGC | 7 | Asp26HI, Asp35HI, Asp36HI, Asp50HI, BsaMI, BsmI, Mva1269I | +| BsaOI | Bacillus stearothermophilus O-122 | CGRYCG | 4 | | +| BsaWI | Bacillus stearothermophilus W1718 | WCCGGW | 1 | | +| BscI | Bacillus sp. | ATCGAT | 2 | BanIII, BavCI, Bci29I, BdiI, Bli41I, BliAI, LplI, PgaI, SpmI | +| Bsc91I | Bacillus sp. | GAAGAC | 8 | | +| BscAI | Bacillus schlegelii S3 | GCATC | 9 | | +| BscBI | Bacillus sp. A11 | GGNNCC | 3 | AspNI,  BmiI, BspLI, NlaIV, PspN4I | +| BscCI | Bacillus sp. 2G | GAATGC | 7 | Asp26HI, Asp27HI, Asp35HI, Asp36HI, BsaMI, BscCI, PctI | +| BscFI | Bacillus sp. JY391 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BtkII, CviAI, Kzo9I, NlaII, SsiBI | +| Bse1I | Bacillus stearothermophilus 1 | ACTGG | 6 | | +| Bse15I | Bacillus sp. 15 | CYCGRG | 1 | Ama87I, AvaI, BcoI, BsoBI, BstSI, Eco88I, NspSAI, OfoI | +| Bse16I | Bacillus sp. 16 | CCWGG | 2 | AeuI, BseBI, BsiLI, BstNI, BstM6I, BthDI, BthEI, EcoRII, MvaI | +| Bse17I | Bacillus sp. 17 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | +| Bse21I | Bacillus sp. 21 | CCTNAGG | 2 | AxyI, BliHKI, BspR7I, Bsu36I, Eco81I, MstII, OxaNI, SshAI | +| Bse24I | Bacillus sp. 24 | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, Psp6I, PspGI | +| Bse64I | Bacillus sp. 64 | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BstPI, EcaI, Eci125I, EcoO65I, NspSAII | +| Bse118I | Bacillus sp. 118 | RCCGGY | 1 | | +| Bse634I | Bacillus sp. 634 | RCCGGY | 1 | | +| BseAI | Bacillus sphaericus | TCCGGA | 1 | AccIII, Aor13HI, BlfI, BsiMI, Bsp13I, BspMII, CauB3I, Kpn2I | +| BseBI | Bacillus stearothermophilus | CCWGG | 2 | AjnI, AorI, Bse17I, Bst1I, BstOI, Bst2UI, EcoRII, MvaI, SleI, ZanI | +| BseCI | Bacillus sp. | ATCGAT | 2 | AagI, BanIII, BavCI, Bsa29I, BspDI, Bsu15I, BsuTUI, ClaI, LcaI | +| BseDI | Bacillus stearothermophilus RFL1434 | CCNNGG | 1 | | +| Bse3DI | Bacillus stearothermophilus 3D | GCAATG | 8 | | +| BseGI | Bacillus stearothermophilus Vs 34-031 | GGATG | 7 | | +| BseKI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseXI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BseMI | Bacillus stearothermophilus Isl 15-111 | GCAATG | 8 | | +| BseMII | Bacillus stearothermophilus Isl 15-111 | CTCAG | 10 | | +| BseNI | Bacillus sp. N | ACTGG | 6 | | +| BsePI | Bacillus stearothermophilus P6 | GCGCGC | 1 | | +| BseQI | Bacillus sp. Q | GGCC | 2 | | +| BseRI | Bacillus sp. R | GAGGAG | 11 | | +| BseSI | Bacillus stearothermophilus Jo-553 | GKGCMC | 5 | | +| BseT9I | Bacillus sp. T9 | GGTNACC | 1 | AcrII, Bse64I, BstEII, BstT9I, EcaI, Eci125I, EcoO65I, NspSAII, PspEI | +| BseT10I | Bacillus sp. T10 | GGTNACC | 1 | AcrII, AspAI, BstEII, BstT10I, BstPI, EcoO128I, EcoO65I, PspEI | +| BseXI | Bacillus stearothermophilus Ra3-212 | GCAGC | 8 | AlwXI, BbvI, BseKI, Bsp423I, Bst12I, Bst71I, BstV1I | +| BseX3I | Bacillus stearothermophilus X3 | CGGCCG | 1 | AaaI, BstZI, EagI, EclXI, Eco52I, SenPT16I, XmaIII | +| BseYI | Bacillus sp. 2521 | CCCAGC | 1 | | +| BseZI | Bacillus sp. Z | CTCTTC | 7 | | +| BsgI | Bacillus sphaericus B922 | GTGCAG | 13 | | +| BshI | Bacillus sphaericus | GGCC | 2 | | +| Bsh45I | Bacillus sphaericus 45 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, BsiHKAI, HgiAI,  HpyF46II, MspV281I | +| Bsh1236I | Bacillus sphaericus RFL1236 | CGCG | 2 | AccII, BceBI, BspFNI, Bsp50I, Csp68KVI, FauBII, MvnI, SelI | +| Bsh1285I | Bacillus sphaericus RFL1285 | CGRYCG | 4 | | +| BshFI | Bacillus sphaericus | GGCC | 2 | | +| BshGI | Bacillus sphaericus | CCWGG | 2 | AeuI, BseBI, Bse16I, Bst2I, BstNI, Bst38I, Bst100I, PspGI, SspAI | +| BshKI | Bacillus sphaericus | GGNCC | 1 | AspS9I, Bac36I, BavAII, Bsp1894I, BspBII, CcuI, MaeK81II, Pde12I | +| BshNI | Bacillus sphaericus TK-45 | GGYRCC | 1 | BanI, BbvBI, BspT107I, Eco64I, HgiCI, HgiHI, MspB4I, PfaAI | +| BshTI | Bacillus sphaericus Jo22-024 | ACCGGT | 1 | AgeI, AsiAI,  AsiGI, CsiAI CspAI, PinAI | +| BsiI | Bacillus sphaericus | CACGAG | 1 | | +| BsiCI | Bacillus sp. | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, Csp45I, FspII, NspV, PpaAI, SfuI | +| BsiEI | Bacillus sp. | CGRYCG | 4 | | +| BsiHKAI | Bacillus stearothermophilus | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I,  Bsm6I, HgiAI, MspV281I | +| BsiHKCI | Bacillus sp. HKC | CYCGRG | 1 | AquI, BcoI, Bse15I, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | +| BsiKI | Bacillus sp. | GGTNACC | 1 | | +| BsiLI | Bacillus sp. | CCWGG | 2 | AglI, BseBI, Bse17I, Bst2I, BstNI, Bst38I, Bst100I, EcoRII, MvaI | +| BsiMI | Bacillus sp. | TCCGGA | 1 | AccIII, BbvAIII, BlfI, Bsp13I, BspMII, Bsu23I, Kpn2I, PinBII | +| BsiQI | Bacillus sp. | TGATCA | 1 | AbaI, BclI, BspXII, BstT7I, FbaI, Ksp22I,  ParI | +| BsiSI | Bacillus sp. | CCGG | 1 | | +| BsiWI | Bacillus sp. | CGTACG | 1 | | +| BsiXI | Bacillus sp. X | ATCGAT | 2 | BscI, BsiXI, Bsp106I, BspDI, Bsu15I, BsuTUI, ClaI, Rme21I | +| BsiZI | Bacillus sp. | GGNCC | 1 | AspS9I, Bac36I, BavAII, BshKI, BspBII, CcuI, MaeK81II, Pde12I | +| BslFI | Bacillus stearothermophilus FI | GGGAC | 9 | | +| BsmI | Bacillus stearothermophilus NUB | GAATGC | 7 | Asp26HI, Asp36HI, Asp40HI, BmaHI, BscCI, Mva1269I, PctI | +| BsmAI | Bacillus stearothermophilus A664 | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsoMAI, BstMAI | +| BsmBI | Bacillus stearothermophilus B61 | CGTCTC | 7 | | +| BsmFI | Bacillus stearothermophilus F | GGGAC | 9 | | +| BsmSI | Bacillus stearothermophilus CP114 | CCWWGG | 1 | | +| Bso31I | Bacillus stearothermophilus E31 | GGTCTC | 7 | | +| BsoBI | Bacillus stearothermophilus JN2091 | CYCGRG | 1 | AquI, BcoI, BsiHKCI, BspLU4I, Eco88I, Nli3877I, PlaAI, PunAI | +| BsoCI | Bacillus stearothermophilus AU891 | GDGCHC | 5 | AocII, BmyI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | +| BsoFI | Bacillus stearothermophilus F66 | GCNGC | 2 | | +| BsoMAI | Bacillus stearothermophilus MA | GTCTC | 6 | Alw26I,  BcoDI, BscQII, BsmAI, BstMAI |","Markdown" +"Bioengineering","telatin/seqfu2","re/Bd-Bp.md",".md","9607","64","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:---------|:--------------------------------|:-----------------------|------:|:--------------------------------------------------------------------| +| BdiI | Brevibacterium divaricatum | ATCGAT | 2 | BavCI, Bci29I, Bli41I, Bli86I, BseCI, BsuTUI, Rme21I, SpmI | +| BdiSI | Bacteroides distasonis | CTRYAG | 1 | | +| BecAII | Brevibacterium sp. A | GGCC | 2 | | +| BepI | Brevibacterium epidermidis | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, BtkI, FalII, FauBII, ThaI | +| BetI | Brevibacterium acetyliticum | WCCGGW | 1 | | +| BfaI | Bacteroides fragilis | CTAG | 1 | | +| BfiI | Bacillus firmus S8120 | ACTGGG | 11 | BmrI | +| Bfi57I | Butyrivibrio fibrisolvens OB157 | GATC | 1 | Bsp105I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, SsiBI | +| Bfi89I | Butyrivibrio fibrisolvens OB189 | YGGCCR | 1 | | +| BfmI | Bacillus firmus S8-336 | CTRYAG | 1 | | +| BfrI | Bacteroides fragilis | CTTAAG | 1 | | +| BfrBI | Bacteroides fragilis BE3 | ATGCAT | 5 | Csp68KIII, EcoT22I, Mph1103I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | +| BfuI | Bacillus firmus Auk 22-m21 | GTATCC | 10 | BciVI | +| BfuAI | Bacillus fusiformis | ACCTGC | 10 | Acc36I, BspMI, BveI | +| BfuCI | Bacillus fusiformis 1226 | GATC | 1 | Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, MkrAI, Sth368I | +| BglII | Bacillus globigii | AGATCT | 1 | | +| BimI | Brevibacterium immotum | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bim19I | Brevibacterium immotum 19 | TTCGAA | 2 | AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bim19II | Brevibacterium immotum 19 | GGCC | 2 | | +| BinI | Bifidobacterium infantis 659 | GGATC | 9 | AclWI, AlwI,  BsrWI, BspPI, BstH9I,  Bth617I, EacI | +| BlfI | Bacillus licheniformis | TCCGGA | 1 | AccIII, Aor13HI, BseAI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | +| Bli41I | Bacillus licheniformis 41 | ATCGAT | 2 | Bci29I, Bli86I, BseCI, BsiXI, BsuTUI, Rme21I, SpmI, Ssp27144I | +| Bli86I | Bacillus licheniformis 86 | ATCGAT | 2 | BliAI, Bli41I, BseDI, BsiXI, Rme21I, SpmI, Ssp27144I, ZhoI | +| Bli736I | Bacillus licheniformis 736 | GGTCTC | 7 | | +| BliAI | Bacillus licheniformis | ATCGAT | 2 | BliRI, Bli41I, BsiXI, BspDI, Rme21I, SpmI, Ssp27144I, ZhoI | +| BliHKI | Bacillus licheniformis HK | CCTNAGG | 2 | AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | +| BliRI | Bacillus licheniformis | ATCGAT | 2 | BciBI, BdiI, Bli41I, BsiXI, BspDI, BspXI, LplI, SpmI, ZhoI | +| BlnI | Brevibacterium linens | CCTAGG | 1 | AspA2I, AvrII, AvrBII, BspA2I, XmaJI | +| BloHI | Bifidobacterium longum E194b | RGATCY | 1 | | +| BloHII | Bifidobacterium longum E194b | CTGCAG | 5 | AjoI, Asp713I, BsuBI, CflI, CfuII, HalII, PstI, SalPI, SflI, Sst12I | +| BlpI | Bacillus lentus | GCTNAGC | 2 | | +| BluI | Brevibacterium luteum | CTCGAG | 1 | AbrI, BssHI, BstVI, PanI, Sau3239I, Sfr274I, TliI, XhoI | +| Bme12I | Bacillus megaterium 12 | GATC | 1 | Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, SsiBI | +| Bme18I | Bacillus megaterium 18 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | +| Bme142I | Bacillus megaterium 142 | RGCGCY | 3 | AccB2I,  BfoI, Bsp143II, BstH2I, HaeII, LpnI | +| Bme216I | Bacillus megaterium 216 | GGWCC | 1 | BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | +| Bme361I | Bacillus megaterium 361 | GGCC | 2 | | +| Bme585I | Bacillus mesentericus 585 | CCCGC | 9 | | +| Bme1390I | Bacillus megaterium RFL1390 | CCNGG | 2 | | +| Bme1580I | Bacillus megaterium 1580 | GKGCMC | 5 | | +| BmgBI | Bacillus megaterium | CACGTC | 3 | | +| BmrI | Bacillus megaterium | ACTGGG | 11 | BfiI | +| BmtI | Bacillus megaterium S2 | GCTAGC | 5 | AceII, AsuNHI,  BspOI, NheI, LlaG2I, PstNHI | +| BmyI | Bacillus mycoides | GDGCHC | 5 | AocII, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | +| BnaI | Bacillus natto B3364 | GGATCC | 1 | AccEBI, BamHI, Bce751I, BstI, CelI, OkrAI, Nsp29132II, Pfl8I, SolI | +| BpcI | Bacillus sphaericus | CTRYAG | 1 | | +| BpiI | Bacillus pumilus sw 4-3 | GAAGAC | 8 | | +| BpmI | Bacillus pumilus | CTGGAG | 12 | | +| BpoAI | Bacillus polymyxa | ATTAAT | 2 | AseI, AsnI, PshBI, Sru4DI, VspI | +| BptI | Bacillus pantothenticus | CCWGG | 2 | AjnI, BseBI, Bse16I, BstNI, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | +| BpuI | Bacillus pumilus AHU1387A | GRGCYC | 5 | | +| Bpu10I | Bacillus pumilus 10 | CCTNAGC | 2 | | +| Bpu14I | Bacillus pumilus 14 | TTCGAA | 2 | AcpI, AsuII, BsiCI, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | +| Bpu95I | Bacillus pumilus 95 | CGCG | 2 | AccII, BepI, BspFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | +| Bpu1102I | Bacillus pumilus RFL1102 | GCTNAGC | 2 | | +| BpuAI | Bacillus pumilus | GAAGAC | 8 | | +| BpuAmI | Bacillus pumilus | GAGCTC | 3 | | +| BpuB5I | Bacillus pumilus | CGTACG | 1 | | +| BpuDI | Bacillus pumilus 1117 | CCTNAGC | 2 | | +| BpuEI | Bacillus pumilus 2187a | CTTGAG | 12 | | +| BpuJI | Bacillus pumilus RFL1458 | CCCGT | 9 | — None on May 2010 — | +| BpuSI | Bacillus pumilus | GGGAC | 8 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/L-N.md",".md","19163","119","| Enzyme | Source | Recognition sequence | Cut | Isoschizomers | +|:-----------|:----------------------------------------|:-----------------------|------:|:---------------------------------------------------------------------| +| LcaI | Lactobacillus casei | ATCGAT | 2 | BdiI, Bli41I, Bsa29I, BscI, Bsp106I, BspDI, Bst28I, LplI, PgaI, ZhoI | +| LlaAI | Lactococcus lactis cremoris W9 | GATC | 1 | Bme12I, Bsp67I, BstENII, ChaI, FnuEI, MgoI, NphI, RalF40I | +| LlaBI | Lactococcus lactis cremoris W56 | CTRYAG | 1 | | +| LlaCI | Lactococcus lactis W15 | AAGCTT | 1 | | +| LlaG2I | Lactococcus lactis cremoris | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, NheI, PstNHI | +| Lmu60I | Listeria murrayi 60 | CCTNAGG | 2 | AocI, AxyI, BspR7I, CvnI, Lmu60I, MstII, SauI, SshAI | +| LplI | Lactobacillus plantarum | ATCGAT | 2 | BanIII, BbvAII, BdiI, Bsa29I, BscI, BstNZ169I, ClaI, LcaI, PgaI | +| LpnI | Legionella pneumophila | RGCGCY | 3 | AccB2I,  BfoI, Bme142I, Bsp143II, BstH2I, HaeII | +| LspI | Lactobacillus sp. | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp45I, PlaII, PpaAI, Ssp1I | +| LweI | Listeria welshimeri RFL131 | GCATC | 8 | | +| MabI | Microbacterium arborescens SE | ACCWGGT | 1 | | +| MaeI | Methanococcus aeolicus PL-15/H | CTAG | 1 | | +| MaeII | Methanococcus aeolicus | ACGT | 1 | | +| MaeIII | Methanococcus aeolicus | GTNAC | 1 | | +| MaeK81I | Microcystis aeruginosa K-81 | CGTACG | 1 | | +| MaeK81II | Microcystis aeruginosa | GGNCC | 1 | AsuI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, Sau96I | +| MavI | Mycobacterium avium | CTCGAG | 1 | BspAAI, BstVI, MlaAI, PaeR7I, SauLPII, SciI, SlaI, Sol10179I, XhoI | +| MbiI | Moraxella bovis Fr1-022 | CCGCTC | 3 | AccBSI, BsrBI, BstD102I, Bst31NI | +| MboI | Moraxella bovis | GATC | 1 | AspMDI, Bsp105I, BspFI, BstMBI, CviAI, Kzo9I, NdeII, Sth368I | +| MboII | Moraxella bovis | GAAGA | 9 | | +| MchI | Micromonospora chalcea | GGCGCC | 2 | | +| MchAI | Mycobacterium chelonei | GCGGCCGC | 2 | | +| MchAII | Mycobacterium chelonei | GGCC | 2 | | +| McrI | Micrococcus cryophilus | CGRYCG | 4 | | +| MfeI | Mycoplasma fermentans | CAATTG | 1 | | +| MflI | Microbacterium flavum | RGATCY | 1 | | +| MfoAI | Mycobacterium fortuitum TMC 1529 | GGCC | 2 | | +| Mgl14481I | Merismopedia glauca 1448-1 | CCSGG | 2 | AseII, AsuC2I, BcnI, BpuMI, CauII, Eco1831I, EcoHI, HgiS22I, NciI | +| MgoI | Mycobacterium gordonae | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, NphI, Sau3AI | +| MhaAI | Mycobacterium habana 206 | CTGCAG | 5 | AliAJI, Asp713I, Bsp63I, CstI, Ecl37kI, HalII, PaePI, PstI, YenI | +| MhlI | Micrococcus halobius SD | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, BspLS2I, MhlI, SduI | +| MkrAI | Micrococcus kristinae | GATC | 1 | Bme12I, BspAI, BstENII, ChaI, FnuEI, MgoI, NphI, Sau3AI | +| MlaI | Mastigocladus laminosus | TTCGAA | 2 | Asp10HI, BimI, BsiCI, BstBI, Csp68KII, LspI, PlaII, Ssp1I | +| MlaAI | Micromonospora lacustris | CTCGAG | 1 | BspAAI, BstVI, PanI, SauLPII, Sbi68I, Sfr274I, SlaI, XhoI | +| MlsI | Micrococcus luteus Ng 16-122 | TGGCCA | 3 | | +| MltI | Micrococcus luteus | AGCT | 2 | AluBI, AluI | +| MluI | Micrococcus luteus | ACGCGT | 1 | | +| Mlu23I | Micrococcus luteus 23 | GGATCC | 1 | | +| Mlu31I | Micrococcus luteus 31 | TGGCCA | 3 | | +| MluB2I | Micrococcus luteus B2 | TCGCGA | 3 | | +| MluNI | Micrococcus luteus N | TGGCCA | 3 | | +| MlyI | Micrococcus lylae | GAGTC | 8 | | +| Mly113I | Micrococcus lylae 113 | GGCGCC | 2 | | +| MmeI | Methylophilus methylotrophus | TCCRAC | 12 | | +| MnlI | Moraxella nonliquefaciens | CCTC | 9 | | +| MnoI | Moraxella nonliquefaciens | CCGG | 1 | | +| Mph1103I | Moraxella phenylpyruvica RFL1103 | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, NsiI, PinBI, Ppu10I, SepI, SspD5II | +| MroI | Micrococcus roseus | TCCGGA | 1 | BbvAIII, BseAI, Bsp13I, BspEI, Bsu23I, CauB3I, PinBII, PtaI | +| MroNI | Micrococcus roseus N | GCCGGC | 1 | | +| MscI | Micrococcus sp. | TGGCCA | 3 | | +| MseI | Micrococcus sp. | TTAA | 1 | | +| MspI | Moraxella sp. | CCGG | 1 | | +| Msp17I | Micrococcus sp. 17 | GRCGYC | 2 | AsuIII, BsaHI, BstACI, HgiGI, HgiHII, Hin1I, Msp17I, PamII | +| Msp20I | Micrococcus sp. | TGGCCA | 3 | | +| Msp67I | Micrococcus sp. MS67 | CCNGG | 2 | | +| MspA1I | Moraxella sp. A1 | CMGCKG | 3 | | +| MspB4I | Moraxella sp. B4 | GGYRCC | 1 | AccB1I, BanI, BshNI, BspT107I, Eco64I, HgiCI, HgiHI, PfaAI | +| MspCI | Micrococcus sp. | CTTAAG | 1 | | +| MspR9I | Micrococcus sp. R9 | CCNGG | 2 | | +| MspSWI | Moraxella sp. SW | ATTTAAAT | 4 | | +| MspV281I | Myxosarcinia sp. V/281 | GWGCWC | 5 | Alw21I, AspHI, Bbv12I, Bsh45I, BsiHKAI,  Bsm6I, HgiAI,  HpyF46II, | +| MspYI | Microcystis sp. J2 | YACGTR | 3 | | +| MssI | Methylobacterium sp. Dd 5-732 | GTTTAAAC | 4 | PmeI | +| MstI | Microcoleus sp. | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, NsbI, PamI, Pun14627I | +| MstII | Microcoleus sp. | CCTNAGG | 2 | AocI, BliHKI, BspR7I, CvnI, Lmu60I, OxaNI, SauI, SshAI | +| MthZI | Methanobacterium thermoformicicum Z-245 | CTAG | 1 | | +| MunI | Mycoplasma sp. | CAATTG | 1 | | +| MvaI | Micrococcus varians RFL19 | CCWGG | 2 | AjnI, BciBII, BptI, Bst1I, BstOI, BstM6I, Bst2UI, SslI, TaqXI, ZanI | +| Mva1269I | Micrococcus varians RFL1269 | GAATGC | 7 | Asp26HI, Asp40HI, Asp50HI, BscCI, BsmI, Mva1269I, PctI | +| MvnI | Methanococcus vannielii | CGCG | 2 | AccII, Bsh1236I, BstFNI, BtkI, Csp68KVI, FalII, FauBII, ThaI | +| MvrI | Micrococcus varians | CGATCG | 4 | Afa22MI, BspCI, EagBI, ErhB9I, Ple19I, PvuI, RshI, XorII | +| MxaI | Myxococcus xanthus F18E | GAGCTC | 3 | | +| NaeI | Nocardia aerocolonigenes | GCCGGC | 3 | | +| NarI | Nocardia argentinensis | GGCGCC | 2 | | +| NblI | Nocardia blackwellii | CGATCG | 4 | Afa16RI, Afa22MI, EagBI, MvrI, Ple19I, Psu161I, RshI, XorII | +| NciI | Neisseria cinerea | CCSGG | 2 | AhaI, AseII, AsuC2I, BpuMI, CauII, EcoHI, HgiS22I, Mgl14481I | +| NcoI | Nocardia corallina | CCATGG | 1 | | +| NcrI | Nocardia carnea C-212 | AGATCT | 1 | | +| NcuI | Neisseria cuniculi | GAAGA | 9 | | +| NdaI | Nocardia dassonvillei | GGCGCC | 2 | | +| NdeI | Neisseria denitrificans | CATATG | 2 | | +| NdeII | Neisseria denitrificans | GATC | 1 | Bce243I, Bsp105I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, Sth368I | +| NgoAIII | Neisseria gonorrhoeae FA1090 | CCGCGG | 4 | | +| NgoAIV | Neisseria gonorrhoeae FA1090 | GCCGGC | 1 | | +| NgoMIV | Neisseria gonorrhoeae MS11 | GCCGGC | 1 | | +| NgoPII | Neisseria gonorrhoeae P9-2 | GGCC | 2 | | +| NgoPIII | Neisseria gonorrhoeae P9-2 | CCGCGG | 4 | | +| NheI | Neisseria mucosa heidelbergensis | GCTAGC | 1 | AceII, AsuNHI, BmtI,  BspOI, LlaG2I, PstNHI | +| NlaII | Neisseria lactamica | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | +| NlaIII | Neisseria lactamica | CATG | 4 | | +| NlaIV | Neisseria lactamica | GGNNCC | 3 | AspNI, BscBI, BmiI, BspLI, PspN4I | +| Nli3877I | Nostoc linckia | CYCGRG | 5 | Ama87I, AvaI, BcoI, BsiHKCI, Eco27kI, Eco88I, NspSAI, OfoI | +| NmeCI | Neisseria meningitidis C114 | GATC | 1 | BscFI, BspAI, BstENII, ChaI, FnuEI, MgoI, RalF40I, Sau3AI | +| NmeRI | Neisseria meningitidis | CAGCTG | 3 | | +| NmuCI | Neisseria mucosa C9-2 | GTSAC | 1 | | +| NopI | Nocardia opaca | GTCGAC | 1 | | +| NotI | Nocardia otitidis-caviarum | GCGGCCGC | 2 | | +| NphI | Neisseria pharyngis C245 | GATC | 1 | AspMDI, BspAI, BstENII, ChaI, FnuEI, MkrAI, RalF40I, Sau3AI | +| NruI | Nocardia rubra | TCGCGA | 3 | | +| NsbI | Neisseria subflava Va-1 | TGCGCA | 3 | Acc16I, AosI, AviII, FdiII, FspI, MstI, PamI, Pun14627I | +| NsiI | Neisseria sicca | ATGCAT | 5 | BfrBI, Csp68KIII, EcoT22I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | +| NsiCI | Neisseria sicca C351 | GATATC | 3 | | +| NspI | Nostoc sp. C | RCATGY | 5 | | +| NspII | Nostoc sp. C | GDGCHC | 5 | AocII, BmyI, BsoCI, Bsp1286I, MhlI, NspII, SduI | +| NspIII | Nostoc sp. C | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BsoBI, Eco27kI, Eco88I, OfoI, PunAI | +| NspIV | Nostoc sp. C | GGNCC | 1 | AvcI, Bal228I, Bce22I, BsiZI, BspF4I, Cfr13I, Nsp7121I, UnbI | +| NspV | Nostoc sp. C | TTCGAA | 2 | Asp10HI, BimI, Bsp119I, BstBI, Csp68KII, MlaI, PlaII, SspRFI | +| Nsp7121I | Nostoc sp. 7121 | GGNCC | 1 | AvcI, Bal228I, Bce22I, Bsp1894I, Bsu54I, Cfr13I, NspIV, UnbI | +| Nsp29132II | Nostoc sp. | GGATCC | 1 | AliI, ApaCI, BamHI, Bce751I, Nsp29132II, Pfl8I, SolI, Uba4009I | +| NspBII | Nostoc sp. | CMGCKG | 3 | | +| NspHI | Nostoc sp. | RCATGY | 5 | | +| NspLKI | Nocardia sp. LK | GGCC | 2 | | +| NspMACI | Nostoc sp. | AGATCT | 1 | | +| NspSAI | Nostoc sp. SA | CYCGRG | 1 | Ama87I, AvaI, Bse15I, BspLU4I, Eco27kI, Nli3877I, OfoI, PunAI | +| NspSAII | Nostoc sp. SA | GGTNACC | 1 | AspAI, Bse64I, BseT9I, BseT10I, BstPI, Eco91I, NspSAII, PspEI | +| NspSAIV | Nostoc sp. SA | GGATCC | 1 | AliI, BamHI, Bsp98I, Bsp4009I, NspSAIV, Pfl8I, SolI, Uba4009I | +| NunII | Nocardia uniformis | GGCGCC | 2 | |","Markdown" +"Bioengineering","telatin/seqfu2","re/scrape.py",".py","4210","146","#!/usr/bin/env python3 +"""""" +Extract enzyme table from wikipedia page. +Input: a text file with the list of Enzyme tables URLs + +Internal use only / Dev +"""""" + +#Note: requires lxml +import pandas as pd +from bs4 import BeautifulSoup +from urllib.request import urlopen +import re +import os, sys + + + +def siteString(site): + # site: 5' GAATTC 3' CTTAAG + # cutsite: 5' ---G AATTC--- 3' 3' ---CTTAA G--- 5' + if not isinstance(site, str): + return """" + + + + # Extract the string from ""5'"" to ""3'"" + regex = ""5'(.*?)3'"" + # Find the cutsite + cutsite = re.search(regex, site).group(1) + # Strip leadingnad trailing whitespaces + + if re.search(""\d"", cutsite): + print(f""Warning: {cutsite} site contains a number"", file=sys.stderr) + return """" + return cutsite.strip() + +def cutPosition(string): + #5' ---AT CGAT--- 3' + regex = ""5' [-]+(.+) (.+)[-]+ 3'"" + # Capture the two groups + match = re.search(regex, string) + if match: + return len(match.group(1))#, match.group(2) + else: + return -1 + +def getTable(url, class_attributes=None, columnName=""Enzyme""): + if class_attributes is None: + class_attributes = [] + + # Get the page from url + if url.lower().startswith(""http""): + page = BeautifulSoup(urlopen(url), ""html.parser"") #nosec - was checked above + else: + raise ValueError(""url must start with http"") + + # Select tables containing all attributes in the list class_attributes + tables = page.find_all(""table"", class_=class_attributes) + + # Select the table from tables having columnName as column name + tables = [table for table in tables if columnName in table.find_all(""tr"")[0].text] + # Return the table + return tables + +def htmlTableToDataFrame(table): + # Create a dataframe from the table + df = pd.read_html(str(table))[0] + # First row is the header + df.columns = df.iloc[0] + # Drop the first row + df = df.drop(df.index[0]) + # First column is the enzyme name (index) + df.index = df.iloc[:,0] + # Drop the first column + df = df.drop(df.columns[0], axis=1) + return df + +def urlToDf(url): + + tables = getTable(url, [""sortable""], ""Enzyme"") + dfs = [] + for table in tables: + df = htmlTableToDataFrame(table) + # From the first column strip the pattern ""\[.*\]"" + df.index = df.index.str.replace(""\[.*\]"", """") + + # Columns to remove + colToRemove = [""PDB code""] + + # Check if colToRemove are in the dataframe + for col in colToRemove: + if col in df.columns: + df = df.drop(col, axis=1) + + # Replace column ""Recognition sequence"" with siteString() + df[""Recognition sequence""] = df[""Recognition sequence""].apply(siteString) + # Remove rows where ""Recognition sequence"" is empty + df = df[df[""Recognition sequence""] != """"] + + # Replace ""Cut"" with cutPosition() + df[""Cut""] = df[""Cut""].apply(cutPosition) + # Drop rows where ""Cut"" is -1 + df = df[df[""Cut""] != -1] + + dfs.append(df) + + df = pd.concat(dfs) + return df + +if __name__ == ""__main__"": + inputfile = sys.argv[-1] + if not os.path.exists(inputfile): + print(""ERROR: file not found: "", inputfile) + sys.exit(1) + + # Load list of urls from file + with open(inputfile, ""r"") as f: + urls = f.readlines() + dataframes = [] + for url in urls: + if not url.lower().startswith(""http""): + continue + + basename = os.path.basename(url) + # Strip after ""#"" + if ""#"" in basename: + basename = basename.split(""#"")[0] + if "":_"" in basename: + basename = basename.split("":_"")[1] + try: + df = urlToDf(url) + print(basename, df.shape, file=sys.stderr) + # Replace nan values with empty string + df = df.fillna("""") + df.to_markdown(basename + "".md"") + dataframes.append(df) + except Exception as e: + print(e) + + if len(dataframes) > 0: + df = pd.concat(dataframes) + print(df.shape) + + df.to_markdown(""enzyme_table.md"") + df.to_csv(""enzyme_table.csv"") +","Python" +"Bioengineering","telatin/seqfu2","src/build.md",".md","1800","71","# Initial build script + +```bash +#!/bin/bash +set -exuo pipefail +OLDWD=$PWD + +PLATFORM="""" +if [[ $(uname) == 'Darwin' ]]; +then + PLATFORM=""_mac"" +fi +DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" + + +nim --version >/dev/null 2>&1 || { echo ""nim compiler not found.""; exit 1; } +RELEASE="""" +if [ ""${NIM_RELEASE+x}"" ]; then + RELEASE="" -d:release ""; +fi + +nim c --hints:off -w:on --opt:speed $RELEASE -p:$DIR/lib -o:$DIR/../bin/seqfu${PLATFORM} $DIR/sfu.nim \ + || { echo ""Compilation failed.""; exit 1; } + +for UTIL in src/fu*.nim; +do + NAME=$(basename ${UTIL%.nim} | sed 's/_/-/g') + THREADS="""" + if [[ $(grep thread ""$UTIL"") ]]; then + THREADS="" --threads:on "" + fi + nim c $THREADS --hints:off -w:on --opt:speed $RELEASE -p:$DIR/lib -o:$DIR/../bin/${NAME}${PLATFORM} $UTIL \ + || { echo ""Util ${NAME} compilation failed.""; exit 2; } +done + +if [ -e ""$DIR/../test/mini.sh"" ]; then + bash $DIR/../test/mini.sh +else + echo ""Minimal test suite not found at: $DIR/../test/mini.sh"" + exit 1; +fi + +VERSION=$(grep return $DIR/seqfu_utils.nim | grep -o \\d\[^\""\]\\+ | head -n 1) +sed -i ""s/version\s\+=\s\+\"".\+\""/version = \""$VERSION\""/"" $DIR/../seqfu.nimble || true + +perl -e ' +$VERSION=shift(@ARGV); +$BIN=shift(@ARGV); +$SPLASH=`$BIN --help 2>&1`; +$TEMPLATE=shift(@ARGV); + +print STDERR ""bin:$BIN;version:$VERSION\n""; +open(I, ""<"", $TEMPLATE); +while () { + while ( $_=~/\{\{ (\w+) \}\}/g ) { + $repl=${$1}; + $match=$1; + $_=~s/\{\{\s*$match\s*\}\}/$repl/g; + } + print; +} +print ""## Some functions\n""; +for my $function (""head"", ""interleave"", ""deinterleave"", ""derep"", ""stats"", ""count"") { + print ""\n### :closed_book: seqfu $function\n\n""; + print ""```\n""; + print `$BIN $function --help`; + print ""```\n"" +} + +' ""$VERSION"" ""$DIR/../bin/seqfu${PLATFORM}"" ""$DIR/README.raw"" > $DIR/../README.md +```","Markdown" +"Bioengineering","telatin/seqfu2","src/countseqs.sh",".sh","697","36","#!/bin/bash + +CAT=""cat"" +# Check if the first parameter was passed +if [ -z ""$1"" ]; then + echo ""Usage: countseqs.sh "" + exit 1 +fi + +# Check if the file exists +if [ ! -f ""$1"" ]; then + echo ""File $1 does not exist"" + exit 1 +fi + +# Check if the filename ends with .gz +if [[ ""$1"" == *.gz ]]; then + #GZIPPED=1 + GUNZIP_PIPE=""gzip -d "" +else + #GZIPPED=0 + GUNZIP_PIPE=""$CAT"" +fi + +# Get the first character of the file +FIRST_CHAR=$($CAT ""$1"" | $GUNZIP_PIPE | head -c 1) + +if [[ ""$FIRST_CHAR"" == "">"" ]]; then + COUNT=$($CAT ""$1"" | $GUNZIP_PIPE | grep -c ""^>"") +elif [[ ""$FIRST_CHAR"" == ""@"" ]]; then + COUNT=$($CAT ""$1"" | $GUNZIP_PIPE | wc -l) + COUNT=$((COUNT / 4)) +fi + +echo $COUNT +","Shell" +"Bioengineering","telatin/seqfu2","src/doc/bench.md",".md","236","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `perl uniq.pl ./input/*.fa*` | 935.7 ± 38.4 | 886.1 | 1027.9 | 8.39 ± 0.36 | +| `derep_Darwin ./input/*.fa*` | 111.5 ± 1.6 | 108.9 | 115.1 | 1.00 | +","Markdown" +"Bioengineering","telatin/seqfu2","src/doc/single_file.md",".md","415","6","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `vsearch --derep_fulllength ./input/filt.fa.gz --output /tmp/vsearch.fa` | 179.1 ± 9.6 | 170.1 | 198.0 | 1.06 ± 0.10 | +| `./bin/derep_Darwin ./input/filt.fa.gz > /tmp/derep.fa` | 169.2 ± 13.1 | 150.0 | 211.8 | 1.00 | +| `perl ./test/uniq.pl ./input/filt.fa.gz > /tmp/uniq.fa ` | 956.9 ± 64.5 | 866.4 | 1063.1 | 5.65 ± 0.58 | +","Markdown" +"Bioengineering","telatin/seqfu2","src/doc/build-seqfu.sh",".sh","110","7","#!/bin/bash + +mkdir -p ""${PREFIX}""/bin +chmod +x ./bin/* +mv ./bin/* ""${PREFIX}""/bin/ +mv seqfu ""${PREFIX}""/bin/ +","Shell" +"Bioengineering","telatin/seqfu2","test/test-rotate.sh",".sh","974","29","#!/bin/bash +ROTATE=$(""$BINDIR""/seqfu rotate -i 14 ""$FILES""/homopolymer.fa| grep -v '^>') +FORROT=$(""$BINDIR""/seqfu rotate -m AAAAAAAAAAC ""$FILES""/homopolymer.fa| grep -v '^>') +REVROT=$(""$BINDIR""/seqfu rotate -r -m GTTTTTTT ""$FILES""/homopolymer.fa| grep -v '^>') + +if [[ $ROTATE = ""AAAAAAAAAACTGCTACTAACACGTACTACTG"" ]]; then + echo -e ""$OK: sequence rotated"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: rotated seq $ROTATE should start with polyA"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $FORROT = ""AAAAAAAAAACTGCTACTAACACGTACTACTG"" ]]; then + echo -e ""$OK: sequence rotated with pattern"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: rotated seq $ROTATE (pattern) should start with polyA"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $REVROT = ""GTTTTTTTTTTCAGTAGTACGTGTTAGTAGCA"" ]]; then + echo -e ""$OK: sequence rotated with reverse pattern"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: rotated seq $ROTATE (reverse pattern) should start with GTTT."" + ERRORS=$((ERRORS+1)) +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/test-tab.sh",".sh","3794","111","#!/bin/bash + +export SEQFU_QUIET=1 + +SE=$(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) + +if [[ $SE == ""5"" ]]; then + echo -e ""$OK: FASTQ sequence tabulated / detabulated"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FASTQ sequence tabulated / detabulated 5 expected, got $SE"" + ERRORS=$((ERRORS+1)) +fi + +FA=$(""$BINDIR""/seqfu tabulate ""$FILES""/numbers.fa | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) +if [[ $FA == ""1000"" ]]; then + echo -e ""$OK: FASTA sequence tabulated / detabulated"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FASTA sequence tabulated / detabulated 1000 expected, got $FA"" + ERRORS=$((ERRORS+1)) +fi + +ILVCOUNT=$(""$BINDIR""/seqfu tabulate ""$FILES""/interleaved.fq.gz -i | wc -l | grep -o '[[:digit:]]\+') +if [[ $ILVCOUNT == ""7"" ]]; then + echo -e ""$OK: FQ interleaved sequence tabulated / detabulated"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FQ interleaved sequence tabulated / detabulated 7 PAIRS (lines) expected, got $ILVCOUNT"" + ERRORS=$((ERRORS+1)) +fi +ILV=$(""$BINDIR""/seqfu tabulate ""$FILES""/interleaved.fq.gz -i | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | ""$BINDIR""/seqfu cnt | cut -f 2) +if [[ $ILV == ""14"" ]]; then + echo -e ""$OK: FQ interleaved sequence tabulated / detabulated"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FQ interleaved sequence tabulated / detabulated 14 expected, got $ILV"" + ERRORS=$((ERRORS+1)) +fi + +## FASTQ SE +SE_LINES=$(getnumber $(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)) + +if [[ $SE_LINES == ""20"" ]]; then + echo -e ""$OK: FASTQ output format: line count $SE_LINES"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FASTQ output format: line count 20 expected, got $SE_LINES"" + ERRORS=$((ERRORS+1)) +fi + + +## FASTQ PE +SE_LINES=$(getnumber $(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fastq | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)) + +if [[ $SE_LINES == ""20"" ]]; then + echo -e ""$OK: FASTQ output format: line count $SE_LINES"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FASTQ output format: line count 20 expected, got $SE_LINES"" + ERRORS=$((ERRORS+1)) +fi + + +## FASTA SE +FA_LINES=$(getnumber ""$(""$BINDIR""/seqfu tabulate ""$FILES""/comments.fasta | SEQFU_QUIET=1 ""$BINDIR""/seqfu tabulate -d | wc -l)"") + +if [[ $FA_LINES == ""8"" ]]; then + echo -e ""$OK: FASTA output format: $FA_LINES"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: FASTA output format: 8 expected, got $FA_LINES"" + ERRORS=$((ERRORS+1)) +fi + +## Pair end? + +TEMPORARY_DIR=$(mktemp -d) +""$BINDIR""/seqfu tabulate -i ""$FILES""/interleaved.fq.gz > ""$TEMPORARY_DIR""/interleaved.tabcheck +EXP=8 +GOT=$(getnumber ""$(""$BINDIR""/fu-tabcheck ""$TEMPORARY_DIR""/interleaved.tabcheck | cut -f 3)"") +if [[ $GOT == ""$EXP"" ]]; then + echo -e ""$OK: Tabulated file has $EXP columns: $GOT"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Tabulated file has not $EXP columns: $GOT"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu tabulate -d ""$TEMPORARY_DIR""/interleaved.tabcheck| ""$BINDIR""/seqfu deinterleave -o ""$TEMPORARY_DIR""/dei - +EXP=7 +GOT=$(getnumber ""$(""$BINDIR""/seqfu cnt -u ""$TEMPORARY_DIR""/dei_R1.fq | cut -f 2)"") +if [[ $GOT == ""$EXP"" ]]; then + echo -e ""$OK: Deinterleaved detabulated has $EXP R1 reads: $GOT"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Deinterleaved detabulated has not $EXP R1 reads: $GOT"" + ERRORS=$((ERRORS+1)) +fi + +GOT=$(getnumber ""$(""$BINDIR""/seqfu cnt -u ""$TEMPORARY_DIR""/dei_R2.fq | cut -f 2)"") +if [[ $GOT == ""$EXP"" ]]; then + echo -e ""$OK: Deinterleaved detabulated has $EXP R2 reads: $GOT"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Deinterleaved detabulated has not $EXP R2 reads: $GOT"" + ERRORS=$((ERRORS+1)) +fi +rm -rf ""$TEMPORARY_DIR"" + +","Shell" +"Bioengineering","telatin/seqfu2","test/interleave.md",".md","3856","115","# Reference interleave.sh script + +```bash +#!/bin/bash + +DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" +PLATFORM="""" +if [[ $(uname) == ""Darwin"" ]]; then + PLATFORM="""" +fi +BIN=$DIR/../bin/seqfu${PLATFORM} +FILES=$DIR/../data/ + +# +iPair1=$FILES/illumina_1.fq.gz +iPair2=$FILES/illumina_2.fq.gz +iPair1a=$FILES/tests/sample1_R1.fq +iPair1b=$FILES/tests/sample1_R2.fq +iPair1b=$FILES/tests/sample1_forward.fq +iPair2b=$FILES/tests/sample1_reverse.fq +iR1LONG1=$FILES/tests/longerone_R1.fq +iR2LONG1=$FILES/tests/longerone_R2.fq +iR1LONG2=$FILES/tests/longertwo_R1.fq +iR2LONG2=$FILES/tests/longertwo_R2.fq +iR1EMPTY=$FILES/tests/empty_R1.fq +iR2EMPTY=$FILES/tests/empty_R2.fq +iAllMISS=$FILES/tests/nonexistent.fq + +ERRORS=0 +echo ""# Testing -interleave- function"" + +# Binary works +$BIN > /dev/null|| { echo ""Binary not working""; exit 1; } +echo ""OK: Running"" + +# Interleave normal R1 and R2 fastq +echo """" +echo ""1. TEST - interleave R1 and R2 fastq"" +echo ""COMMAND: $BIN ilv -v -o testtmpSample1.fq -1 $iPair1a -2 $iPair2a"" +$BIN ilv -v -o testtmpSample1.fq -1 $iPair1a -2 $iPair2a +if [[ $(cat testtmpSample1.fq | wc -l) == $(cat $iPair1a $iPair1a | wc -l ) ]]; then + echo ""OK: Interleave fastq _R1 and _R2"" +else + echo ""ERR: Interleave fastq _R1 and _R2"" + ERRORS=$((ERRORS+1)) +fi + + +# Interleave normal gzipped - find _2 by only giving _1 +echo """" +echo ""2. TEST - interleave gesipped fastq - _1 and let _2 automatically find"" +echo ""COMMAND: BIN ilv -v -o testtmpS1.fq -1 $iPair1"" +$BIN ilv -v -o testtmpS1.fq -1 $iPair1 +if [[ $(cat testtmpS1.fq | wc -l) == $(cat $iPair1 $iPair2 | gunzip | wc -l ) ]]; then + echo ""OK: Interleave fastq _1 and _2"" +else + echo ""ERR: Interleave fastq _1 and _2"" + ERRORS=$((ERRORS+1)) +fi + +# Interleave normal custom extension +echo """" +echo ""3. TEST - interleave _forward and let _reverse automatically find by specifying -f and -r "" +echo ""COMMAND: $BIN ilv -v -o testtmpS2.fq -1 $iPair1b -f forward -r reverse"" +$BIN ilv -v -o testtmpS2.fq -1 $iPair1b -f forward -r reverse +if [[ $(cat testtmpS2.fq | wc -l) == $(cat $iPair1b $iPair2b | wc -l ) ]]; then + echo ""OK: Interleave fastq _forward and _reverse"" +else + echo ""ERR: Interleave fastq _forward and _reverse"" + ERRORS=$((ERRORS+1)) +fi + + +# Interleave unbalanced reads +echo """" +echo ""4. TEST - interleave R1 (more reads) and R2 (fewer reads) of fastq"" +echo ""COMMAND: $BIN ilv -v -o testtmpLong1.fq -1 $iR1LONG1 -2 $iR2LONG1 2> testtmpnope"" +$BIN ilv -v -o testtmpLong1.fq -1 $iR1LONG1 -2 $iR2LONG1 + +# Interleave unbalanced reads +echo """" +echo ""5. TEST - interleave R1 (fewer reads) and R2 (more reads) of fastq"" +echo ""COMMAND: $BIN ilv -v -o testtmpLong2.fq -1 $iR1LONG2 -2 $iR2LONG2 2> testtmpnope2"" +$BIN ilv -v -o testtmpLong2.fq -1 $iR1LONG2 -2 $iR2LONG2 + +# Interleave two same fastq +# FATAL ERROR: First file and second file are equal. +echo """" +echo ""6. TEST - interleave two same fastq files"" +echo ""COMMAND: $BIN ilv -v -1 $iPair1a -2 $iPair1a"" +$BIN ilv -v -1 $iPair1a -2 $iPair1a + +# Interleave two empty fastq +# needed: warning if input files are empty ""no sequenes in file X""; at the moment: produces empty output but no warning +echo """" +echo ""7. TEST - interleave two empty fastq files"" +echo ""COMMAND: $BIN ilv -v -o testtmpintempty.fq -1 $iR1EMPTY -2 $iR2EMPTY"" +$BIN ilv -v -o testtmpintempty.fq -1 $iR1EMPTY -2 $iR2EMPTY +if [[ $(cat testtmpintempty.fq | wc -l ) == "" 0"" ]]; then + echo ""OK: Two empty input files resulted in one empty output file"" +else + echo ""ERR: interleave two empty fastq files"" + ERRORS=$((ERRORS+1)) +fi + +# Interleave nonexistent R2 +# needed: warning if input R2 file is nonexistent; at the moment: error +#echo """" +#echo ""8. TEST - interleave one existent R1 fastq file with one non-existent file"" +#echo ""COMMAND: $BIN ilv -v -o testtmpmiss -1 $iPair1a -2 $iAllMISS"" +#$BIN ilv -v -o testtmpmiss -1 $iPair1a -2 $iAllMISS + +rm testtmp* + +``` ","Markdown" +"Bioengineering","telatin/seqfu2","test/build.bash",".bash","63","3","nim c speed/imported.nim +nim c -p:../src/lib speed/native.nim +","Bash" +"Bioengineering","telatin/seqfu2","test/bin.sh",".sh","845","36","#!/bin/bash + +SCRIPT_DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" && pwd )"" + +echo ""Building fresh binary"" +echo ""============================="" + +VER=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE ' +my ($tag, $val) = split /:/, $_; +if ($tag=~/tag_name/) { + my @tag = split /""/, $val; + for my $i (@tag) { + $i =~s/[^0-9.]//g; + say $i if (length($i) > 2); + } +}') + + +if [[ $(uname) == ""Darwin"" ]]; then + PLAT='Darwin'; +else + PLAT='Linux-x86_64' +fi + +DEST=""$SCRIPT_DIR/../releases/zips/""; +mkdir -p ""$DEST"" + +echo ""Last version online: $VER"" +echo ""Local version: $LOCALVER"" +nimble build +LOCAL_RELEASE=$(./bin/seqfu version) +zip -r ""$DEST""/SeqFu-v""${LOCAL_RELEASE}""-""${PLAT}"".zip bin/* + +echo ""Last version online: $VER"" +echo ""Local version: $LOCAL_RELEASE"" +echo ""$DEST/SeqFu-v${LOCAL_RELEASE}-${PLAT}.zip""","Shell" +"Bioengineering","telatin/seqfu2","test/test-bases.sh",".sh","3604","141"," +#!/bin/bash + +export SEQFU_QUIET=1 +TEMPFILENAME=$(mktemp) +### SINGLE END +""$BINDIR""/seqfu bases ""$FILES""/{base,base_extra,bases_lower}.fa > ""$TEMPFILENAME"" +""$BINDIR""/seqfu bases -c ""$FILES""/{base,base_extra,bases_lower}.fa > ""$TEMPFILENAME.raw"" +""$BINDIR""/seqfu bases ""$FILES""/upper-{lower,none,only}.fa > ""$TEMPFILENAME.upper"" +WC=$(getnumber $(cat ""$TEMPFILENAME"" | wc -l)) + + +MSG=""Counted files"" +EXP=3 +if [[ $EXP == $WC ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $WC)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $WC)"" + ERRORS=$((ERRORS+1)) +fi + +# Check table +""$BINDIR""/fu-tabcheck ""$TEMPFILENAME"" > ""$TEMPFILENAME.check"" + +IS_TABLE=$(cat ""$TEMPFILENAME.check"" | cut -f 2) +NUM_COLS=$(getnumber $(cat ""$TEMPFILENAME.check"" | cut -f 3)) +MSG=""Output is a table"" +EXP=""Pass"" +if [[ $EXP == $IS_TABLE ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_TABLE)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_TABLE)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Output is a table with 9 columns"" +EXP=10 +if [[ $EXP == $NUM_COLS ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $NUM_COLS)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $NUM_COLS)"" + ERRORS=$((ERRORS+1)) +fi + + +### RAw checks +MSG=""Raw counts of extra bases"" +EXP=10 +GOT=$(getnumber $(cat ""$TEMPFILENAME.raw"" | grep extra | cut -f 8 )) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Raw counts of lowercase bases"" +EXP=15 +GOT=$(getnumber $(cat ""$TEMPFILENAME.raw"" | grep lower | cut -f 2 )) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi +#/// + +MSG=""Count ratio of As in bases_lower"" +EXP=""33.33"" +GOT=$(cat ""$TEMPFILENAME"" | grep lower | cut -f 3 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Count ratio of As in base.fa"" +EXP=""50.00"" +GOT=$(cat ""$TEMPFILENAME"" | grep base.fa | cut -f 3 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Count ratio of Gs in base.fa"" +EXP=""0.00"" +GOT=$(cat ""$TEMPFILENAME"" | grep base.fa | cut -f 5 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Uppercase ratio: none"" +EXP=""0.00"" +GOT=$(cat ""$TEMPFILENAME.upper"" | grep none | cut -f 10 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Uppercase ratio: all"" +EXP=""100.00"" +GOT=$(cat ""$TEMPFILENAME.upper"" | grep only | cut -f 10 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Uppercase ratio: mixed"" +EXP=""50.00"" +GOT=$(cat ""$TEMPFILENAME.upper"" | grep lower | cut -f 10 ) +if [[ $EXP == $GOT ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $GOT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $GOT)"" + ERRORS=$((ERRORS+1)) +fi +rm ""$TEMPFILENAME""*","Shell" +"Bioengineering","telatin/seqfu2","test/compare-grep.sh",".sh","311","15","#!/bin/bash + +for FILE in data/numbers.fa data/filt.fa.gz; +do + for PATTERN in 12$ filt.598..; + do + for SWITCH in ""-w"" ""-f""; + do + echo ""=== $PATTERN $SWITCH"" + hyperfine ""bin/seqfu grep $SWITCH -r $PATTERN $FILE"" \ + ""bin/seqfu grep2 $SWITCH -r $PATTERN $FILE"" + done + done +done +","Shell" +"Bioengineering","telatin/seqfu2","test/test-index.sh",".sh","2975","131","#!/bin/bash + +# Single file +TMP=$(mktemp) +echo "" Temp file: $TMP"" +""$BINDIR""/fu-index ""$iPair1"" ""$iPair2"" > ""$TMP"" + + +MSG=""Checking output expecting 2 lines:"" +EXP=2 +OBS=$(cat ""$TMP"" | wc -l | grep -o ""[[:digit:]]\+"" | head -n 1) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + cat ""$TMP"" + echo --- + #cat ""$TMP"" | wc -l | '[[:digit:]]\+' + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Got expected index:"" +EXP=""TACGCTGC+CTATTAAG"" +OBS=$(cat ""$TMP"" | cut -f 2 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $EXP / $OBS"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Got expected index ratio:"" +EXP=""1.00"" +OBS=$(cat ""$TMP"" | cut -f 3 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Got expected pass:"" +EXP=""PASS"" +OBS=$(cat ""$TMP"" | cut -f 4 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Got expected instrument:"" +EXP=""A00709"" +OBS=$(cat ""$TMP"" | cut -f 5 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Got expected flowcell:"" +EXP=""HYG25DSXX"" +OBS=$(cat ""$TMP"" | cut -f 7 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $EXP / $OBS: $(cat ""$TMP"")"" + ERRORS=$((ERRORS+1)) +fi + +# --- + +""$BINDIR""/fu-index ""$iAmpli"" > ""$TMP"" + +MSG=""Checking output expecting 1 line:"" +EXP=1 +OBS=$(wc -l ""$TMP"" | grep -o '[[:digit:]]\+' | head -n 1) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP / got=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checking failed sample (no index):"" +EXP="""" +OBS=$(cat ""$TMP"" | cut -f 2 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checking failed sample (status):"" +EXP=""--"" +OBS=$(cat ""$TMP"" | cut -f 4 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" + ERRORS=$((ERRORS+1)) +fi + + +# --- + +""$BINDIR""/fu-index ""$FILES""/mixed_index.fq.gz > ""$TMP"" +MSG=""Checking failed sample (ratio):"" +EXP=""0.50"" +OBS=$(cat ""$TMP"" | cut -f 3 | sort | uniq) +if [[ ""$OBS"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG: $EXP / $OBS"" + PASS=$((PASS+1)) +else + echo -e """"$FAIL: $MSG: $EXP / $OBS: $(cat $TMP)"""" + ERRORS=$((ERRORS+1)) +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/test-orflegacy.sh",".sh","1388","45","#!/bin/bash +ORFFOR=$(""$BINDIR""/fu-orf ""$FILES""/orf.fa.gz --min-size 500 | grep "">"" | wc -l) +ORFREV=$(""$BINDIR""/fu-orf ""$FILES""/orf.fa.gz --min-size 500 --scan-reverse | grep "">"" | wc -l) + +if [[ $ORFFOR -eq 1 ]]; then + echo -e ""$OK: ONE large ORF found in forward mode"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Expected ONE large ORF found in forward mode [found: $ORFFOR]"" + ERRORS=$((ERRORS+1)) +fi +if [[ $ORFREV -eq 2 ]]; then + echo -e ""$OK: Two large ORFs found in for/rev mode"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Expected Two large ORFs found in forward/reverse mode [found: $ORFREV]"" + ERRORS=$((ERRORS+1)) +fi + +CODE1=$(""$BINDIR""/fu-orf ""$FILES""/codons.fa --min-size 3 --min-read-len 6 -c 1 | grep -v "">"") +CODE5=$(""$BINDIR""/fu-orf ""$FILES""/codons.fa --min-size 3 --min-read-len 6 -c 5 | grep -v "">"") +if [[ $CODE1 != $CODE5 ]]; then + PASS=$((PASS+1)) + echo -e ""$OK: Genetic code implemented"" +else + echo -e ""$FAIL: Genetic code match $CODE1 $CODE5"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $CODE1 =~ ""RRI"" ]]; then + echo -e ""$OK: Standard genetic code [1]"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Standard genetic code error $CODE1 != RRI"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $CODE5 =~ ""SSM"" ]]; then + echo -e ""$OK: Genetic code #5"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Genetic code 5 error $CODE5 != SSM"" + ERRORS=$((ERRORS+1)) +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/merge.md",".md","234","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu merge -o /tmp/ data/lane` | 2.6 ± 0.9 | 1.6 | 10.4 | 1.00 | +| `bash /tmp/merge.sh data/lane/` | 31.8 ± 4.0 | 25.4 | 49.5 | 12.42 ± 4.46 | +","Markdown" +"Bioengineering","telatin/seqfu2","test/test-cat.sh",".sh","1816","78","#!/bin/bash + +# Single file +TMP=$(mktemp) +""$BINDIR""/seqfu stats --basename ""$iAmpli"" > ""$TMP"" + + +MSG=""Precheck input file has 1000 sequences"" +if [[ $(count ""$FILES""/numbers.fa) == 1000 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu cat --skip 2 ""$FILES""/numbers.fa > ""$TMP"" +OBS=$(count ""$TMP"") +EXP=500 +MSG=""Checking cat --skip 2, expecting 500 sequences, got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu cat --skip-first 500 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" +OBS=$(count ""$TMP"") +EXP=250 +MSG=""Checking cat --skip 2 and --skip-first 500, expecting $EXP sequences, got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu cat --skip-first 500 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" +OBS=$(count ""$TMP"") +EXP=250 +MSG=""Checking cat --skip 2 and --skip-first 500, expecting $EXP sequences, got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu cat --skip-first 500 --max-bp 200 --skip 2 ""$FILES""/numbers.fa > ""$TMP"" +OBS=$(bp ""$TMP"") +EXP=200 +MSG=""Checking --max-bp 200, got $OBS <= $EXP"" +if [[ ! $OBS -gt $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu cat --jump-to 500 ""$FILES""/numbers.fa > ""$TMP"" +OBS=$(count ""$TMP"") +EXP=500 +MSG=""Checking --jump-to NAME (exclusive), got $OBS expecting $EXP"" +if [[ ! $OBS -gt $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + + +","Shell" +"Bioengineering","telatin/seqfu2","test/minimal-markdown-linter.py",".py","3485","118","#!/usr/bin/env python +"""""" +Read a Markdown file and save it back out, but with some +minimal changes to make it pass the Markdown linter. +"""""" + +import sys +import os + +def eprint(*args, **kwargs): + print(*args, file=sys.stderr, **kwargs) + +def remove_trailing_whitespace(lines): + """""" + Remove trailing space from a line. + """""" + + lines = [line.rstrip() for line in lines] + return lines + +def fenced_code_blocks(lines): + """""" + Fenced code blocks should be surrounded by blank lines + """""" + opened = False + for i in range(len(lines)): + if lines[i].startswith('```'): + if i == 0 or lines[i-1] != '': + if not opened: + lines.insert(i, '') + opened = True + continue + elif i == len(lines)-1 or lines[i+1] != '': + if opened: + lines.insert(i+1, '') + opened = False + continue + + + + return lines + +def headerlines_withspace(lines): + """""" + Markdown headers have a variable number of '#' + and after a space must be present + """""" + + for index in range(len(lines)): + line = lines[index] + if line.startswith('#'): + for pos, char in enumerate(line): + if char != '#' and line[pos+1] != ' ': + lines[index] = line[:pos] + ' ' + line[pos:] + break + return lines + +def headerlines_surrounded(lines): + """""" + Headers should be surrounded by blank lines + """""" + + for i in range(len(lines)): + if lines[i].startswith('##'): + if i == 0 or lines[i-1] != '': + lines.insert(i, '') + if i == len(lines)-1 or lines[i+1] != '': + lines.insert(i+1, '') + + return lines + +def long_lines(lines): + """""" + Split long lines to be no longer than 60 characters + """""" + + for L in range(len(lines)): + if len(lines[L]) > 60: + for i, char in enumerate(lines[L]): + if char == ' ' or char == '\t': + lastwhite = i + if i > 60: + # replace character lastwhite with a newline + lines[L] = lines[L][:lastwhite] + lines.insert(L+1, lines[L][lastwhite+1:]) + break + return lines + + +if __name__ == '__main__': + import argparse + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('infile', nargs='+', type=argparse.FileType('r')) + parser.add_argument('-d', '--dry', action='store_true', default=False, help='dry run') + parser.add_argument('-v', '--verbose', action='store_true', default=False, help='verbose') + args = parser.parse_args() + + for file in args.infile: + eprint('Processing {}'.format(file.name)) + lines = file.readlines() + file.close() + + lines = remove_trailing_whitespace(lines) + lines = fenced_code_blocks(lines) + lines = headerlines_withspace(lines) + lines = headerlines_surrounded(lines) + #lines = long_lines(lines) + + if args.dry: + eprint('Dry run: not writing file:\n-------------------------') + print('\n'.join(lines)) + else: + # Make backup + eprint('Writing {}'.format(file.name)) + os.rename(file.name, file.name + '.bak') + with open(file.name, 'w') as f: + f.writelines('\n'.join(lines)) +","Python" +"Bioengineering","telatin/seqfu2","test/test-rc.sh",".sh","1056","54","#!/bin/bash + +export SEQFU_QUIET=1 + +FOR=""CAGATA"" +RC=""TATCTG"" + +OBS=$(""$BINDIR""/seqfu rc ""$FOR"") +MSG=""Reverse complement of $FOR: exp=$RC got=$OBS"" +if [[ $RC == $OBS ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +OBS=$(""$BINDIR""/seqfu rc ""$RC"") +MSG=""Reverse complement of $RC: exp=$FOR got=$OBS"" +if [[ $OBS == $FOR ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +#>polya +#cagataaaaaaa +#TTTTTTTATCTG +OBS=$(""$BINDIR""/seqfu rc ""$FILES""/rc.fa | grep -v "">"") +EXP=""TTTTTTTATCTG"" +MSG=""Reverse complement of rc.fa: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +## IUPAC + +IUPAC=""ACGTWSKY"" +EXP=""RMSWACGT"" +OBS=$(""$BINDIR""/seqfu rc $IUPAC) +MSG=""Reverse complement iupac $IUPAC: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi ","Shell" +"Bioengineering","telatin/seqfu2","test/test-tabcheck.sh",".sh","1279","52","#!/bin/bash + +# Single file +TABLE=""$FILES""/table-demo.tsv +COMPR=""$FILES""/tablegz.tsv.gz +WRONG=""$FILES""/table2.tsv + +for F in ""$TABLE"" ""$COMPR"" ""$WRONG""; do + if [[ -e ""$F"" ]]; then + echo -e ""$OK: Files exist: $F"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: Files do not exist: $F"" + ERRORS=$((ERRORS+1)) + fi +done + + +# ----------------------------------------------------------------------------- + +EXP=1 +MSG=""Check valid table"" +OBS=$(""$BINDIR""/fu-tabcheck ""$TABLE"" | grep Pass | wc -l | grep -o '[[:digit:]]\+') +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +EXP=0 +MSG=""Check wrong table"" +OBS=$(""$BINDIR""/fu-tabcheck ""$WRONG"" | grep Pass | wc -l | grep -o '[[:digit:]]\+') +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +EXP=0 +MSG=""Check details"" +OBS=$(""$BINDIR""/fu-tabcheck ""$TABLE"" -i | grep Pass | wc -l | grep -o '[[:digit:]]\+') +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi","Shell" +"Bioengineering","telatin/seqfu2","test/speed.sh",".sh","288","9","#!/bin/bash + +for FILE in /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq /local/qi/data/SC/CEL/reads/F09.fastq.gz ""$@""; +do + seqfu count ""$FILE"" + BASE=$(basename ""$FILE"" | cut -f1 -d.) + hyperfine ""./speed/native $FILE"" ""./speed/imported $FILE"" --export-markdown speed/""$BASE"".md +done +","Shell" +"Bioengineering","telatin/seqfu2","test/test-comp.sh",".sh","364","14","#!/bin/bash +NATIVE=$(grep -v "">"" ""$FILES""/homopolymer.fa| wc -c) +COMPRESSED=$(""$BINDIR""/fu-homocomp ""$FILES""/homopolymer.fa | grep -v "">"" | wc -c) + +if [[ $NATIVE -gt $COMPRESSED ]]; then + echo -e ""$OK: compression from $NATIVE to $COMPRESSED"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: compression from $NATIVE to $COMPRESSED"" + ERRORS=$((ERRORS+1)) +fi + + +","Shell" +"Bioengineering","telatin/seqfu2","test/test-split.sh",".sh","3260","124","#!/bin/bash + +PY=$(command -v python) +PYERR=$? +if [[ -e ""$BINDIR""/fu-split ]] && [[ $PYERR == 0 ]]; then + +python --version +export SEQFU_BIN=""$BINDIR""/seqfu +# Single file +OUTDIR=$(mktemp -d) +echo "" * Outdir: $OUTDIR"" + + +if [[ ! -d ""$OUTDIR"" ]]; then + echo ""Error: output directory not created"" + exit 1 +fi + +touch ""$OUTDIR""/test.txt +EXP=7 + +""$BINDIR""/fu-split -i ""$i16S"" -n $EXP -o ""$OUTDIR""/splitParts-00000.fa.gz +# -------------------------------------------------------------------------------- +OBS=$(ls ""$OUTDIR""/splitParts-*.fa.gz | wc -l | grep -o '[[:digit:]]\+') +MSG=""Split in $EXP files: got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ls -lh ""$OUTDIR""/splitParts-*.fa.gz + ERRORS=$((ERRORS+1)) +fi + +EXP=$(count ""$i16S"") +OBS=$(""$BINDIR""/seqfu cat ""$OUTDIR""/splitParts-*.fa.gz | ""$BINDIR""/seqfu count | cut -f 2) +MSG=""Total sequences from splitParts-*.fa.gz equal source: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + + +# Check total bases +BASES=500000 +""$BINDIR""/fu-split -i ""$i16S"" -b $BASES -o ""$OUTDIR""/splitBases-00000.fa.gz +# -------------------------------------------------------------------------------- +EXP=$(bp ""$i16S"") +OBS=$(bp ""$OUTDIR""/splitBases-*.fa.gz) +MSG=""Split by $BASES bases: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +EXP=4 +OBS=$(ls ""$OUTDIR""/splitBases-*.fa.gz | wc -l | grep -o '[[:digit:]]\+') +MSG=""Split by bases: expecting $EXP files: got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ""$BINDIR""/seqfu stats -b -n ""$OUTDIR""/splitBases-*.fa.gz + ERRORS=$((ERRORS+1)) +fi + +# Each file should contain less than $BP bases +for FILE in ""$OUTDIR""/splitBases*; +do + F=$(basename ""$FILE"") + BP=$(bp ""$FILE"") + if [[ ! $BP -gt $BASES ]]; then + echo -e ""$OK: $F contains $BP bp: no more than $BASES"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: $F contains $BP bp: more than $BASES"" + ERRORS=$((ERRORS+1)) + fi +done +# ============================================================================== +# Check total seqs +SEQS=1000 +""$BINDIR""/fu-split -i ""$i16S"" -s $SEQS -o ""$OUTDIR""/splitSeqs-00000.fa.gz +# -------------------------------------------------------------------------------- +EXP=$(bp ""$i16S"") +OBS=$(bp ""$OUTDIR""/splitSeqs-*.fa.gz) +MSG=""Split by $SEQS seqs: exp=$EXP got=$OBS "" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +# Each file should contain less than $SEQS sequences +for FILE in ""$OUTDIR""/splitSeqs*; +do + COUNT=$(count ""$FILE"") + F=$(basename ""$FILE"") + if [[ ! $COUNT -gt $SEQS ]]; then + echo -e ""$OK: $F contains $COUNT sequences: no more than $SEQS"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: $F contains $COUNT sequences: more than $SEQS"" + ERRORS=$((ERRORS+1)) + fi +done + +if [[ $ERRORS == 0 ]]; then + rm -rf ""$OUTDIR"" +fi + +else + echo -e ""SKIP: python not found ($PY) or fu-split not in $BINDIR"" +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/test-stats.sh",".sh","5419","194","#!/bin/bash + +# Single file +TMP=$(mktemp) +""$BINDIR""/seqfu stats --basename ""$iAmpli"" > ""$TMP"" + +WC=$(cat ""$TMP"" | wc -l | grep -o '[[:digit:]]\+') +SEQS=$(cat ""$TMP"" | tail -n 1 | cut -f 2) +TOT=$(cat ""$TMP"" | tail -n 1 | cut -f 3) +N50=$(cat ""$TMP"" | tail -n 1 | cut -f 5) + +MSG=""Checking normal output expecting 2 lines: <$WC>"" +if [[ $WC == 2 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Checking normal output expecting total seqs 78730: <$SEQS>"" +if [[ ""$SEQS"" == 78730 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checking normal output expecting total bases 24299931: <$TOT>"" +if [[ ""$TOT"" == 24299931 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checking normal N50 to be 316: <$N50>"" +if [[ $N50 == 316 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats --basename --csv ""$iAmpli"" > ""$TMP"" +N50=$(cat ""$TMP"" | tail -n 1 | cut -f 5 -d ,) +MSG=""Checking CSV output N50 is 316, got: <$N50>"" +if [[ $N50 == 316 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +# Nice output +""$BINDIR""/seqfu stats --basename --nice ""$iAmpli"" > ""$TMP"" +WC=$(cat ""$TMP"" | grep . | wc -l | grep -o '[[:digit:]]\+') +if [[ ""$WC"" == 5 ]]; then + echo -e ""$OK: Checking nice output expecting 5 lines: <$WC>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Checking nice output expecting 5 lines: <$WC>"" + ERRORS=$((ERRORS+1)) +fi + +# Json +TMP2=$(mktemp) +""$BINDIR""/seqfu stats --basename --json --multiqc ""$TMP2"" ""$iAmpli"" > ""$TMP"" +WC=$(cat ""$TMP"" | grep . | wc -l | grep -o '[[:digit:]]\+') +WC2=$(cat ""$TMP2"" | grep . | wc -l | grep -o '[[:digit:]]\+') +if [[ ""$WC2"" == 39 ]]; then + echo -e ""$OK: Checking MultiQC output expecting 39 lines: <$WC2>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Checking MultiQC output expecting 39 lines: <$WC2>"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $WC == 1 ]]; then + echo -e ""$OK: Experimental JSON output on 1 line: <$WC>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Experimental JSON output on 1 line: <$WC>"" + ERRORS=$((ERRORS+1)) +fi +# Multi file + +# Default sort +""$BINDIR""/seqfu stats --basename ""$iAmpli"" ""$iSort"" ""$iMini"" > ""$TMP"" +# Sort by N50 descending +""$BINDIR""/seqfu stats --basename --sort n50 --reverse ""$iAmpli"" ""$iSort"" ""$iMini"" > ""$TMP2"" + +FILT=$(cat ""$TMP"" | head -n 2 | tail -n 1 | cut -f 1) +MSG=""Checking default starting by 'filt': <$FILT>"" +if [[ ""$FILT"" == ""filt"" ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +FILT=$(cat ""$TMP2"" | head -n 2 |tail -n 1 | cut -f 1) +MSG=""Checking default N50 starting by 'sort': <$FILT>"" +if [[ ""$FILT"" == ""sort"" ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +#///// + + +""$BINDIR""/seqfu stats -a ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" + +MSG=""Check absolute paths"" +if [[ $(grep ^/ ""$TMP"" | cut -c 1 | sort | head -n 1 ) == ""/"" ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: "" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Check sort orded when not specified"" +A=$(basename $(head -n 1 ""$TMP"" | cut -f 1 ) ) +if [[ ""$A"" == ""prot.faa"" ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: $A"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats -a --sort tot ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" +MSG=""Check sort: tot seq sorted at 3300"" +if [[ $(head -n 1 ""$TMP"" | cut -f 3 ) == 3300 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG:$(head -n 1 ""$TMP"" | cut -f 3 ) "" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats -a --sort tot --reverse ""$FILES""/prot.faa ""$FILES""/prot2.faa ""$FILES""/test.fa ""$FILES""/test.fasta ""$FILES""/test.fastq ""$FILES""/test2.fastq ""$FILES""/test_4.fa.gz | grep -v ""Total bp"" > ""$TMP"" +MSG=""Check reverse sort: tot seq sorted at 3300"" +if [[ $(tail -n 1 ""$TMP"" | cut -f 3 ) == 3300 ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG:$(head -n 1 ""$TMP"" | cut -f 3 ) "" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats --gc ""$FILES""/gc/1.fa | grep -v ""Total bp"" > ""$TMP"" +MSG=""%GC check at 1.00"" +OUT=$(cut -f 11 ""$TMP"" ) +if [[ ""$OUT"" == 1.00 ]]; then + echo -e ""$OK: $MSG: <$OUT>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG expected 1.00 got $OUT"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats --gc ""$FILES""/gc/2.fa | grep -v ""Total bp"" > ""$TMP"" +MSG=""%GC check at 0.00"" +OUT=$(cut -f 11 ""$TMP"" ) +if [[ ""$OUT"" == 0.00 ]]; then + echo -e ""$OK: $MSG: <$OUT>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG expected 0.00 got $OUT"" + ERRORS=$((ERRORS+1)) +fi + +""$BINDIR""/seqfu stats --gc ""$FILES""/gc/3.fa | grep -v ""Total bp"" > ""$TMP"" +MSG=""%GC check at 0.50"" +OUT=$(cut -f 11 ""$TMP"" ) +if [[ ""$OUT"" == 0.50 ]]; then + echo -e ""$OK: $MSG: <$OUT>"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG expected 0.50 got $OUT"" + ERRORS=$((ERRORS+1)) +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/mini.sh",".sh","11120","432","#!/bin/bash +export SEQFU_QUIET=1 +DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" + +BINDIR=""$DIR/../bin/"" +BIN=""$BINDIR""/seqfu +FILES=""$DIR""/../data/ + +iInterleaved=""$FILES""/interleaved.fq.gz +iPair1=""$FILES""/illumina_1.fq.gz +iPair2=""$FILES""/illumina_2.fq.gz +iAmpli=""$FILES""/filt.fa.gz +iSort=""$FILES""/sort.fa +iMini=""$FILES""/target.fa +i16S=""$FILES""/primers/16S_R1.fq.gz +export iComments=""$FILES""/comments.fastq +export iNum=""$FILES""/numbers.fa + +OK='\033[0;32mOK\033[0m' +FAIL='\033[0;31mFAIL\033[0m' +STAR='\033[1;34m->\033[0m' +NOTE='\033[0;34m' +BOLD='\033[1m' +YELLOW='\033[1;33m' +NC='\033[0m' +ERRORS=0 + +getnumber() { + echo ""$1"" | grep -o '[0-9]*' +} +count() { + + ""$BINDIR""/seqfu count ""$1"" | cut -f 2 +} +bp() { + ""$BINDIR""/seqfu cat ""$@"" | ""$BINDIR""/seqfu stats | grep -v ""Total bp"" | cut -f 3 +} + +function separator { + # if length $1 > 0; then + # echo -e ""\n$1\n"" + if [[ $1 ]]; then + echo -e ""${YELLOW}\033[1m $1 \033[0m"" + fi + DIV_BAR=""${YELLOW}\033[1m------------------------------------------------------------ \033[0m"" + echo -e ""$DIV_BAR"" +} + +separator ""Minimal test suite"" +# Binary works +""$BIN"" > /dev/null || { echo ""Binary not working: $BIN""; exit 1; } +echo -e ""$OK: Binary running"" + +BINCOUNT=0 +for MOD in head tail view qual derep sort count stats grep rc interleave deinterleave count; +do + BINCOUNT=$((BINCOUNT+1)) + echo -e "" $STAR $BINCOUNT. $MOD"" + ""$BIN"" ""$MOD"" --help >/dev/null 2>&1 || { echo ""Help for $MOD returned non-zero""; exit 1; } +done + +# Check version + +VERSION=$(""$BIN"" version) +if [[ ""$VERSION"" == """" ]]; +then + echo ""Version not found"" + ERRORS=$((ERRORS+1)) +else + grep ""$VERSION"" ""$DIR""/../seqfu.nimble +fi + +PASS=0 +ERRORS=0 +# Dereiplicate +if [[ $(""$BIN"" derep ""$iAmpli"" | grep -c '>') -eq ""18664"" ]]; then + echo -e ""$OK: Dereplicate"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Dereplicate didnt return 18664 seqs"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" derep ""$iAmpli"" -m 10000 2>/dev/null | grep -c '>') -eq ""1"" ]]; then + echo -e ""$OK: Dereplicate, min size"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Dereplicate, min size"" + ERRORS=$((ERRORS+1)) +fi + +# Grep +if [[ $(""$BIN"" grep -n seq.1 ""$FILES""/comm.fa | grep -c '>') -eq ""1"" ]]; then + echo -e ""$OK: grep, name"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: grep, name"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" grep -c -n size=3 ""$FILES""/comm.fa | grep -c '>') -eq ""1"" ]]; then + echo -e ""$OK: grep, size"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: grep, size"" + ERRORS=$((ERRORS+1)) +fi + +# List +if [[ $(""$BIN"" list ""$FILES""/prot.list ""$FILES""/prot.faa | grep -c '>') -eq ""5"" ]]; then + echo -e ""$OK: list, default"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: list, default not 5"" + ERRORS=$((ERRORS+1)) +fi +if [[ $(""$BIN"" list -c ""$FILES""/prot.list ""$FILES""/prot.faa | grep -c '>') -eq ""4"" ]]; then + echo -e ""$OK: list, with comments"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: list, with comments not 4"" + ERRORS=$((ERRORS+1)) +fi + +# Homopolymer +HOMO=""$(dirname ""$BIN"")""/fu-homocomp +if [[ -e ""$HOMO"" ]]; then + ORIGINAL=$(grep . ""$FILES""/homopolymer.fq | wc -c | grep -o ""[[:digit:]]\+"") + COMPRESSED=$($HOMO ""$FILES""/homopolymer.fq | wc -c | grep -o ""[[:digit:]]\+"") + if [[ $ORIGINAL -gt $COMPRESSED ]]; then + echo -e ""$OK: homopolymer pass $ORIGINAL > $COMPRESSED"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: homopolymer failed $ORIGINAL original length, $COMPRESSED compressed length"" + ERRORS=$((ERRORS+1)) + fi +fi + +# Interleave +if [[ $(""$BIN"" ilv -1 ""$iPair1"" -2 ""$iPair2"" | wc -l) == $(cat ""$iPair1"" ""$iPair2"" | gzip -d | wc -l ) ]]; then + echo -e ""$OK: Interleave"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Interleave differs cat/wc"" + ERRORS=$((ERRORS+1)) +fi + +# Deinterleave +""$BIN"" dei ""$iInterleaved"" -o testtmp +if [[ $(grep . testtmp_R{1,2}.fq | wc -l) == $(gzip -dc ""$iInterleaved"" | wc -l ) ]]; then + echo -e ""$OK: Deinterleave"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Deinterleave "" + ERRORS=$((ERRORS+1)) +fi +rm testtmp_* + +# Count +if [[ $(""$BIN"" count ""$iAmpli"" | cut -f 2) == $(gzip -dc ""$iAmpli"" | grep -c '>' ) ]]; then + echo -e ""$OK: Count"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Count \""$BIN\"" count \""$iAmpli\"": differs grep/wc"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" count ""$iPair1"" ""$iPair2"" | wc -l) -eq 1 ]]; then + echo -e ""$OK: Count pairs"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Count pairs"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" count -u ""$iPair1"" ""$iPair2"" | wc -l) -eq 2 ]]; then + echo -e ""$OK: Count pairs, split"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Count pairs, split"" + ERRORS=$((ERRORS+1)) +fi + + +## Sort by size (asc) +OUTPUT=$(""$BIN"" sort --asc ""$iSort"" | head -n 1| cut -c 2-6) +if [[ $OUTPUT == 'short' ]]; then + echo -e ""$OK: Sort by size"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Sort by size failed, exp short got '$OUTPUT'"" + ERRORS=$((ERRORS+1)) +fi + +## Head +if [[ $(""$BIN"" head -n 1 ""$iInterleaved"" | wc -l) -eq 4 ]]; then + echo -e ""$OK: Head 1 sequence"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Head failed"" + ERRORS=$((ERRORS+1)) +fi + + + +## Tail +if [[ $(""$BIN"" tail -n 1 ""$iInterleaved"" | wc -l) -eq 4 ]]; then + echo -e ""$OK: tail 1 sequence"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Tail failed"" + ERRORS=$((ERRORS+1)) +fi + + + +##QUal +if [[ $(""$BIN"" qual ""$iInterleaved"" | grep 'Illumina-1.8' | wc -l ) -eq 1 ]]; then + echo -e ""$OK: qual tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: qual failed"" + ERRORS=$((ERRORS+1)) +fi + +## External + +# Seqfu ORF +ORF1=$(""$BINDIR""/fu-orf -1 ""$iPair1"" -m 29 -r | grep -c '>') +if [[ $ORF1 -eq 20 ]]; then + echo -e ""$OK: fu-orf [-1] tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-orf [-1] test failed: $ORF1 != 20"" + ERRORS=$((ERRORS+1)) +fi + +ORFSE=$(""$BINDIR""/fu-orf ""$iPair1"" -m 29 -r | grep -c '>') +if [[ $ORFSE -eq 20 ]]; then + echo -e ""$OK: fu-orf [Single] tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-orf [Single] test failed: $ORFSE != 20"" + ERRORS=$((ERRORS+1)) +fi + +ORF2=$(""$BINDIR""/fu-orf -r -m 29 -1 ""$iPair1"" -2 ""$iPair2"" | grep -c '>') +if [[ $ORF2 -gt 4 ]]; then + echo -e ""$OK: fu-orf [Paired] tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-orf [Paired] test failed: $ORF2 != 5"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BINDIR""/fu-sw -q ""$FILES""/query.fa -t ""$FILES""/target.fa | grep -c -w '^Query') -eq 1 ]]; then + echo -e ""$OK: fu-sw tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-sw header: test failed: != 1"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BINDIR""/fu-sw -q ""$FILES""/query.fa -t ""$FILES""/target.fa | grep -c '16S_') -eq 2 ]]; then + echo -e ""$OK: fu-sw tested"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-sw alignments: test failed: != 2"" + ERRORS=$((ERRORS+1)) +fi +## STREAMING + +if [[ $( gzip -dc ""$iInterleaved"" | ""$BIN"" head -n 1 2>/dev/null | wc -l) -eq 4 ]]; then + echo -e ""$OK: Head 1 sequence (stream)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: Head failed"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(gzip -dc ""$iInterleaved"" | ""$BIN"" tail -n 1 2>/dev/null | wc -l) -eq 4 ]]; then + echo -e ""$OK: tail 1 sequence (stream)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: tail failed"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" head -n 6 ""$iInterleaved"" | ""$BIN"" tail -n 2 2>/dev/null | wc -l) -eq 8 ]]; then + echo -e ""$OK: head/tail 1 sequence (stream)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: head/tail failed"" + ERRORS=$((ERRORS+1)) +fi + +# CAT +if [[ $(""$BIN"" cat ""$iMini"" | head -n 1) == "">ecoli comment"" ]]; then + echo -e ""$OK: cat: default"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: cat: default"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" cat ""$iMini"" -s | head -n 1) == "">ecoli"" ]]; then + echo -e ""$OK: cat: strip comment"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: cat: strip comment"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" cat -z -p test_ ""$iMini"" | head -n 1) == "">test_1 comment"" ]]; then + echo -e ""$OK: cat: prefix"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: cat: prefix stripped didnt work: got $( ""$BIN"" cat -z -p test_ ""$iMini"" | head -n 1)"" + ERRORS=$((ERRORS+1)) +fi + +if [[ $(""$BIN"" cat -b ""$iMini"" -s | head -n 1) != "">target_ecoli"" ]]; then + echo -e ""$FAIL: cat: basename not added"" + ERRORS=$((ERRORS+1)) +else + echo -e ""$OK: cat: added basename"" + PASS=$((PASS+1)) +fi + +## fu-cov +TOTFILT=$(""$BINDIR""/fu-cov ""$FILES/ctgs.fa.gz"" -c 100 -x 200 2>/dev/null | grep -c '>') +if [[ $((TOTFILT+0)) -eq 1 ]]; then + echo -e ""$OK: fu-cov"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: fu-cov was supposed to select 1 sequence, $TOTFILT found "" + ERRORS=$((ERRORS+1)) +fi + +echo """" +SEARCH_DONE=0 +for TEST in ""$DIR""/test-*.sh; +do + UTIL=$(basename ""$TEST"" | cut -f 1 -d '.' | cut -f 2 -d -) + PREVPASS=$PASS + PREVERR=$ERRORS + + if [[ $SEARCH_DONE -eq 1 ]]; then + break + fi + if [[ ! -z ${1+x} ]] && [[ ""$1"" != ""$UTIL"" ]]; then + echo Skipping $UTIL: looking for $1 + continue + fi + + if [[ -e $TEST ]]; then + echo """" + separator "" Testing module: $(basename ""$TEST"" .sh | cut -f 2 -d - )"" + source ""$TEST"" + + if [[ $ERRORS -gt $PREVERR ]]; + then + echo -e ""$FAIL: Finished with $((PASS-PREVPASS)) passed, $((ERRORS-PREVERR)) failed"" + else + echo -e ""$NOTE# Finished with $((PASS-PREVPASS)) passed, $((ERRORS-PREVERR)) failed${NC}"" + fi + fi + + if [[ ! -z ${1+x} ]] && [[ ""$1"" == ""$UTIL"" ]]; then + SEARCH_DONE=1 + break + fi +done + +if [[ ! -z ${1+x} ]]; then + exit 0 +fi + +## Check docs +separator ""\n Checking docs"" + +for SUB in utilities tools; +do + echo "" - Utilities sort order in $SUB"" + # Note: perl not installed in Github CI + perl --version >/dev/null && grep ^sort: ""$DIR/../docs/$SUB/""[a-z]* | grep -v README | \ + cut -f 2,3 -d : | \ + sort | uniq -c | perl -mTerm::ANSIColor -ne ' + if ($_=~/^\s*(\S)/) + { if ($1 != ""1"") + { print Term::ANSIColor::color(""red""), "" >>> RELEASE WARNING:"", + Term::ANSIColor::color(""reset""), "" Wrong sort order: duplicate entry(es)\n""; + die; + } + }' || grep ^sort: ""$DIR/../docs/$SUB/""[a-z]* | \ + rev | \ + sort -n | \ + rev +done + +## Check release +separator ""\n Checking release (GitHub)"" +LOCAL_RELEASE=$(grep version ""$DIR/../seqfu.nimble"" | cut -f 2 -d = | sed 's/["" ]//g') +GH_RELEASE=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE 'my ($tag, $val) = split /:/, $_; if ($tag=~/tag_name/) { my @tag = split /""/, $val; for my $i (@tag) { $i =~s/[^0-9.]//g; say $i if (length($i) > 2); } }') + +if [[ $LOCAL_RELEASE == $GH_RELEASE ]]; then + echo "" ****************************************************************************"" + echo "" Local $LOCAL_RELEASE matches remote $GH_RELEASE"" + echo "" Set RELEASE=1 to make this warning fatal (e.g. when preparing a new release)"" + echo "" ****************************************************************************"" + echo + if [[ $RELEASE == 1 ]]; + then + echo -e ""$FAIL: Release matches last version on GitHub"" + ERRORS=$((ERRORS+1)) + fi +else + echo -e ""$OK: Local Nimble release $LOCAL_RELEASE != $GH_RELEASE (remote)"" + PASS=$((PASS+1)) +fi + +echo "" Binary version $(""$BINDIR""/seqfu version)"" + +### Check failures +separator +if [[ $ERRORS -gt 0 ]]; then + echo -e ""$FAIL: $ERRORS test failed ($PASS passed)"" + exit 1 +else + echo -e ""$OK: All $PASS tests passed"" +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/test-tofasta.sh",".sh","5662","176","#!/bin/bash + +export SEQFU_QUIET=1 +TEMPFILENAME=$(mktemp) +TOFASTA_DIR=""$FILES/tofasta"" + +# Test files +CLUSTAL_FILE=""$TOFASTA_DIR/test.clw.gz"" +GENBANK_FILE=""$TOFASTA_DIR/test.gbk.gz"" +GFF_FILE=""$TOFASTA_DIR/test.gff.gz"" + +### Test 1: Convert Clustal format +""$BINDIR""/seqfu tofasta ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.clw"" +WC=$(grep -c '^>' ""$TEMPFILENAME.clw"") + +MSG=""tofasta: Clustal format conversion"" +EXP=3 +if [[ $EXP == $WC ]]; then + echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 2: Convert GenBank format +""$BINDIR""/seqfu tofasta ""$GENBANK_FILE"" > ""$TEMPFILENAME.gbk"" +WC=$(grep -c '^>' ""$TEMPFILENAME.gbk"") + +MSG=""tofasta: GenBank format conversion"" +EXP=75 +if [[ $EXP == $WC ]]; then + echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 3: Convert GFF format +""$BINDIR""/seqfu tofasta ""$GFF_FILE"" > ""$TEMPFILENAME.gff"" 2>/dev/null +WC=$(grep -c '^>' ""$TEMPFILENAME.gff"") + +MSG=""tofasta: GFF format conversion"" +EXP=226 +if [[ $EXP == $WC ]]; then + echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 4: Uppercase transformation +""$BINDIR""/seqfu tofasta -u ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.upper"" +# Check if sequences are uppercase (should not contain lowercase letters) +LOWERCASE_COUNT=$(grep -v '^>' ""$TEMPFILENAME.upper"" | grep -o '[a-z]' | wc -l | tr -d ' ') + +MSG=""tofasta: uppercase transformation"" +EXP=0 +if [[ $EXP == $LOWERCASE_COUNT ]]; then + echo -e ""$OK: $MSG (no lowercase letters found)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (found $LOWERCASE_COUNT lowercase letters, expected 0)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 5: Lowercase transformation +""$BINDIR""/seqfu tofasta -l ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.lower"" +# Check if sequences are lowercase (should not contain uppercase letters) +UPPERCASE_COUNT=$(grep -v '^>' ""$TEMPFILENAME.lower"" | grep -o '[A-Z]' | wc -l | tr -d ' ') + +MSG=""tofasta: lowercase transformation"" +EXP=0 +if [[ $EXP == $UPPERCASE_COUNT ]]; then + echo -e ""$OK: $MSG (no uppercase letters found)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (found $UPPERCASE_COUNT uppercase letters, expected 0)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 6: Replace IUPAC ambiguous bases +""$BINDIR""/seqfu tofasta -n ""$CLUSTAL_FILE"" > ""$TEMPFILENAME.iupac"" +# Check if R (in gene01: ATGCRAGGAT) was replaced with N +R_COUNT=$(grep -v '^>' ""$TEMPFILENAME.iupac"" | grep -o 'R' | wc -l | tr -d ' ') + +MSG=""tofasta: replace non-IUPAC with N"" +EXP=0 +if [[ $EXP == $R_COUNT ]]; then + echo -e ""$OK: $MSG (R was replaced)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (found $R_COUNT 'R' characters, expected 0)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 7: Multiple files with output file +""$BINDIR""/seqfu tofasta -o ""$TEMPFILENAME.multi"" ""$CLUSTAL_FILE"" ""$GENBANK_FILE"" 2>/dev/null +if [[ -f ""$TEMPFILENAME.multi"" ]]; then + WC=$(grep -c '^>' ""$TEMPFILENAME.multi"") + MSG=""tofasta: multiple files to output file"" + EXP=78 # 3 from Clustal + 75 from GenBank + if [[ $EXP == $WC ]]; then + echo -e ""$OK: $MSG (expected $EXP sequences, got $WC)"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: $MSG (expected $EXP sequences, got $WC)"" + ERRORS=$((ERRORS+1)) + fi +else + echo -e ""$FAIL: tofasta: output file was not created"" + ERRORS=$((ERRORS+1)) +fi + +### Test 8: Verbose mode stderr output +VERBOSE_OUTPUT=$(""$BINDIR""/seqfu tofasta -v ""$CLUSTAL_FILE"" 2>&1 >/dev/null) +if echo ""$VERBOSE_OUTPUT"" | grep -q ""Format: Clustal""; then + echo -e ""$OK: tofasta: verbose mode works"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: tofasta: verbose mode did not print format"" + ERRORS=$((ERRORS+1)) +fi + +### Test 9: Check sequence correctness (GenBank ID) +GB_HEADER=$(head -n 1 ""$TEMPFILENAME.gbk"") +if echo ""$GB_HEADER"" | grep -q ""NZ_AHMY02000075""; then + echo -e ""$OK: tofasta: GenBank sequence ID correct"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: tofasta: GenBank sequence ID not found (got: $GB_HEADER)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 10: Check sequence correctness (Clustal IDs) +GENE01_FOUND=$(grep -c '^>gene01' ""$TEMPFILENAME.clw"") +GENE02_FOUND=$(grep -c '^>gene02' ""$TEMPFILENAME.clw"") +GENE03_FOUND=$(grep -c '^>gene03' ""$TEMPFILENAME.clw"") + +MSG=""tofasta: Clustal sequence IDs correct"" +if [[ $GENE01_FOUND == 1 ]] && [[ $GENE02_FOUND == 1 ]] && [[ $GENE03_FOUND == 1 ]]; then + echo -e ""$OK: $MSG (all 3 genes found)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (gene01=$GENE01_FOUND, gene02=$GENE02_FOUND, gene03=$GENE03_FOUND)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 11: Sequence content preservation (check gaps were removed) +# Clustal alignment has gaps (-), FASTA output should not +GAP_COUNT=$(grep -v '^>' ""$TEMPFILENAME.clw"" | grep -o '\-' | wc -l | tr -d ' ') + +MSG=""tofasta: gaps preserved in output"" +# We expect gaps to be preserved in the sequence (they are valid FASTA characters) +if [[ $GAP_COUNT -gt 0 ]]; then + echo -e ""$OK: $MSG (found $GAP_COUNT gaps as expected)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (no gaps found, expected some)"" + ERRORS=$((ERRORS+1)) +fi + +### Test 12: Help text +if ""$BINDIR""/seqfu tofasta --help 2>&1 | grep -q ""Convert various sequence formats""; then + echo -e ""$OK: tofasta: help text available"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: tofasta: help text not found"" + ERRORS=$((ERRORS+1)) +fi + +# Cleanup +rm -f ""$TEMPFILENAME""* +","Shell" +"Bioengineering","telatin/seqfu2","test/deinterleave.md",".md","2795","88","# Reference deinterleave.sh script + +```bash +#!/bin/bash + +DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" +PLATFORM="""" +if [[ $(uname) == ""Darwin"" ]]; then + PLATFORM="""" +fi +BIN=$DIR/../bin/seqfu${PLATFORM} +FILES=$DIR/../data/ + +# Files +iInterleaved=$FILES/interleaved.fq.gz +iInterleavedFQ=$FILES/tests/interleavedFQ.fq +iInterUNEVEN=$FILES/tests/unevenInterleaved.fq +iInterLONG1=$FILES/tests/longerone.fq +iInterLONG2=$FILES/tests/longertwo.fq +iAllEMPTY=$FILES/tests/empty.fq +iAllMISS=$FILES/tests/nonexistent.fq + +ERRORS=0 +echo ""# Testing -deinterleave- function"" + +# Binary works +$BIN > /dev/null|| { echo ""Binary not working""; exit 1; } +echo ""OK: Running"" + +# Deinterleave normal gzipped +echo """" +echo ""1. TEST - de-interleave a gzipped fastq file"" +echo ""COMMAND: $BIN dei -v -o testtmp $iInterleaved"" +$BIN dei -v -o testtmp $iInterleaved +if [[ $(cat testtmp_R1.fq testtmp_R2.fq | wc -l) == $(cat $iInterleaved | gunzip | wc -l ) ]]; then + echo ""OK: Deinterleave gzipped fastq"" +else + echo ""ERR: Deinterleave gzipped fastq"" + ERRORS=$((ERRORS+1)) +fi + +# Deinterleave normal +echo """" +echo ""2. TEST - de-interleave a fastq file"" +echo ""COMMAND: $BIN dei -v -o testtmpFQ $iInterleavedFQ"" +$BIN dei -v -o testtmpFQ $iInterleavedFQ +if [[ $(cat testtmpFQ_R1.fq testtmpFQ_R2.fq | wc -l) == $(cat $iInterleavedFQ | wc -l ) ]]; then + echo ""OK: Deinterleave fastq"" +else + echo ""ERR: Deinterleave fastq"" + ERRORS=$((ERRORS+1)) +fi + +# Deinterleave normal other extension +echo """" +echo ""3. TEST - de-interleave a fastq file into custom extension"" +echo ""COMMAND: $BIN dei -v -f _forward.fq -r _reverse.fq -o testtmpcus $iInterleaved"" +$BIN dei -v -f _forward.fq -r _reverse.fq -o testtmpcus $iInterleaved +if [[ $(cat testtmpcus_forward.fq testtmpcus_reverse.fq | wc -l) == $(cat $iInterleaved | gunzip | wc -l ) ]]; then + echo ""OK: Deinterleave fastq custom extension"" +else + echo ""ERR: Deinterleave fastq custom extension"" + ERRORS=$((ERRORS+1)) +fi + +# Deinterleave uneven fastq +# needed: warning if more reads of either R1 or R2 +echo """" +echo ""4. TEST - de-interleave a fastq file with uneven number of reads"" +echo ""COMMAND: $BIN dei -v -o testtmpuneven $iInterUNEVEN"" +$BIN dei -v -o testtmpuneven $iInterUNEVEN + +# Deinterleave empty fastq +# needed: warning if input file is empty ""no sequenes in file X""; at the moment: produces empty R1 and R2 but no warning +#echo """" +#echo ""5. TEST - de-interleave empty fastq file"" +#echo ""COMMAND: $BIN dei -v -o testtmpempty $iAllEMPTY"" +#$BIN dei -v -o testtmpempty $iAllEMPTY + +# Deinterleave nonexistent +# needed: warning if input file is nonexistent; at the moment: error +#echo """" +#echo ""6. TEST - de-interleave a non-existent fastq file"" +#echo ""COMMAND: $BIN dei -v -o testtmpmiss $iAllMISS"" +#$BIN dei -v -o testtmpmiss $iAllMISS + +rm testtmp* +```","Markdown" +"Bioengineering","telatin/seqfu2","test/test-split_nozip.sh",".sh","2902","120","#!/bin/bash + +PY=$(command -v python) + +if [[ -e ""$BINDIR""/fu-split ]] && [[ $PYERR == 0 ]]; then + +python --version + +# Single file +OUTDIR=$(mktemp -d) + + + +if [[ ! -d ""$OUTDIR"" ]]; then + echo ""Error: output directory not created"" + exit 1 +fi + +touch ""$OUTDIR""/test.txt +EXP=7 + +""$BINDIR""/fu-split -i ""$i16S"" -n $EXP -o ""$OUTDIR""/splitParts-00000.fa +OBS=$(ls ""$OUTDIR""/splitParts-*.fa | wc -l | grep -o '[[:digit:]]\+') +MSG=""Split in $EXP files: got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ls -lh ""$OUTDIR""/splitParts-*.fa + ERRORS=$((ERRORS+1)) +fi + +EXP=$(count ""$i16S"") +OBS=$(""$BINDIR""/seqfu cat ""$OUTDIR""/splitParts-*.fa | ""$BINDIR""/seqfu count | cut -f 2) +MSG=""Total sequences from splitParts-*.fa equal source: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + + +# Check total bases +BASES=500000 +""$BINDIR""/fu-split -i ""$i16S"" -b $BASES -o ""$OUTDIR""/splitBases-00000.fa +EXP=$(bp ""$i16S"") +OBS=$(bp ""$OUTDIR""/splitBases-*.fa) +MSG=""Split by $BASES bases: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +EXP=4 +OBS=$(ls ""$OUTDIR""/splitBases-*.fa | wc -l | grep -o '[[:digit:]]\+') +MSG=""Split by bases in $EXP files: got $OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ""$BINDIR""/seqfu stats -b -n ""$OUTDIR""/splitBases-*.fa + ERRORS=$((ERRORS+1)) +fi + +# Each file should contain less than $BP bases +for FILE in ""$OUTDIR""/splitBases*; +do + F=$(basename ""$FILE"") + BP=$(bp ""$FILE"") + if [[ ! $BP -gt $BASES ]]; then + echo -e ""$OK: $F contains $BP bp: no more than $BASES"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: $F contains $BP bp: more than $BASES"" + ERRORS=$((ERRORS+1)) + fi +done +# ============================================================================== +# Check total seqs +SEQS=1000 +""$BINDIR""/fu-split -i ""$i16S"" -s $SEQS -o ""$OUTDIR""/splitSeqs-00000.fa +EXP=$(bp ""$i16S"") +OBS=$(bp ""$OUTDIR""/splitSeqs-*.fa) +MSG=""Split by $SEQS seqs: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +# Each file should contain less than $SEQS sequences +for FILE in ""$OUTDIR""/splitSeqs*; +do + COUNT=$(count ""$FILE"") + F=$(basename ""$FILE"") + if [[ ! $COUNT -gt $SEQS ]]; then + echo -e ""$OK: $F contains $COUNT sequences: no more than $SEQS"" + PASS=$((PASS+1)) + else + echo -e ""$FAIL: $F contains $COUNT sequences: more than $SEQS"" + ERRORS=$((ERRORS+1)) + fi +done +if [[ $ERRORS == 0 ]] +then + rm -rf ""$OUTDIR"" +fi +else + echo -e ""SKIP: python not found ($PY) or fu-split not in $BINDIR"" +fi +","Shell" +"Bioengineering","telatin/seqfu2","test/test-check.sh",".sh","8056","311"," +#!/bin/bash + +export SEQFU_QUIET=1 +TEMPFILENAME=$(mktemp) +### SINGLE END +""$BINDIR""/seqfu check ""$FILES""/illumina_nocomm.fq > ""$TEMPFILENAME"" +IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") +COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) +LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) +EXIT=$? + + +MSG=""Checked single end exit status"" +EXP=0 +if [[ $EXIT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $EXIT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $EXIT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked single end OK"" +EXP=1 +if [[ $IS_OK == ""$EXP"" ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked single end libtype"" +EXP=""SE"" +if [[ $LIBRARY == ""$EXP"" ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked single end sequence count"" +EXP=7 +if [[ $COUNT == ""$EXP"" ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" + ERRORS=$((ERRORS+1)) +fi + +### BAD SE, SINGLE END, DEEP +""$BINDIR""/seqfu check --deep ""$FILES""/bad.fastq > ""$TEMPFILENAME"" +IS_OK=$(grep -c ""ERR"" ""$TEMPFILENAME"" ) +COUNT=$(cut -f 4 ""$TEMPFILENAME"") +LIBRARY=$(cut -f 2 ""$TEMPFILENAME"" ) +EXIT=$? + + +MSG=""Checked BAD single end exit status with --deep"" +EXP=1 +if [[ $IS_OK == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi +MSG=""Counts checking BAD single end exit status with --deep"" +EXP=0 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi + +### BAD PE, DEEP +""$BINDIR""/seqfu check --deep --dir ""$FILES""/check/pe/ > ""$TEMPFILENAME"" +IS_OK=$(grep -c ""ERR"" ""$TEMPFILENAME"" ) +COUNT=$(cut -f 4 ""$TEMPFILENAME"" | awk '{ sum += $1 } END { print sum }') +LIBRARY=$(cut -f 2 ""$TEMPFILENAME"" ) +EXIT=$? + + +MSG=""Checked BAD paired end exit status with --deep"" +EXP=2 +if [[ $IS_OK == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi +MSG=""Counts checking BAD paired end exit status with --deep"" +EXP=0 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" + ERRORS=$((ERRORS+1)) +fi + + +### BAD SE, SINGLE END, NO DEEP +""$BINDIR""/seqfu check ""$FILES""/bad.fastq > ""$TEMPFILENAME"" +IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") +COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) +LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) +EXIT=$? + + +MSG=""Checked BAD single end exit status without --deep"" +EXP=1 +if [[ $IS_OK == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi +MSG=""Counts checking BAD single end exit status without --deep"" +EXP=0 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi +### PAIRED END +""$BINDIR""/seqfu check ""$FILES""/illumina_1.fq.gz > ""$TEMPFILENAME"" +EXIT=$? +IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") +COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) +LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) + +MSG=""Checked paired end"" +EXP=1 +if [[ $IS_OK == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked paired end exit status"" +EXP=0 +if [[ $EXIT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $EXIT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $EXIT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked paired end libtype"" +EXP=""PE"" +if [[ $LIBRARY == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked single end sequence count (2xSE)"" +EXP=14 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" + ERRORS=$((ERRORS+1)) +fi + +## INVALID PE +""$BINDIR""/seqfu check ""$FILES""/longerone_R1.fq.gz > ""$TEMPFILENAME"" +EXIT=$? +IS_OK=$(cat ""$TEMPFILENAME"" | grep -c ""OK"") +COUNT=$(cat ""$TEMPFILENAME"" |cut -f 4) +LIBRARY=$(cat ""$TEMPFILENAME"" |cut -f 2) + +MSG=""Checked INVALID paired end"" +EXP=0 +if [[ $IS_OK == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $IS_OK)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $IS_OK)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked INVALID paired end exit status"" +EXP=0 +if [[ $EXIT -gt $EXP ]]; then + echo -e ""$OK: $MSG (got $EXIT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (got $EXIT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked INVALID paired end libtype"" +EXP=""PE"" +if [[ $LIBRARY == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $LIBRARY)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $LIBRARY)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked INVALID paired end sequence count (2xSE)"" +EXP=""-"" +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT)"" + ERRORS=$((ERRORS+1)) +fi + +### CHECK INVALID DIR +LSDIR=$(ls -lh ""$FILES""/primers) +$BINDIR/seqfu check --verbose --dir ""$FILES/primers"" > ""$TEMPFILENAME"" 2> ""$TEMPFILENAME.log"" +EXIT=$? +WC=$(getnumber $(cat ""$TEMPFILENAME"" | wc -l)) +WC_ERR=$(getnumber $(cat ""$TEMPFILENAME"" | grep -v OK | grep ERR | wc -l)) + + +MSG=""Checked INVALID directory ($FILES/primers) exit status"" +if [[ $EXIT -gt 0 ]]; then + echo -e ""$OK: $MSG (expected > 0, got $EXIT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected > 0, got $EXIT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked INVALID directory line count"" +EXP=14 +if [[ $WC == $EXP ]]; then + echo -e ""$OK: $MSG (got $WC expected $EXP)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (got $WC expected $EXP)\n$(cat ""$TEMPFILENAME"")\n$LSDIR"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Checked INVALID directory line error count"" +EXP=2 +if [[ $WC_ERR == $EXP ]]; then + echo -e ""$OK: $MSG (got $WC_ERR expected $EXP)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (got $WC_ERR expected $EXP)\n$(cat ""$TEMPFILENAME"")\n$LSDIR"" + ERRORS=$((ERRORS+1)) +fi + + + +### CHECK VALID DIR: WHICH ONE? +TMP_CHECK_DIR_VALID=$(mktemp -d SEQFU_TMPDIR_XXXXXX) +cp ""$FILES""/illumina_{1,2}.fq.gz ""$TMP_CHECK_DIR_VALID""/ +""$BINDIR""/seqfu check --verbose --dir ""$TMP_CHECK_DIR_VALID"" > ""$TMP_CHECK_DIR_VALID/out"" 2> ""$TMP_CHECK_DIR_VALID/log"" +EXIT=$? + +WC=$(getnumber ""$( wc -l < ""$TMP_CHECK_DIR_VALID/out"")"" ) +WC_ERR=$(getnumber ""$( grep -v OK ""$TMP_CHECK_DIR_VALID/out"" | grep -c ""ERR"")"" ) +rm -rf ""$TMP_CHECK_DIR_VALID"" + + +MSG=""Checked valid directory $TMP_CHECK_DIR_VALID exit status"" +if [[ $EXIT -eq 0 ]]; then + echo -e ""$OK: $MSG (expected 0, got $EXIT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected 0, got $EXIT)\n"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""Checked valid directory line count $TMP_CHECK_DIR_VALID/out"" +EXP=1 +if [[ ""$WC"" == ""$EXP"" ]]; then + echo -e ""$OK: $MSG (got $WC expected $EXP)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (got $WC expected $EXP)"" + ERRORS=$((ERRORS+1)) +fi + + +MSG=""Checked valid directory line error count"" +EXP=0 +if [[ $WC_ERR == $EXP ]]; then + echo -e ""$OK: $MSG (got $WC_ERR expected $EXP)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (got $WC_ERR expected $EXP)"" + ERRORS=$((ERRORS+1)) +fi + + +rm ""$TEMPFILENAME""","Shell" +"Bioengineering","telatin/seqfu2","test/test-grep.sh",".sh","4635","173","#!/bin/bash + +# Single file +TMP=$(mktemp) +echo "" Temp file: $TMP"" + + +## Get SEQ3 +EXP=1 +MSG=""Extracting one exact match (SEQ3)"" +OBS=$(""$BINDIR""/seqfu grep -n SEQ3 ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Get SEQ3 (-v) +EXP=4 +MSG=""Extracting one exact match (SEQ3), invert (-v)"" +OBS=$(""$BINDIR""/seqfu grep -v -n SEQ3 ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi +## Get SEQ +EXP=5 +MSG=""Get all SEQ matches"" +OBS=$(""$BINDIR""/seqfu grep -n SEQ ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Get seq *none* +EXP=0 +MSG=""Extracting all 'seq' matches"" +OBS=$(""$BINDIR""/seqfu grep -n seq ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Get seq *none* +EXP=5 +MSG=""Extracting all 'seq' matches, but case insensitive"" +OBS=$(""$BINDIR""/seqfu grep -i -n seq ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Get seq with regex +EXP=10 +MSG=""Regex '1.3' matches (-r)"" +OBS=$(""$BINDIR""/seqfu grep -r 1.3 ""$iNum"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Get seq full +EXP=1 +MSG=""Full '13' matches (-f)"" +OBS=$(""$BINDIR""/seqfu grep -n 13 -f ""$iNum"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + + +## Search patter +EXP=0 +MSG=""Search 'two' (is only in comments)"" +OBS=$(""$BINDIR""/seqfu grep -n two ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Search in comments +EXP=3 +MSG=""Search 'two' (INCLUDING comments)"" +OBS=$(""$BINDIR""/seqfu grep -c -n two ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +## Search oligo +EXP=1 +MSG=""Search oligo"" +OBS=$(""$BINDIR""/seqfu grep -o ACGTACGTACGTAGCTGATCGATCGTACGTAGCTGACA ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + + + +EXP=1 +MSG=""Search oligo, revcompl and lowercase"" +OBS=$(""$BINDIR""/seqfu grep -o tgtcagctacgtacgatcgatcagctacgtacgtacgt ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +EXP=1 +MSG=""Search oligo (lower case in UC seq)"" +OBS=$(""$BINDIR""/seqfu grep -o acgtacgtacgtagctgatcgatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +EXP=1 +MSG=""Search oligo (partial with 'N' inside)"" +OBS=$(""$BINDIR""/seqfu grep -o tacgtacgtagctgatcNatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + +EXP=1 +MSG=""Search oligo (partial with 'IUPAC' inside)"" +OBS=$(""$BINDIR""/seqfu grep -o acgtacgtacgtaSStgatcgatcgtacgtagctgaca ""$iComments"" | ""$BINDIR""/seqfu count | cut -f 2 ) +if [[ $OBS -eq $EXP ]]; then + echo -e ""$OK: $MSG: exp=$EXP obs=$OBS"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG: exp=$EXP obs=$OBS"" + ERRORS=$((ERRORS+1)) +fi + ","Shell" +"Bioengineering","telatin/seqfu2","test/test-tail.sh",".sh","572","31","#!/bin/bash + +export SEQFU_QUIET=1 +TMP=$(mktemp) + +$(""$BINDIR""/seqfu tail ""$iNum"" > ""$TMP"") +OBS=$(count ""$TMP"") +EXP=10 +MSG=""Last seqs (default) $TMP: exp=$EXP got=$OBS"" +if [[ $EXP == $OBS ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +EXP=50 +$(""$BINDIR""/seqfu tail -n $EXP ""$iNum"" > ""$TMP"") +OBS=$(count ""$TMP"") +MSG=""Last '-n $EXP' seqs $TMP: exp=$EXP got=$OBS"" +if [[ $EXP == $OBS ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi +rm ""$TMP"" + +","Shell" +"Bioengineering","telatin/seqfu2","test/makezip.sh",".sh","944","39","#!/bin/bash +set -euxo pipefail +check_gh() { + # Check if `gh` command is available + if command -v gh >/dev/null 2>&1; then + echo ""OK: GitHub CLI 'gh' found"" + gh --version + return 0 + else + echo ""ERROR: GitHub CLI 'gh' was not found"" + echo ""Please install it from https://cli.github.com/"" + return 1 + fi +} + +getversion() { + new_tag=""v$(grep version ""$DIR""/../seqfu.nimble | cut -f 2 -d \"")"" + # check if gh() + if check_gh; then + new_tag=$(gh release list -L 1 | grep -o ""v\d\+\.\d\+\.\d\+"") + else + echo ""Could not get remote release"" + fi +} +DIR=""$( cd ""$( dirname ""${BASH_SOURCE[0]}"" )"" >/dev/null && pwd )"" +BINDIR=""$DIR""/../bin/ +DESTDIR=""$DIR""/../releases/zips/ + +programName=""SeqFu"" +os_tag=""$(uname -s)-$(uname -m)"" +new_tag=""unknown"" +getversion + +mkdir -p ""$DESTDIR"" +ZIP=""$DESTDIR""/${programName}-${new_tag}-${os_tag}.zip +zip -j ""$ZIP"" ""$BINDIR""/* + +gh release upload ${new_tag} ""$ZIP"" +","Shell" +"Bioengineering","telatin/seqfu2","test/screenshot.sh",".sh","644","26","#!/usr/bin/env bash +# Automate screeshots with termshot + +# Check if termshot is available +if ! command -v termshot &> /dev/null +then + echo ""termshot could not be found"" + echo ""Install it with:"" + echo ""brew install homeport/tap/termshot"" + exit +fi +echo ""termshot found, continuing..."" +make +echo ""Setting up test environment..."" +export PATH=$PWD/bin:$PATH + + +for PROG in cat count deinterleave derep grep head interleave lanes metadata rc rotate stats tab tail; +do + + termshot --show-cmd --filename docs/img/screenshot-${PROG}.png -- seqfu $PROG --help + +done +termshot --show-cmd --filename docs/img/screenshot-seqfu.png -- seqfu + +","Shell" +"Bioengineering","telatin/seqfu2","test/release.py",".py","8435","296","#!/usr/bin/env python3 +"""""" +LOCAL_RELEASE=$(cat ""$DIR/../seqfu.nimble"" | grep version | cut -f 2 -d = | sed 's/["" ]//g') +GH_RELEASE=$(curl -s https://api.github.com/repos/telatin/seqfu2/releases/latest | perl -nE 'my ($tag, $val) = split /:/, $_; if ($tag=~/tag_name/) { my @tag = split /""/, $val; for my $i (@tag) { $i =~s/[^0-9.]//g; say $i if (length($i) > 2); } }') +"""""" + +import subprocess +import sys +import json +import urllib.request +import os +import re +import hashlib +programName='SeqFu' + + +def eprint(*args, **kwargs): + # import sys + print(*args, file=sys.stderr, **kwargs) + +def jsonFromURL(uri): + operUrl = urllib.request.urlopen(uri) + if(operUrl.getcode()==200): + data = operUrl.read() + jsonData = json.loads(data) + else: + eprint(""Error receiving data"", operUrl.getcode()) + return jsonData + +def get_os(): + arch = subprocess.getoutput(['uname -m']) + machine = subprocess.getoutput(['uname -s']) + return machine + '-' + arch + +def check_gh(): + command = ['gh', 'version'] + expected_return_code = 0 + try: + result = subprocess.run(command, stdout=subprocess.PIPE) + if result.returncode == expected_return_code: + return True + else: + return False + except Exception as e: + eprint(f""WARNING: checking `gh` failed:\n{e}."") + return False + +def get_last_release(): + """""" + Retrieve the last release tag from Github + """""" + releaseInfo = jsonFromURL('https://api.github.com/repos/telatin/seqfu2/releases/latest') + if 'tag_name' in releaseInfo: + return releaseInfo['tag_name'] + else: + eprint(""ERROR: Unable to get the last release"") + quit(1) + +def get_curr_release(file): + """""" + Extract the last version from Nimble + """""" + try: + with open(file, 'r') as fd: + content = fd.read() + match = re.search('version\s+=\s+""(.+?)""', content) + if match.group(1) is not None: + return match.group(1) + else: + eprint(f""WARNING: Version not found in {file}"") + return """" + except Exception as e: + eprint(f""ERROR loading {file}:\n{e}"") + quit(1) + + +def get_output(bin): + result = subprocess.run([bin], stdout=subprocess.PIPE) + return result.stdout.decode(""utf-8"") + +def md5sum(rootdir, filename, blocksize=2**20): + m = hashlib.md5() + with open( os.path.join(rootdir, filename) , ""rb"" ) as f: + while True: + buf = f.read(blocksize) + if not buf: + break + m.update( buf ) + return m.hexdigest() +def list_files_md(bindir): + """""" + list files in a directory + """""" + files = os.listdir(bindir) + md = """" + list = {} + for f in files: + if f == 'seqfu': + continue + help_page = f""{bindir}/../docs/utilities/{f}.md"" + md5 = md5sum(bindir, f) + list[f] = md5 + if not os.path.exists(help_page): + eprint(f""WARNING: {help_page} not found"") + md += f"" * {f}\n"" + else: + md += "" * ["" + f + ""]({{site.baseurl}}/utilities/"" + f + "".html)\n"" + + return [md, list] + + +def get_core_utils(dir): + md = """" + for file in os.listdir(dir): + module = file.split(""."") + md += f"" * [seqfu {module[0]}]("" + ""{{site.baseurl}}/tools/"" + module[0] + "".html)\n"" + return md + +def init_markdown(file, release, changes, bindir): + """""" + create an empty markdown page + """""" + splash = get_output(f""{bindir}/seqfu"") + core = get_core_utils(f""{bindir}/../docs/tools/"") + #changes = """" + utils, data = list_files_md(bindir) + template = f""""""# {programName} {release} + +### Changes + +{changes} + +### Splash screen + +```text +{splash} +``` + + """""" + try: + with open(file, 'w') as f: + print(template, file=f) + except Exception as e: + eprint(f""ERROR trying to write MD file to {file}:\n{e}"") + + +def print_as_json(data, file): + try: + with open(file, 'w+') as fp: + fp.write(json.dumps(data)) + except Exception as e: + eprint(f""ERROR: Unable to print JSON to {file}:\n{e}"") + quit(1) + +if __name__ == ""__main__"": + import argparse + parser = argparse.ArgumentParser(description=f'Release a new version of {programName}') + parser.add_argument(""-s"", ""--skip-build"", help=""Skip build step"", action=""store_true"") + parser.add_argument(""-D"", ""--delete"", help=""delete the readme file"", action=""store_true"") + parser.add_argument(""-x"", ""--skip-test"", help="""", action=""store_true"") + parser.add_argument(""-v"", ""--verbose"", help=""Enable verbose output"", action=""store_true"") + parser.add_argument(""-r"", ""--release"", help=""Make release"", action=""store_true"") + + args = parser.parse_args() + + if not check_gh(): + eprint(""ERROR: `gh` is required."") + quit(1) + + + # Relevant variables + last_release = get_last_release() + script_dir = os.path.dirname(os.path.realpath(__file__)) + curr_release = get_curr_release(f""{script_dir}/../{programName.lower()}.nimble"") + basedir = f""{script_dir}/../"" + bindir = f""{basedir}/bin/"" + bin = f""{bindir}/seqfu"" + new_tag = f""v{curr_release}"" + changelog = f""{basedir}/releases/changes.md"" + os_tag = get_os() + + release_text = """" + try: + with open(changelog) as ch: + release_text = ch.read() + except Exception as e: + eprint(f""ERROR: Change log not found {changelog}.\n{e}"") + quit(1) + if len(release_text) == 0: + eprint(""No release notes"") + quit(1) + if args.verbose: + eprint(f""Last GH release:\t{last_release}"") + eprint(f""Current release:\t{new_tag}"") + eprint(f""Platform: \t{os_tag}"") + + # Build + if not args.skip_build: + os.chdir(f""{script_dir}/.."") + for f in os.listdir(f""{script_dir}/../bin/""): + path = os.path.join(f""{script_dir}/../bin"", f) + eprint(f""Removing {path}"") + os.remove(path) + build = subprocess.run(['nimble', 'build']) + if build.returncode != 0: + eprint(""Build failed."") + quit(1) + + # Test + if not args.skip_test: + subprocess.run(['bash', f'{script_dir}/../test/mini.sh']) + + release_notes = f""{script_dir}/../docs/releases/{new_tag}.md"" + release_dir = f""{basedir}/releases/"" + + # Make directory ${release_dir}/zips if not exists + zip_dir = os.path.join(release_dir, ""zips"") + if not os.path.exists(zip_dir): + os.makedirs(zip_dir) + # Prepare zip + zipfile = f""{release_dir}/zips/{programName}-{new_tag}-{os_tag}.zip"" + binaries = ['zip', '-q', '-j', zipfile] + for file in os.listdir(bindir): + binaries.append(os.path.join(bindir, file)) + eprint(f""Making zip file: {zipfile}"") + subprocess.run(binaries) + + # Check that there's a new release + if last_release == new_tag: + eprint(f""ERROR: Update the release first: {new_tag} already published"") + quit(1) + + # Prepare release dir + eprint(f""Release dir: {release_dir}"") + + # Prepare splash screen archive + # CORE + splashes = {} + try: + for coreManPage in os.listdir(f""{basedir}/docs/tools/""): + if coreManPage == 'README.md': + continue + core = coreManPage.split('.')[0] + splash = subprocess.run([f'{bindir}/seqfu', core, '--help'], stdout=subprocess.PIPE) + splash_screen = splash.stdout.decode('utf-8') + splashes[f""seqfu {core}""] = splash_screen + except Exception as e: + quit() + + # UTILS: + try: + for utilManPage in os.listdir(f""{basedir}/docs/utilities/""): + if utilManPage == 'README.md': + continue + core = utilManPage.split('.')[0] + eprint([core, '--help']) + splash = subprocess.run([f'{bindir}/{core}', '--help'], stdout=subprocess.PIPE) + splash_screen = splash.stdout.decode('utf-8') + splashes[core] = splash_screen + except Exception as e: + eprint(f""Error in {utilManPage}: {e}"") + quit() + + #print_as_json(splashes, os.path.join(release_dir, f""{new_tag}.splashes.json"")) + + # Generate new release document + if False:# and not os.path.exists(release_notes) or args.delete: + eprint(f""Generating new page: {release_notes}"") + splash = get_output(bin) + + init_markdown(release_notes, new_tag, release_text, bindir) + + title = f""SeqFu {new_tag}"" + + status = subprocess.run(['git', 'status', '-s'], stdout=subprocess.PIPE) + + + + if len(status.stdout.decode('utf-8')) > 0: + eprint(""Uncommitted changes!"") + quit(args.release) + + if not args.release: + quit() + + eprint(""Preparing release"") + release_cmd = ['gh', 'release', 'create', new_tag, zipfile, '--title', title, '--notes-file', changelog] + try: + subprocess.run(release_cmd) + except Exception as e: + eprint(f""Failed to release: {e}.\n# {release_cmd.join(' ')}"") + + try: + os.rename(changelog, f""{basedir}/releases/{new_tag}.md"") + except Exception as e: + eprint(f""ERROR: Unable to rename {changelog}"")","Python" +"Bioengineering","telatin/seqfu2","test/test-shred.sh",".sh","1788","67","#!/bin/bash + +export SEQFU_QUIET=1 +TEMPFILENAME=$(mktemp) +INPUT=""$FILES""/16S_coli.fa +### SINGLE END +""$BINDIR""/fu-shred ""$INPUT"" -l 100 -s 150 > ""$TEMPFILENAME"" +COUNT=$(cat ""$TEMPFILENAME"" | ""$BINDIR""/seqfu count - | cut -f 2) +LEN=$(cat ""$TEMPFILENAME"" | ""$BINDIR""/seqfu stats - | cut -f 3 | tail -n 1) +EXIT=$? + + +MSG=""SE: 10 sequences"" +EXP=10 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT from $INPUT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT from $INPUT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""SE: Total length 1000bp "" +EXP=1000 +if [[ $LEN == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $LEN from $INPUT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $LEN from $INPUT)"" + ERRORS=$((ERRORS+1)) +fi + +TEMPORARY_DIR=$(mktemp -d) +FWD=""$TEMPORARY_DIR""/illuminate_R1.fq +REV=""$TEMPORARY_DIR""/illuminate_R2.fq +""$BINDIR""/fu-shred ""$INPUT"" -f 100 -l 50 -s 150 -o ""$TEMPORARY_DIR""/illuminate + +MSG=""Output found $FWD,$REV "" +if [[ -e ""$FWD"" ]] && [[ -e ""$REV"" ]]; then + echo -e ""$OK: $MSG "" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +COUNT=$(cat ""$FWD"" | ""$BINDIR""/seqfu count - | cut -f 2) +LEN=$(cat ""$FWD"" | ""$BINDIR""/seqfu stats - | cut -f 3 | tail -n 1) +MSG=""PE: 10 sequences"" +EXP=10 +if [[ $COUNT == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $COUNT from $INPUT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $COUNT from $INPUT)"" + ERRORS=$((ERRORS+1)) +fi + +MSG=""PE: Total length 1000bp "" +EXP=500 +if [[ $LEN == $EXP ]]; then + echo -e ""$OK: $MSG (expected $EXP, got $LEN from $INPUT)"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG (expected $EXP, got $LEN from $INPUT)"" + ERRORS=$((ERRORS+1)) +fi ","Shell" +"Bioengineering","telatin/seqfu2","test/hpc.sh",".sh","481","12","#!/bin/bash +set -exuo pipefail +VERSION=$(grep version seqfu.nimble | grep -oP \\d\+\.\\d\+\.\\d\+) +make +mkdir -p ""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/"" +mv -v ""bin""/* ""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/"" +BINSCRIPT=""/nbi/software/testing/bin/seqfu-${VERSION}"" +echo '#!/bin/bash' > $BINSCRIPT +echo ""VERSION=${VERSION}"" >> $BINSCRIPT +echo 'export PATH=""/nbi/software/testing/seqfu/${VERSION}/x86_64/bin/:$PATH""' >> $BINSCRIPT +chmod +x $BINSCRIPT +","Shell" +"Bioengineering","telatin/seqfu2","test/convert.sh",".sh","506","19","FILE=$1 +if [[ ! -e $FILE ]];then + echo exiting.. + exit 1 +fi + +if [[ ! -d src/ ]]; then + echo src should be where the script is invoked + exit 1 +fi +set -euxo pipefail +DIR=$(dirname $FILE) +cp -r /Users/telatina/.choosenim/toolchains/nim-1.6.6/lib $DIR/ +cp -r /Users/telatina/.nimble/pkgs $DIR/ +cp -r ./src $DIR/ +sed ""s'/Users/telatina/.choosenim/toolchains/nim-1.6.6/'./'g"" $FILE | sed ""s'/Users/telatina/git/seqfu2/'./'g"" > $DIR/compile.sh +sed -i.bak 's|/Users/telatina/.nimble/pkgs/|./pkgs/|g' $DIR/*.c + +","Shell" +"Bioengineering","telatin/seqfu2","test/test-metadata.sh",".sh","1028","43","#!/bin/bash + +export SEQFU_QUIET=1 + +READS_DIR=""$FILES""/reads/ + +SEQFU_TEMP_DIR=$(mktemp -d) +META_DEFAULT=$($BINDIR/seqfu metadata $READS_DIR > ""$SEQFU_TEMP_DIR""/metadata.tsv) +META_IRIDA=$($BINDIR/seqfu metadata -f irida -P 100 $READS_DIR > ""$SEQFU_TEMP_DIR""/irida.csv) +## IUPAC + +EXP=3 +OBS=$(""$BINDIR""/fu-tabcheck ""$SEQFU_TEMP_DIR""/metadata.tsv | cut -f 3) +MSG=""Default table columns: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +EXP=6 +OBS=$(""$BINDIR""/fu-tabcheck ""$SEQFU_TEMP_DIR""/metadata.tsv | cut -f 4) +MSG=""Default table rows: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi + +EXP=7 +OBS=$(getnumber $(grep . ""$SEQFU_TEMP_DIR""/irida.csv | wc -l)) +MSG=""Irida lines: exp=$EXP got=$OBS"" +if [[ $OBS == $EXP ]]; then + echo -e ""$OK: $MSG"" + PASS=$((PASS+1)) +else + echo -e ""$FAIL: $MSG"" + ERRORS=$((ERRORS+1)) +fi ","Shell" +"Bioengineering","telatin/seqfu2","test/speed/hg38-fasta.md",".md","349","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `./speed/native /local/qi/db/hg38/Homo_sapiens.GRCh38.dna_sm.toplevel.fa` | 2485.163 ± 395.734 | 2050.087 | 3031.333 | 1.00 ± 0.52 | +| `./speed/imported /local/qi/db/hg38/Homo_sapiens.GRCh38.dna_sm.toplevel.fa` | 2474.497 ± 1214.150 | 303.033 | 3061.138 | 1.00 | +","Markdown" +"Bioengineering","telatin/seqfu2","test/speed/F09.md",".md","307","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `./speed/native /local/qi/data/SC/CEL/reads/F09.fastq.gz` | 141.438 ± 2.189 | 138.283 | 145.046 | 1.00 | +| `./speed/imported /local/qi/data/SC/CEL/reads/F09.fastq.gz` | 206.206 ± 1.747 | 203.614 | 208.992 | 1.46 ± 0.03 | +","Markdown" +"Bioengineering","telatin/seqfu2","test/speed/7794_51_R1.md",".md","313","5","| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `./speed/native /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq` | 155.0 ± 4.7 | 149.8 | 165.8 | 1.00 | +| `./speed/imported /local/qi/import/AN/EG/Lcr/reads/7794_51_R1.fastq` | 368.5 ± 17.8 | 356.0 | 412.3 | 2.38 ± 0.14 | +","Markdown" +"Bioengineering","telatin/seqfu2","test/byte/validate_fastq.c",".c","5188","156","#include +#include +#include + +#define MAX_LINE_LENGTH 4096 +#define QSCORE_OFFSET 33 +int main(int argc, char *argv[]) { + FILE *fp; + + int opt_offset = QSCORE_OFFSET; + int opt_strict = 0; + int opt_help = 0; + int opt_verbose = 0; + char *filename = NULL; // Initialize to NULL + + // Parse command-line arguments + for (int i = 1; i < argc; i++) { + if (strcmp(argv[i], ""-s"") == 0) { + opt_strict = 1; + } else if (strcmp(argv[i], ""-o"") == 0 && i < argc - 1) { + opt_offset = atol(argv[i + 1]); + i++; + } else if (strcmp(argv[i], ""-v"") == 0) { + opt_verbose = 1; + } else if (strcmp(argv[i], ""-h"") == 0) { + opt_help = 1; + } else { + filename = argv[i]; + } + } + + // Check for the correct number of command-line arguments + if (opt_help) { + // create a string that is the program's basename + char *program_name = strrchr(argv[0], '/'); + if (program_name != NULL) { + program_name++; + } else { + program_name = argv[0]; + } + printf(""Usage: %s [-s] [-o offset] filename\n"", program_name); + printf(""\nParameters:\n""); + printf("" -s : Validate quality (optional).\n""); + printf("" -o OFFSET : The offset for quality score (optional, default: 33).\n""); + printf("" filename : The name of the file to be processed (optional, default: stdin)\n""); + return 1; + } + + // if defined filename open it else use stdin + if ( filename != NULL ) { + // print to stderr if verbose + if (opt_verbose) { + fprintf(stderr, ""Opening file %s\n"", filename); + } + + fp = fopen(filename, ""r""); + + if (fp == NULL) { + fprintf(stderr, ""Error opening file %s\n"", filename); + return 1; + } + } else { + // print to stderr if verbose + if (opt_verbose) { + fprintf(stderr, ""Reading from stdin\n""); + } + fp = stdin; + } + char first_seq[MAX_LINE_LENGTH]; + char last_seq[MAX_LINE_LENGTH]; + char line[MAX_LINE_LENGTH]; + int line_count = 0; + int seq_count = 0; + int seq_len = 0; + int valid = 1; + while (fgets(line, sizeof(line), fp)) { + line_count++; + + if (line_count % 4 == 1) { + // Remove the trailing newline character + line[strcspn(line, ""\n"")] = 0; + + // seq name: remove first character and split to the first space + + char *seq_name = strtok(line+1, "" ""); + + if (seq_count == 0) { + strcpy(first_seq, seq_name); + } + strcpy(last_seq, seq_name); + + // check if first character is '@' + if (line[0] != '@') { + printf(""ERROR: Line %d in sequence %d does not start with '@'\n"", line_count, seq_count); + valid = 0; + break; + } + } else if (line_count % 4 == 2) { + // Remove the trailing newline character + line[strcspn(line, ""\n"")] = 0; + seq_len = strlen(line); + + // Check if the line is only composed by A, C, G, T and N + for (int i = 0; i < seq_len; i++) { + if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { + printf(""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); + valid = 0; + break; + } + } + } else if (line_count % 4 == 3) { + if (line[0] != '+') { + printf(""ERROR: Line %d in sequence %d does not start with '+'\n"", line_count, seq_count); + valid = 0; + break; + } + } else if (line_count % 4 == 0) { + line[strcspn(line, ""\n"")] = 0; + if (seq_len != strlen(line)) { + printf(""ERROR: Line %d in sequence %d has a different length than the sequence: %ld vs %d\n"", line_count, seq_count, (long)(line ? strlen(line) : 0), seq_len), seq_len); + valid = 0; + break; + } + // Check if the quality line is composed by ASCII values from 0 to 60 + if (opt_strict) { + int qscore_int = 0; + for (int i = 0; i < seq_len; i++) { + qscore_int = (int) line[i] - opt_offset; + if (qscore_int < 0 || qscore_int > 60) { + printf(""ERROR: Line %d in sequence %d contains an invalid quality score: %c = %d\n"", line_count, seq_count, line[i], qscore_int); + valid = 0; + break; + } + } + } + + seq_count++; + } + + + } + // create status_string + char status[4]; + if (valid) { + strcpy(status, ""OK""); + } else { + strcpy(status, ""ERR""); + } + printf(""%s\t%d\t%s\t%s\n"", status, seq_count, first_seq, last_seq); + + if (fp != stdin) { + fclose(fp); + } + return 0; +} +","C" +"Bioengineering","telatin/seqfu2","test/byte/shifter.c",".c","5194","149","#include +#include +#include + +#define START_BYTE_DEFAULT 128 +#define BYTE_STEP_DEFAULT 64 +#define MAX_BYTE_CAP_DEFAULT 256000 + +/* + This C program allows for the manipulation of binary data within a file. + It provides a versatile method to modify specific bytes within the file based on user-defined criteria. + Users can choose to either increment or decrement selected bytes in the file. + + Usage: + - To modify the file: Run the program with the desired input file as the argument. + - To revert modifications: Include the '-u' option followed by the input file. + + The program offers flexibility by specifying the starting byte position, step size, + and maximum byte cap for byte manipulation within the file. + + Usage: + ./program_name [-u] [-s start_byte] [-j step_size] [-m max_byte] filename + + Options: + -u : Reverts modifications made to the file (optional). + -s start_byte: The starting byte position for byte manipulation (optional, default: 128). + -j step_size : The step size for byte manipulation (optional, default: 64). + -m max_byte : The maximum byte cap for file size (optional, default: 256000). + filename : The name of the file to be processed. + + + Andrea Telatin, QIB, 2021 +*/ +int main(int argc, char *argv[]) { + int unscramble = 0; + long substitutions = 0; + long start_byte = START_BYTE_DEFAULT; + long byte_step = BYTE_STEP_DEFAULT; + long max_byte_cap = MAX_BYTE_CAP_DEFAULT; + char *filename; + + // Parse command-line arguments + for (int i = 1; i < argc; i++) { + if (strcmp(argv[i], ""-u"") == 0) { + unscramble = 1; + } else if (strcmp(argv[i], ""-s"") == 0 && i < argc - 1) { + start_byte = atol(argv[i + 1]); + i++; + } else if (strcmp(argv[i], ""-j"") == 0 && i < argc - 1) { + byte_step = atol(argv[i + 1]); + i++; + } else if (strcmp(argv[i], ""-m"") == 0 && i < argc - 1) { + max_byte_cap = atol(argv[i + 1]); + i++; + } else { + filename = argv[i]; + } + } + + // Check for the correct number of command-line arguments + if (argc < 2 || filename == NULL) { + // create a string that is the program's basename + char *program_name = strrchr(argv[0], '/'); + if (program_name != NULL) { + program_name++; + } else { + program_name = argv[0]; + } + printf(""Usage: %s [-u] [-s start_byte] [-j step_size] [-m max_byte] filename\n"", program_name); + printf(""\nParameters:\n""); + printf("" -u : Reverts modifications made to the file (optional).\n""); + printf("" -s START_BYTE : The starting byte position for byte manipulation (optional, default: 128).\n""); + printf("" -j STEP_SIZE : The step size for byte manipulation (optional, default: 64).\n""); + printf("" -m MAX_BYTE : The maximum byte cap for file size (optional, default: 256000).\n""); + printf("" filename : The name of the file to be processed.\n""); + return 1; + } + + FILE *file = fopen(filename, ""rb+""); + if (file == NULL) { + fprintf(stderr, ""ERROR: Error opening file: %s\n"", filename); + return 1; + } + + // Get the file size + fseek(file, 0, SEEK_END); + long file_size = ftell(file); + fseek(file, 0, SEEK_SET); + + // Cap the file_size if it exceeds max_byte_cap + if (file_size > max_byte_cap) { + fprintf(stderr, ""INFO:\tCapping file size to %ld bytes\n"", max_byte_cap); + file_size = max_byte_cap; + } + + // Allocate memory for reading/writing + unsigned char *buffer = malloc(file_size); + if (buffer == NULL) { + perror(""ERROR: Memory allocation error""); + fclose(file); + return 1; + } + + // Read the file into the buffer + if (fread(buffer, 1, file_size, file) != file_size) { + perror(""ERROR: Error reading file""); + fclose(file); + free(buffer); + return 1; + } + + if (unscramble) { + // Unscramble the file by reverting every byte_step-th byte starting from start_byte + for (long i = start_byte; i < file_size; i += byte_step) { + if (buffer[i] == 0) { + buffer[i] = 255; // Wrap around to the maximum value + } else { + buffer[i] -= 1; + } + substitutions++; + } + } else { + // Scramble the file by changing every byte_step-th byte to its following, starting from start_byte + for (long i = start_byte; i < file_size; i += byte_step) { + if (buffer[i] == 255) { + buffer[i] = 0; // Wrap around to 0 when reaching the maximum + } else { + buffer[i] += 1; + } + substitutions++; + } + } + + // Rewind the file and write the modified buffer back to it + rewind(file); + if (fwrite(buffer, 1, file_size, file) != file_size) { + perror(""Error writing to file""); + fclose(file); + free(buffer); + return 1; + } + + fclose(file); + free(buffer); + + // Print the number of substitutions + printf(""INFO:\tSubstitutions: %ld\n"", substitutions); + return 0; +}","C" +"Bioengineering","telatin/seqfu2","test/byte/validate.c",".c","7680","222","/* + Description: + This program reads a FASTQ file (compressed with zlib) and validates its format. + It checks that the file follows the FASTQ format rules, such as having the '@' character + at the beginning of the sequence identifier lines, containing only valid DNA characters, + and optionally checking the quality scores for valid ASCII values. + + Usage: + ./fastq_validator [-s] [-o offset] filename + + Parameters: + -s : Validate quality (optional). + -o OFFSET : The offset for quality score (optional, default: 33). + filename : The name of the file to be processed (optional, default: stdin) +*/ + +#include +#include +#include +#include // Include zlib header + +#define MAX_LINE_LENGTH 4096 +#define QSCORE_OFFSET 33 + +int main(int argc, char *argv[]) { + gzFile fp; // Use gzFile instead of FILE* + + int opt_offset = QSCORE_OFFSET; + int opt_strict = 0; + int opt_help = 0; + int opt_verbose = 0; + char *filename = NULL; // Initialize to NULL + + + // Parse command-line arguments + for (int i = 1; i < argc; i++) { + if (strcmp(argv[i], ""-s"") == 0) { + opt_strict = 1; + } else if (i < argc - 1 && strcmp(argv[i], ""-o"") == 0 ) { + opt_offset = atol(argv[i + 1]); + i++; + } else if (strcmp(argv[i], ""-v"") == 0) { + opt_verbose = 1; + } else if (strcmp(argv[i], ""-h"") == 0) { + opt_help = 1; + } else { + filename = argv[i]; + + } + } + + // Check for the correct number of command-line arguments + if (opt_help) { + // create a string that is the program's basename + char *program_name = strrchr(argv[0], '/'); + if (program_name != NULL) { + program_name++; + } else { + program_name = argv[0]; + } + printf(""Usage: %s [-s] [-o offset] filename\n"", program_name); + printf(""\nParameters:\n""); + printf("" -s : Validate quality (optional).\n""); + printf("" -o OFFSET : The offset for quality score (optional, default: 33).\n""); + printf("" filename : The name of the file to be processed (optional, default: stdin)\n""); + return 1; + } + + // if defined filename open it else use stdin + if (filename != NULL) { + // print to stderr if verbose + if (opt_verbose) { + fprintf(stderr, ""Opening file %s\n"", filename); + } + + fp = gzopen(filename, ""r""); // Use gzopen instead of fopen + + if (fp == NULL) { + fprintf(stderr, ""Error opening file %s\n"", filename); + return 1; + } + } else { + // print to stderr if verbose + if (opt_verbose) { + fprintf(stderr, ""Reading from stdin\n""); + } + fp = gzdopen(fileno(stdin), ""r""); // Use gzdopen to wrap stdin + } + char first_seq[MAX_LINE_LENGTH]; + char last_seq[MAX_LINE_LENGTH]; + char line[MAX_LINE_LENGTH]; + int line_count = 0; + int seq_count = 0; + int seq_len = 0; + int valid = 1; + + char first_char; + // read the first character + if (gzread(fp, &first_char, 1) != 1) { + fprintf(stderr, ""ERROR: File is empty\n""); + return 1; + } + + if (first_char == '>') { + while (gzgets(fp, line, sizeof(line))) { + line_count++; + if (line_count == 1 || line[0] == '>') { + // header + seq_count++; + line[strcspn(line, ""\n"")] = 0; + char *seq_name = strtok(line, "" ""); + if (seq_count == 1) { + strcpy(first_seq, seq_name); + } + strcpy(last_seq, seq_name+1); + } else { + // sequence + line[strcspn(line, ""\n"")] = 0; + seq_len = strlen(line); + + // Check if the line is only composed by A, C, G, T and N + for (int i = 0; i < seq_len; i++) { + if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { + // print to stderr the error + + fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); + valid = 0; + break; + } + } + } + } + + } else if (first_char == '@') { + while (gzgets(fp, line, sizeof(line))) { // Use gzgets instead of fgets + line_count++; + + if (line_count % 4 == 1) { + // Remove the trailing newline character + line[strcspn(line, ""\n"")] = 0; + + // seq name: remove first character and split to the first space + + char *seq_name = strtok(line, "" ""); + + if (seq_count == 0) { + strcpy(first_seq, seq_name); + } + strcpy(last_seq, seq_name+1); + + // check if first character is '@' + if (line_count != 1 && line[0] != '@') { + printf(""ERROR: Line %d in sequence %d does not start with '@'\n"", line_count, seq_count); + valid = 0; + break; + } + } else if (line_count % 4 == 2) { + // Remove the trailing newline character + line[strcspn(line, ""\n"")] = 0; + seq_len = strlen(line); + + // Check if the line is only composed by A, C, G, T and N + for (int i = 0; i < seq_len; i++) { + if (line[i] != 'A' && line[i] != 'C' && line[i] != 'G' && line[i] != 'T' && line[i] != 'N') { + // print to stderr the error + + fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid character: %c\n"", line_count, seq_count, line[i]); + valid = 0; + break; + } + } + } else if (line_count % 4 == 3) { + if (line[0] != '+') { + fprintf(stderr,""ERROR: Line %d in sequence %d does not start with '+'\n"", line_count, seq_count); + valid = 0; + break; + } + } else if (line_count % 4 == 0) { + line[strcspn(line, ""\n"")] = 0; + if (seq_len != strlen(line)) { + fprintf(stderr, ""ERROR: Line %d in sequence %d has a different length than the sequence: %ld vs %d\n"", line_count, seq_count, (long)(strlen(line) + 1), seq_len); + valid = 0; + break; + } + // Check if the quality line is composed by ASCII values from 0 to 60 + if (opt_strict) { + int qscore_int = 0; + for (int i = 0; i < seq_len; i++) { + qscore_int = (int) line[i] - opt_offset; + if (qscore_int < 0 || qscore_int > 60) { + fprintf(stderr,""ERROR: Line %d in sequence %d contains an invalid quality score: %c = %d\n"", line_count, seq_count, line[i], qscore_int); + valid = 0; + break; + } + } + } + + seq_count++; + } + + + } + + } + + + // create status_string + char status[4]; + if (valid) { + strcpy(status, ""OK""); + } else { + strcpy(status, ""ERR""); + } + printf(""%s\t%d\t%s\t%s\n"", status, seq_count, first_seq, last_seq); + + + if (fp != gzdopen(fileno(stdin), ""r"")) { // Check against gzdopen(fileno(stdin), ""r"") instead of stdin + gzclose(fp); // Use gzclose instead of fclose + } + + return 0; +}","C" +"Bioengineering","telatin/seqfu2","test/byte/fastx_count.c",".c","2469","88","#include +#include +#include +#include + +#define BUFFER_SIZE 1024 + +// Function to check if the file is gzipped +int is_gzipped(const char *filename) { + int len = strlen(filename); + return len > 3 && strcmp(filename + len - 3, "".gz"") == 0; +} + +// Function to open the file appropriately based on its type +FILE *open_file(const char *filename) { + if (is_gzipped(filename)) { + return (FILE *)gzopen(filename, ""rb""); + } else { + return fopen(filename, ""r""); + } +} + +// Function to read a line from the file +char *read_line(FILE *file, char *buffer, int gzipped) { + if (gzipped) { + return gzgets((gzFile)file, buffer, BUFFER_SIZE); + } else { + return fgets(buffer, BUFFER_SIZE, file); + } +} + +// Function to check if the file is FASTQ +int is_fastq(const char *filename) { + return strstr(filename, "".fq"") != NULL || strstr(filename, "".fastq"") != NULL; +} + +// Main function for parsing the FASTQ or FASTA file +int main(int argc, char *argv[]) { + if (argc < 2) { + fprintf(stderr, ""Usage: %s \n"", argv[0]); + return 1; + } + + const char *filename = argv[1]; + int gzipped = is_gzipped(filename); + FILE *file = open_file(filename); + if (!file) { + fprintf(stderr, ""Error opening file: %s\n"", filename); + return 1; + } + + char buffer[BUFFER_SIZE]; + unsigned long total_length = 0; + int total_sequences = 0; + int isFasta = !is_fastq(filename); + int line_number = 0; + + while (read_line(file, buffer, gzipped) != NULL) { + if (isFasta) { + if (buffer[0] == '>') { // Header line in FASTA + if (line_number > 0) total_sequences++; + } else { + total_length += strlen(buffer) - 1; // -1 to exclude the newline character + } + line_number++; + } else { + line_number++; + if (line_number % 4 == 2) { // Sequence line in FASTQ + total_length += strlen(buffer) - 1; // -1 to exclude the newline character + total_sequences++; + } + } + } + + // Adjust sequence count for the last sequence in FASTA + if (isFasta && line_number > 0) total_sequences++; + + if (gzipped) { + gzclose((gzFile)file); + } else { + fclose(file); + } + + printf(""Total number of sequences: %d\n"", total_sequences); + printf(""Total length of sequences: %lu\n"", total_length); + + return 0; +}","C" +"Bioengineering","telatin/seqfu2","test/byte/count.cpp",".cpp","3825","132","#include +#include +#include +#include +#include + +int main(int argc, char* argv[]) { + std::istream* input_stream = nullptr; + gzFile gz_input_stream = nullptr; + std::ifstream file; + + bool use_gzip = false; + bool use_verbose = false; + bool use_stdin = true; + char *input_filename = nullptr; + + + + // Check if -z flag is present + for (int i = 1; i < argc; ++i) { + if (strcmp(argv[i], ""-z"") == 0) { + use_gzip = true; + } else if (strcmp(argv[i], ""-v"") == 0) { + use_verbose = true; + + } else { + input_filename = argv[i]; + use_stdin = false; + // check if filename ends with .gz + int len = strlen(input_filename); + if (len > 3 && strcmp(input_filename + len - 3, "".gz"") == 0) { + use_gzip = true; + } + } + } + + // Verbose + if (use_verbose) { + std::cout << ""use_gzip: "" << use_gzip << std::endl; + std::cout << ""use_stdin: "" << use_stdin << std::endl; + std::cout << ""input_filename: "" << input_filename << std::endl; + } + if ( ! use_stdin ) { + if (use_gzip) { + gz_input_stream = gzopen(input_filename, ""rb""); + if (!gz_input_stream) { + std::cerr << ""Error opening gzipped file: "" << input_filename << std::endl; + return 1; + } + } else { + file.open(input_filename); + if (!file) { + std::cerr << ""Error opening file: "" << input_filename << std::endl; + return 1; + } + input_stream = &file; + } + } else { + input_stream = &std::cin; + if (use_gzip) { + gz_input_stream = gzdopen(0, ""rb""); // 0 is the file descriptor for stdin + } + } + + char first_char; + if (use_gzip) { + gzread(gz_input_stream, &first_char, 1); + } else { + first_char = input_stream->get(); + } + + int greater_than_count = 0; + int newline_count = 0; + const int chunk_size = 1024; + std::vector buffer(chunk_size); + + if (use_gzip) { + int bytes_read; + while ((bytes_read = gzread(gz_input_stream, buffer.data(), chunk_size)) > 0) { + for (int i = 0; i < bytes_read; i++) { + if (buffer[i] == '>') { + greater_than_count++; + } else if (buffer[i] == '\n') { + newline_count++; + } + } + } + } else { + while (input_stream->read(buffer.data(), chunk_size)) { + for (int i = 0; i < chunk_size; i++) { + if (buffer[i] == '>') { + greater_than_count++; + } else if (buffer[i] == '\n') { + newline_count++; + } + } + } + + // Handle the remaining characters (less than chunk_size) + int remaining = input_stream->gcount(); + for (int i = 0; i < remaining; i++) { + if (buffer[i] == '>') { + greater_than_count++; + } else if (buffer[i] == '\n') { + newline_count++; + } + } + } + + if (file.is_open()) { + file.close(); + } + if (gz_input_stream) { + gzclose(gz_input_stream); + } + + if (first_char == '>') { + std::cout << greater_than_count + 1 << ""\tFASTA"" << std::endl; + } else if (first_char == '@') { + int approx = newline_count / 4; + std::cout << approx << ""\tFASTQ"" << std::endl; + } else { + std::cerr << ""Error: first character is not '>' or '@'"" << std::endl; + if (use_stdin) { + std::cerr << ""If the stream is gzipped try adding -z"" << std::endl; + } + return 1; + } + + return 0; +} +","C++" +"Bioengineering","telatin/seqfu2","test/byte/fastx_counter.c",".c","1794","71","#include +#include +#include +#include + +#define BUFFER_SIZE 1024 + +// Function to check if the file is gzipped +int is_gzipped(const char *filename) { + int len = strlen(filename); + return len > 3 && strcmp(filename + len - 3, "".gz"") == 0; +} + +// Function to open the file appropriately based on its type +FILE *open_file(const char *filename) { + if (is_gzipped(filename)) { + return (FILE *)gzopen(filename, ""rb""); + } else { + return fopen(filename, ""r""); + } +} + +// Function to read a line from the file +char *read_line(FILE *file, char *buffer, int gzipped) { + if (gzipped) { + return gzgets((gzFile)file, buffer, BUFFER_SIZE); + } else { + return fgets(buffer, BUFFER_SIZE, file); + } +} + +// Main function for parsing the FASTQ file +int main(int argc, char *argv[]) { + if (argc < 2) { + fprintf(stderr, ""Usage: %s \n"", argv[0]); + return 1; + } + + const char *filename = argv[1]; + int gzipped = is_gzipped(filename); + FILE *file = open_file(filename); + if (!file) { + fprintf(stderr, ""Error opening file: %s\n"", filename); + return 1; + } + + char buffer[BUFFER_SIZE]; + unsigned long total_length = 0; + int total_sequences = 0; + int line_number = 0; + + while (read_line(file, buffer, gzipped) != NULL) { + line_number++; + if (line_number % 4 == 2) { // Sequence line + total_length += strlen(buffer) - 1; // -1 to exclude the newline character + total_sequences++; + } + } + + if (gzipped) { + gzclose((gzFile)file); + } else { + fclose(file); + } + + printf(""Total number of sequences: %d\n"", total_sequences); + printf(""Total length of sequences: %lu\n"", total_length); + + return 0; +} +","C" +"Bioengineering","telatin/seqfu2","test/byte/mnt.c",".c","2326","82","#include +#include +#include // Required for gzipped files + +// Function to process a regular file +void processRegularFile(FILE *file) { + // Variables to keep count of sequences and total length + unsigned long sequenceCount = 0; + unsigned long totalLength = 0; + char line[100024]; // Assuming each line will not be longer than 1024 characters + + while (fgets(line, sizeof(line), file)) { + if (line[0] == '@') { // Sequence identifier line + sequenceCount++; + if (fgets(line, sizeof(line), file)) { // Sequence line + totalLength += strlen(line) - 1; // -1 to remove newline character + + + } + } + } + + printf(""Number of sequences: %lu\n"", sequenceCount); + printf(""Total length: %lu\n"", totalLength); +} + +void processGzippedFile(gzFile file) { + unsigned long sequenceCount = 0; + unsigned long totalLength = 0; + char line[1024]; // Buffer for each line + + while (gzgets(file, line, sizeof(line))) { + //printf(""Debug: Read line: %s"", line); // Debugging line + if (line[0] == '@') { + sequenceCount++; + if (gzgets(file, line, sizeof(line))) { + totalLength += strlen(line) - 1; // -1 to remove newline character + + + } + // discard next two lines + gzgets(file, line, sizeof(line)); + gzgets(file, line, sizeof(line)); + } + } + + printf(""Number of sequences: %lu\n"", sequenceCount); + printf(""Total length: %lu\n"", totalLength); +} + + +int main(int argc, char *argv[]) { + if (argc != 2) { + fprintf(stderr, ""Usage: %s \n"", argv[0]); + return 1; + } + + FILE *file; + gzFile gzfile; + + // Check if the file is gzipped or not + if (strstr(argv[1], "".gz"")) { + gzfile = gzopen(argv[1], ""r""); + if (!gzfile) { + fprintf(stderr, ""Could not open gzipped file: %s\n"", argv[1]); + return 1; + } + processGzippedFile(gzfile); + gzclose(gzfile); + } else { + file = fopen(argv[1], ""r""); + if (!file) { + fprintf(stderr, ""Could not open file: %s\n"", argv[1]); + return 1; + } + processRegularFile(file); + fclose(file); + } + + return 0; +} +","C" +"Bioengineering","telatin/seqfu2","templates/make.sh",".sh","128","5","#!/bin/bash + +nim c --threads:on -d:release --opt:speed fastx_multithreaded_utility +nim c -d:release --opt:speed fastx_utility_1 +","Shell" +"Bioengineering","telatin/seqfu2","templates/perl/getdata.sh",".sh","241","6","#!/bin/bash +set -euxo pipefail +## https://umi-tools.readthedocs.io/en/latest/Single_cell_tutorial.html#step-1-obtaining-the-data +wget ""http://cf.10xgenomics.com/samples/cell-exp/1.3.0/hgmm_100/hgmm_100_fastqs.tar"" +tar -x hgmm_100_fastqs.tar +","Shell" +"Bioengineering","telatin/seqfu2","releases/v1.20.0.md",".md","90","3","* Added paired end support for `fu-shred` +* Added `--noheader` in `seqfu stats` +* Bugfixes","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.14.0.md",".md","557","8","* **SeqFu grep** will die if fed with non existing files (to ensure no wrong parameters were passed) +* **SeqFu grep** will match oligos case insensitive by default +* Addedd invert match `-v` to `seqfu grep` +* Improved `fu-tabcheck`, notably added `--inspect` option to print columns info +* `fu-split` now can use a different SeqFu than specified in path, setting `$SEQFU_BIN` or `--bin` option +* `fu-split` version check fixed +* :warning: Bugfix in `seqfu tab`: was not working with FASTA files +* **SeqFu head** and **SeqFu tail** migrated to readfq library","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.10.0.md",".md","103","3","* Added support for MetaPhage to **seqfu metadata** +* Added `--header` to **fu-tabcheck** +* Minor fixes","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.8.7.md",".md","39","2","* Improved performance +* Added Makefile","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.9.0.md",".md","347","5","* `seqfu grep` now has `-w` (word) and `-f` (full) match options. default behaviour unchanged. +* `seqfu cat` now has a filter for Ns (`--max-ns INT`) +* `seqfu cat` now has a filter for the total expected errors (`--max-ee FLOAT`), and can report `--add-ee` and `--add-initial-ee` +* Added header line in `seqfu metadata` when using ""irida"" formats +","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.9.3.md",".md","203","3"," +* **bugfix**: `seqfu cat` controls the length of operations (truncate, trim) +* *improved*: `seqfu cat` improved renaming options (basename and strip-name will now add a progressive number automatically)","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.13.2.md",".md","179","2","* added `--print-last` option to **seqfu cat** and **seqfu heda** +* updated `fu-split`, with support for paired end reads, improved performance thanks to `--print-last`, new tests","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.20.1.md",".md","117","2","* Bugfix in `seqfu metadata` when producing a **Manifest file** for **single end** +* Added `--translate` to `fu-orf`","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.8.9.md",".md","21","1","* Improved **fu-msa**","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.8.8.md",".md","67","2","* Introduced the experimental multiple alignment viewer **fu-msa** +","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.12.0.md",".md","36","2","* Improved ""fu-index"" +* Minor bugfix","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.9.1.md",".md","130","2","* Test suite will not fail if the version matches the remote version. Set `RELEASE=1` to enable the previous behaviour (for devs) +","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.20.3.md",".md","36","1","* Bugfix interleave/deinterleave #21","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.13.1.md",".md","33","1","* added `fu-split` (experimental)","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.9.2.md",".md","30","3","- Bugfix on Seqfu Detabulate + +","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.11.0.md",".md","242","4","* Improved `seqfu stats`: added sorting option and JSON output, added GC content, improved test suite. +* **bugfix** Seqfu tabulate `-d` (detabulate) was too stringent in requiring forward and reverse reads to have the same length :facepalm: + +","Markdown" +"Bioengineering","telatin/seqfu2","releases/v1.13.0.md",".md","221","2","* `seqfu cat` now can skip a set of initial sequences (`--skip-first INT`) or start from a specific sequence (`--jump-to`) +* Minor updates in the test suite, github actions (including rich_codex) and documentation updates","Markdown" +"Bioengineering","telatin/seqfu2","docs/install.md",".md","1494","46","--- +layout: default +title: Installation +nav_order: 2 +permalink: /installation +--- + +# Installation + +## Install via Miniconda + +The **recommended** installation method is via BioConda, +which is supported from both **Linux** and **macOS**. +If you have _conda_ installed ([how to install it](https://docs.conda.io/en/latest/miniconda.html)): + +```bash +# Ensure a recent version will be installed: 0.x is a very old and unsupported tool +conda install -c conda-forge -c bioconda ""seqfu>1.10"" +``` + +More info on [installing conda](https://telatin.github.io/microbiome-bioinformatics/Install-Miniconda/). + +:warning: It is _possible_ to compile the program for Windows, +but we cannot provide support for this platform at the moment. + +## Pre-compiled binaries + +Pre-compiled core binaries are distributed with the [releases](https://github.com/telatin/seqfu2/releases), +as zip files containing all the tools, labeled as ""Linux"" and ""Darwin"" as they target Linux and macOS respectively. +When possible, we recommend to install SeqFu via Miniconda (see above), +as it provides the full set of tools. + +## Manual compilation + +### Linux and macOS + +1) If `nim` is not installed, install it +(**[see instructions](https://nim-lang.org/install_unix.html)**). +We suggest - when available - the `choosenim` method + +2) Clone the repository (`git clone https://github.com/telatin/seqfu2`) + +3) Compile with `nimble build`, that will download the required packages + +4) The binaries will be available in the `./bin` directory +","Markdown" +"Bioengineering","telatin/seqfu2","docs/intro.md",".md","4539","96","--- +layout: default +title: Overview +nav_order: 3 +permalink: /intro +--- + +# Overview + +SeqFu consists of core programs, accessible as subcommands, and a set +of corollary utilities, having the prefix `fu-`. + +Type `seqfu` alone to list the core subprograms, +and `seqfu {command} --help` +to access the help of each specific subcommand. + +To simply print the version type `seqfu version` and to print the +citation `seqfu cite`. + +## Basic operations: cat, head, tail, grep, rc + +These commands have been inspired by the common *GNU commands*, and all can +read from the standard input. + +Their usage is quite intuitive, so here we highlight some special feature. + +**[seqfu cat]({{site.baseurl}}/tools/cat.html)** can read mixed FASTA and +FASTQ files, and be forced to output in either FASTA or FASTQ format. +Some basic manipulations are bundled, like: + +* Forcing FASTA or FASTQ output +* Manipulating sequence name (prefix, suffix, prepend filename, remove comments...) +* Add infos in the header (length, gc content, original name) +* Filter by length (minimum length, maximum length, trim bases at the beginning or the end...) +* ... + +**[seqfu grep]({{site.baseurl}}/tools/grep.html)** can be used to +extract sequences by matching oligonucleotides, that would be scanned +also in the reverse strand and allowing for mismatches or +partial matches. +The oligo can be in IUPAC alphabet with ambiguous bases +(e.g. degenerate primers). + +**[seqfu head]({{site.baseurl}}/tools/head.html)** can skip a +number of sequences (_i. e._ print the first _N_ sequences +taking one every _M_), to extract a small subset sampling deeper. + +The _reverse complement_ function +(**[seqfu rc]({{site.baseurl}}/tools/rc.html)**) +is unique in taking as input both +files and sequences, and properly supports IUPAC degenerate bases. + +## Getting an idea: view, qual, stats, count + +**[seqfu view]({{site.baseurl}}/tools/view.html)** +is only for interactive use, and can be used to have a visual +feedback on the quality values and on the presence of oligonucleotides: + +![View]({{site.baseurl}}/img/view.png) + +**[seqfu stats]({{site.baseurl}}/tools/stats.html)** +can print the total number of sequences, bases, average, +N50, N75, N90 and AuN, minimum and maximum length of a dataset, +both in TSV format and with a nicer console oriented output: + +```text +┌────────────────────┬───────┬──────────┬───────┬─────┬─────┬─────┬────────┬─────┬─────┐ +│ File │ #Seq │ Total bp │ Avg │ N50 │ N75 │ N90 │ auN │ Min │ Max │ +├────────────────────┼───────┼──────────┼───────┼─────┼─────┼─────┼────────┼─────┼─────┤ +│ filt.fa.gz │ 78730 │ 24299931 │ 308.6 │ 316 │ 316 │ 220 │ 0.385 │ 180 │ 485 │ +│ illumina_1.fq.gz │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ +│ illumina_2.fq.gz │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ +│ illumina_nocomm.fq │ 7 │ 630 │ 90.0 │ 90 │ 90 │ 90 │ 12.857 │ 90 │ 90 │ +└────────────────────┴───────┴──────────┴───────┴─────┴─────┴─────┴────────┴─────┴─────┘ +``` + +## Managing datasets: interleave, deinterleave, lanes + +Very common tasks when dealing with Illumina Paired-End sequences are +interleaving and deinterleaving the datasets. + +**[seqfu interleave]({{site.baseurl}}/tools/interleave.html)** and +**[seqfu deinterleave]({{site.baseurl}}/tools/deinterleave.html)** +can do that, with high speed and lower corruption risks. + +Multiple lanes can be quickly merged with **[seqfu lanes]({{site.baseurl}}/tools/merge_lanes.html)**. + +## Sorting, dereplicating + +**[seqfu sort]({{site.baseurl}}/tools/sort.html)** can sort sequences by length. + +**[seqfu derep]({{site.baseurl}}/tools/derep.html)** can be used to dereplicate +datasets, printing the number of identical sequences. In particular, this information +can be used also from the input dataset, allowing to dereplicating a +set of dereplicated files keeping trace of the number of sequences. +","Markdown" +"Bioengineering","telatin/seqfu2","docs/index.md",".md","2130","44","--- +layout: home +title: Home +nav_order: 1 +--- + + + + + +# SeqFu + +[![Seqfu-Nim-Build](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml/badge.svg)](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml) +[![pages-build-deployment](https://github.com/telatin/seqfu2/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/telatin/seqfu2/actions/workflows/pages/pages-build-deployment) +[![GitHub Stars](https://img.shields.io/github/stars/telatin/seqfu2?label=⭐️)](https://github.com/telatin/seqfu2) +[![Latest release](https://img.shields.io/github/v/release/telatin/seqfu2)](https://github.com/telatin/seqfu2/releases) +[![Bioconda Downloads](https://img.shields.io/conda/dn/bioconda/seqfu?label=Bioconda%20Downloads)](https://anaconda.org/bioconda/seqfu) + +📦 See the **[repository](https://github.com/telatin/seqfu2)** | 💾 **[releases](https://github.com/telatin/seqfu2/releases)** + +A general-purpose program to manipulate and parse information from FASTA/FASTQ files, +supporting gzipped input files. +Includes functions to _interleave_ and _de-interleave_ FASTQ files, +to _rename_ sequences and to _count_ and print _statistics_ on sequence lengths. +SeqFu is available for Linux and MacOS. + +* A compiled program delivering high performance analyses +* Supports FASTA/FASTQ files, also Gzip compressed +* A growing collection of handy utilities, also for quick inspection of the datasets +* UNIX like commands but specific for sequences like `seqfu cat`, `seqfu head`, `seqfu tail`, `seqfu grep` +* Terminal friendly reports from `seqfu stats` or `seqfu count`... + +Can be easily [installed](installation) via conda: + +```bash +conda install -c conda-forge -c bioconda ""seqfu>1.0"" +``` + +## Citation + +Telatin A, Fariselli P, Birolo G. *SeqFu: A Suite of Utilities for the Robust +and Reproducible Manipulation of Sequence Files*. +Bioengineering 2021, 8, 59. [doi.org/10.3390/bioengineering8050059](https://doi.org/10.3390/bioengineering8050059) +","Markdown" +"Bioengineering","telatin/seqfu2","docs/usage.md",".md","2398","62","--- +layout: default +title: Usage Guide +nav_order: 4 +permalink: /usage +--- + +# Short guide + +*SeqFu* is composed by a main program with multiple subprograms, and a set of utilities. +Check the complete documentation for each [tool]({{site.baseurl}}/tools), that contains the detailed +documentation. + +SeqFu has tools for: + +* Make life easier when working from the command line + (`seqfu head`, `seqfu tail`, `seqfu rc`...) +* Provide a visual feedback of datasets (like `seqfu view`) +* Get statistics (`seqfu count` and `seqfu stats`) +* Perform common operations with a reliable tool (`seqfu interleave`, `seqfu deinterleave`) +* Perform specialistic operations with added ease of use or features + +## Main program + +If invoked without parameters, *SeqFu* will print the list of subprograms: + +```text +SeqFu - Sequence Fastx Utilities +version: 1.8.5 + + · count [cnt] : count FASTA/FASTQ reads, pair-end aware + · deinterleave [dei] : deinterleave FASTQ + · derep [der] : feature-rich dereplication of FASTA/FASTQ files + · interleave [ilv] : interleave FASTQ pair ends + · lanes [mrl] : merge Illumina lanes + · list [lst] : print sequences from a list of names + · metadata [met] : print a table of FASTQ reads (mapping files) + · sort [srt] : sort sequences by size (uniques) + · stats [st] : statistics on sequence lengths + + · cat : concatenate FASTA/FASTQ files + · grep : select sequences with patterns + · head : print first sequences + · rc : reverse complement strings or files + · tab : tabulate reads to TSV (and viceversa) + · tail : view last sequences + · view : view sequences with colored quality and oligo matches + +Type 'seqfu version' or 'seqfu citation' to print the version and paper, respectively. +Add --help after each command to print its usage. +``` + +## Subprograms + +*SeqFu* is bundled with an (increasing) set of utilities sharing the FASTX parsing library: + +* **fu-orf** to extract ORFs from Paired-End libraries +* **fu-cov** to extract contigs from the most commonly used assembly programs using the coverage information printed in the headers +* **fu-homocomp** to compress homopolymers (e.g. for Nanopore applications) +* ... +* See the **[full list](https://telatin.github.io/seqfu2/utilities/)**. +","Markdown" +"Bioengineering","telatin/seqfu2","docs/notes.md",".md","3573","88","--- +layout: default +title: About +nav_order: 8 +permalink: /about +--- + +# About SeqFu + +## Citing + +Telatin A, Fariselli P, Birolo G. +**SeqFu: A Suite of Utilities for the Robust and +Reproducible Manipulation of Sequence Files**. +Bioengineering 2021, 8, 59. +[https://doi.org/10.3390/bioengineering8050059](doi.org/10.3390/bioengineering8050059) + +## Why + +There are several tools for the analysis of FASTQ/FASTA files. +My personal choice has been (and is) **[SeqKit](https://bioinf.shenwei.me/seqkit/)**, +a general purpose toolkit. + +As many other bioinformaticians, I found myself coding small _ad hoc_ scripts, for example: + +* A tool to extract the _index_ from Illumina FASTQ files +(taking the most common occurrence from the first 1000 reads) +* A tool to extract contigs using a list from a predictor +* Scripts to interleave/deinterleave FASTQ files + +The problem was distributing a very small script to users lacking the library I was using (like the excellent [pyfastx](https://pypi.org/project/pyfastx/) or our +[FASTX::Reader](https://metacpan.org/release/FASTX-Reader)). + +The possibility to distribute self-contained binaries was an option that was both +boosting the performance of the program, and solving the dependency hell for minor +applications. + +This led to the start of the project. + +## How + +The main parsing library is `klib.nim` by Heng Li ([lh3/biofast](https://github.com/lh3/biofast)), that provides good performances. + +For some utilities the *readfq* library has been used ([andreas-wilm/nimreadfq](https://github.com/andreas-wilm/nimreadfq)). This is based on the +C version of Heng Li's parsed, wrapped in an object oriented module. + +## About the name + +The name of the program was modeled after ""[ScriptFu](https://docs.gimp.org/en/gimp-concepts-script-fu.html)"", +a set of macros built in the image manipulation **GIMP**. + +[Apparently](https://twitter.com/StevenSalzberg1/status/1439704488508526599?s=20), +in the US this might sound offensive. + +

I love it that these guys got away with creating a tool called 'seqfu', and even put it in the title of their paper (https://t.co/dCCUStKTEB). Did the editors/reviewers realize what this word sounds like in English? 😉 h/t @telatin https://t.co/fHvOxsKXKx

— Steven Salzberg (@StevenSalzberg1) September 19, 2021
+ +![How to get away]({{site.baseurl}}/img/howtoget.png) + +So we after a consultation with Microsoft (and thanks to their previous experience with Minesweep), +offer a tool to rename the program to **SeqFlower**. + +![SeqFlower]({{site.baseurl}}/img/flowers.png) + +The renaming script is called `flower.sh` in the _src_ directory. + +## Developer's details + +### Perl module + +A Perl version of the parser is available both from +**[MetaCPAN](https://metacpan.org/release/FASTX-Reader)** and from Bioconda: + +``` +conda install -c bioconda perl-fastx-reader +``` + +### Templates + +The repository contains some templates to quickly write +FASTX parser-based applications (in Nim or in Perl). + +:package: [seqfu2/templates](https://github.com/telatin/seqfu2/tree/main/templates) + +## Outreach + +* [Slides](https://www.icloud.com/keynote/0cfGObtl14rWj_q4nZ7lFy7fg#seqfu_2) +* [Slides, PDF)(http://seqfu.it/slides.pdf) +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/tail.md",".md","1043","35","--- +layout: default +title: seqfu tail +parent: Core Tools +--- + + +# seqfu tail + +*tail* is one of the core subprograms of *SeqFu*. + +It will print the last sequences of a FASTX file (like GNU tail), but +can be instructed to skip a number of sequences between each printed one. + +```text +Usage: tail [options] [ ...] + +Options: + -n, --num NUM Print the first NUM sequences [default: 10] + -k, --skip SKIP Print one sequence every SKIP [default: 0] + -p, --prefix STRING Rename sequences with prefix + incremental number + -s, --strip-comments Remove comments + -b, --basename prepend basename to sequence name + --fasta Force FASTA output + --fastq Force FASTQ output + --sep STRING Sequence name fields separator [default: _] + -q, --fastq-qual INT FASTQ default quality [default: 33] + -v, --verbose Verbose output + -h, --help Show this help +``` + + +## Screenshot + +![Screenshot of ""seqfu tail""]({{site.baseurl}}/img/screenshot-tail.svg ""SeqFu tail"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/bases.md",".md","4656","83","--- +layout: default +title: seqfu bases +parent: Core Tools +--- + +# seqfu bases + +Counts the number of A, C, G, T and Ns in FASTA and FASTQ files. + +```note +Introduced in SeqFu 1.15.1 as experimental feature +``` + +Calculates the composition of DNA sequences + +```text +Usage: bases [options] [ ...] + +Print the DNA bases, and %GC content, in the input files + +Options: + -c, --raw-counts Print counts and not ratios + -t, --thousands Print thousands separator + -a, --abspath Print absolute path + -b, --basename Print the basename of the file + -n, --nice Print terminal table + -d, --digits INT Number of digits to print [default: 2] + -H, --header Print header (auto enabled with --nice) + -v, --verbose Verbose output + --debug Debug output + --help Show this help +``` + +### Output + +The output is a table with the following columns (`-H` to print the header): + +1. Filename (`-a` for absolute path, `-b` for basename) +2. Total bases (`-t` to add thousand separator) +3. Ratio of **A** bases over total bases (`-c` to print raw counts) +4. Ratio of **C** bases over total bases (`-c` to print raw counts) +5. Ratio of **G** bases over total bases (`-c` to print raw counts) +6. Ratio of **T** bases over total bases (`-c` to print raw counts) +7. Ratio of **N** bases over total bases (`-c` to print raw counts) +8. Ratio of **Other** characters (either IUPAC DNA or invalid chars) over total bases (`-c` to print raw counts) +9. %GC ratio +10. Ratio of **Uppercase** bases over total bases (if enabled by `-u`) + +### Example + +A simple example: + +```text +seqfu bases --header data/illumina_* + +#Filename Total A C G T N Other %GC +data/illumina_1.fq.gz 630 18.57 18.57 18.57 18.57 18.57 0.00 59.21 +data/illumina_2.fq.gz 630 21.43 21.43 21.43 21.43 21.43 0.00 60.48 +data/illumina_nocomm.fq 630 18.57 18.57 18.57 18.57 18.57 0.00 59.21 +``` + +when using `-n` the output is a nice table: + +```text +┌─────────────────────┬───────┬────────┬────────┬────────┬────────┬──────┬───────┬────────┬───────────┐ +│ File │ Bases │ A │ C │ G │ T │ N │ Other │ %GC │ Uppercase │ +├─────────────────────┼───────┼────────┼────────┼────────┼────────┼──────┼───────┼────────┼───────────┤ +│ data/base_at.fa │ 33 │ 42.42 │ 0.00 │ 0.00 │ 57.58 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ +│ data/bases_lower.fa │ 15 │ 33.33 │ 26.67 │ 20.00 │ 13.33 │ 6.67 │ 0.00 │ 46.67 │ 0.00 │ +│ data/base_c.fa │ 5 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ +│ data/base.fa │ 2 │ 50.00 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 100.00 │ +│ data/upper-none.fa │ 7 │ 42.86 │ 14.29 │ 28.57 │ 14.29 │ 0.00 │ 0.00 │ 42.86 │ 0.00 │ +│ data/base_t.fa │ 5 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ +│ data/base_a.fa │ 5 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ +│ data/upper-lower.fa │ 10 │ 50.00 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 50.00 │ +│ data/base_g.fa │ 1 │ 0.00 │ 0.00 │ 100.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 100.00 │ +│ data/upper-only.fa │ 9 │ 44.44 │ 11.11 │ 44.44 │ 0.00 │ 0.00 │ 0.00 │ 55.56 │ 100.00 │ +│ data/base_extra.fa │ 20 │ 50.00 │ 0.00 │ 0.00 │ 0.00 │ 0.00 │ 50.00 │ 0.00 │ 100.00 │ +│ data/base_cg.fa │ 25 │ 0.00 │ 52.00 │ 48.00 │ 0.00 │ 0.00 │ 0.00 │ 100.00 │ 100.00 │ +└─────────────────────┴───────┴────────┴────────┴────────┴────────┴──────┴───────┴────────┴───────────┘ +``` +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/interleave.md",".md","3334","81","--- +layout: default +title: seqfu interleave +parent: Core Tools +--- + + +# seqfu interleave + +*interleave* (or *ilv*) is one of the core subprograms of *SeqFu*. +It's used to produce an _interleaved FASTQ file_ from two separate +files containing the forward and the reverse read of a paired-end +fragment. + +```text +ilv: interleave FASTQ files + + Usage: ilv [options] -1 [-2 ] + + -f --for-tag string identifying forward files [default: auto] + -r --rev-tag string identifying forward files [default: auto] + -o --output save file to instead of STDOUT + -c --check enable careful mode (check sequence names and numbers) + -v --verbose print verbose output + + -s --strip-comments skip comments + -p --prefix ""string"" rename sequences (append a progressive number) + +guessing second file: + by default is scanned for _R1. and substitute with _R2. + if this fails, the patterns _1. and _2. are tested. + +example: + + ilv -1 file_R1.fq > interleaved.fq +``` + +## What are interleaved files? + +[Paired end sequences](https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html) can be stored in two separate files +(usually denoted with the **_R1** and **_R2** strings) or in a single sequence where each sequence pair is +stored as two subsequent sequences. + +A simple example is depicted below: + +```text +======================================================================= +File_R1.fq File_R2.fq Interleaved.fq +======================================================================= + + +@seq1 @seq1 @seq1 +TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG ++ + + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII +@seq2 @seq2 @seq1 +GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC ++ + + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII +@seq3 @seq3 @seq2 +AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA ++ + + +IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII + @seq2 + TTTTTTTTTTTTTTTTTTT + + + IIIIIIIIIIIIIIIIIII + @seq3 + AGAGTGTCTGATAGCA + + + IIIIIIIIIIIIIIII + @seq3 + GATAGCAG + + + IIIIIIII +``` + + +## Screenshot + +![Screenshot of ""seqfu interleave""]({{site.baseurl}}/img/screenshot-interleave.svg ""SeqFu interleave"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/cat.md",".md","4048","88","--- +layout: default +title: seqfu cat +parent: Core Tools +--- + +# seqfu cat + +Concatenate multiple FASTA/FASTQ files, in a similar way of the GNU `cat` utility. + +```text +Usage: cat [options] [ ...] + +Concatenate multiple FASTA or FASTQ files. + +Options: + -k, --skip STEP Print one sequence every STEP [default: 0] + --skip-first INT Skip the first INT records [default: -1] + --jump-to STR Start from the record after the one named STR + (overrides --skip-first) + --print-last Print the name of the last sequence to STDERR (Last:NAME) + +Sequence name: + -p, --prefix STRING Rename sequences with prefix + incremental number + -z, --strip-name Remove the original sequence name + -a, --append STRING Append this string to the sequence name [default: ] + --sep STRING Sequence name fields separator [default: _] + + -b, --basename Prepend file basename to the sequence name (before prefix) + --split CHAR Split basename at this char [default: .] + --part INT After splitting the basename, take this part [default: 1] + --basename-sep STRING Separate basename from the rest with this [default: _] + --zero-pad INT Zero pad the counter to INT digits [default: 0] + +Sequence comments: + -s, --strip-comments Remove original sequence comments + --comment-sep CHAR Comment separator [default: ] + --add-len Add 'len=LENGTH' to the comments + --add-initial-len Add 'original_len=LENGTH' to the comments + --add-gc Add 'gc=%GC' to the comments + --add-initial-gc Add 'original_gc=%GC' to the comments + --add-name Add 'original_name=INITIAL_NAME' to the comments + --add-ee Add 'ee=EXPECTED_ERROR' to the comments + --add-initial-ee Add 'original_ee=EXPECTED_ERROR' to the comments + +Filtering: + -n, --max-ns INT Discard sequences with more than INT Ns [default: -1] + -m, --min-len INT Discard sequences shorter than INT [default: 1] + -x, --max-len INT Discard sequences longer than INT, 0 to ignore [default: 0] + --max-ee FLOAT Discard sequences with higher than FLOAT expected error [default: -1.0] + --trim-front INT Trim INT base from the start of the sequence [default: 0] + --trim-tail INT Trim INT base from the end of the sequence [default: 0] + --truncate INT Keep only the first INT bases, 0 to ignore [default: 0] + Negative values to print the last INT bases + --max-bp INT Stop printing after INT bases [default: 0] + +Output: + --fasta Force FASTA output + --fastq Force FASTQ output + --report FILE Save a report to FILE (original name, new name) + --list Output a list of sequence names + --anvio Output in Anvio format (-p c_ -s -z --zeropad 12 --report rename_report.txt) + -q, --fastq-qual INT FASTQ default quality [default: 33] + -v, --verbose Verbose output + --debug Debug output + -h, --help Show this help +``` + +## Input + +One or more FASTA or FASTQ files. If no files are provided, the program will read from _standard input_. +Additionally, you can add _standard input_ to the list of input files. +by adding `-`. + +## Output + +It is possible to mix FASTA and FASTQ files, and by default the program will produce a mixed output. +Using `--fasta` or `--fastq` will force a specific output formats. For FASTA sequences a default quality values will be used. +Using `--list` the simple list of records matching the criteria will be printed. + +## Anvi'o shortcut + +If you use `--anvio` you will automatically suppress names and comments, and add a prefix `c_` to the sequence names and leading zeros to the counter, and write the report to `rename_report.txt`. +If you specify a different `--report` file, this will of course override the default report file. + +## Splashscreen + +![Screenshot of ""seqfu cat""]({{site.baseurl}}/img/screenshot-cat.svg ""SeqFu cat"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/list.md",".md","1600","61","--- +layout: default +title: seqfu list +parent: Core Tools +--- + + +# seqfu list + +Extract sequences from sequence files using a list of requested items. +Introduced in **SeqFu 1.8**. + +```text +Usage: list [options] ... + +Print sequences that are present in a list file. +Duplicated entries in the list will be ignored + +Other options: + -c, --with-comments Include comments in the list file + -p, --partial-match Allow partial matches (UNSUPPORTED) + -m, --min-len INT Skip entries smaller than INT [default: 1] + + -v, --verbose Verbose output + -r, --report Print report of found sequences + --help Show this help +``` + + +## Input + +The **list** file is a simple text file with sequence names, +that can contain the comments and +they can have a leading `>` or `@` characters +(which would be discarded). + +By default, if comments are present in the list they are ignored +and the match is only at the sequence name level, unless +the `--with-comments` option is used. + +## Output + +The standard output is in the same format as the input files, +either FASTA or FASTQ. + +With `--report` the full input list is printed with the total +number of sequences printed. + +Example report: + +``` +# SEQUENCES REPORT +# Sequence 'protein.1c;size=5372' found 1 times +# Sequence 'protein.1d;size=5372' found 1 times +# Sequence 'protein.missing' found 0 times +# Sequence 'protein.1a;size=5372' found 1 times +# Sequence 'protein.1f;size=5372' found 1 times +# Sequence 'protein.notfound' found 0 times +# Sequence 'protein.1b;size=5372' found 1 times +Total sequences found: 5/7 +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/rc.md",".md","1551","66","--- +layout: default +title: seqfu rc +parent: Core Tools +--- + + +# seqfu rc + +*rc* is one of the core subprograms of *SeqFu*, that allows +to print the _reverse complement_ of sequences, either from +input files or provided as strings. IUPAC DNA characters allowed. + +```text +Usage: rc [options] [...] + +Print the reverse complementary of sequences in files or sequences +given as parameters + +Options: + -s, --seq-name NAME Sequence name if coming as string [default: string] + --strip-comments Remove sequence comments + -v, --verbose Verbose output + --help Show this help +``` + +## Reverse complement strings + +To print the reverse complement of sequence, for example of universal primers with degenerate bases: +``` +seqfu rc CCTACGGGNGGCWGCAG GGACTACHVGGGTATCTAATCC +``` + +will produce: +```text +>string_1 +CTGCWGCCNCCCGTAGG +>string_2 +GGATTAGATACCCBDGTAGTCC +``` + +**Note**: if a single sequence (string) is provided, the output is not in FASTA format but a plain string. This makes easier +a programmatic use like: +```bash +removePrimersScript.sh --for $FOR --rev $(seqfu rc $REV) +``` + +## Reverse commplement files +When supplying input files, the whole file will be complemented. If the file is in FASTQ format the +quality will be reversed as well. The program can process multiple files. +``` +seqfu rc data/test.fasta +``` + +will produce: +```text +>SEQ1_BamHI-EcoRI +ACGTGTACCAGCTACGATCGTGTGTAGCTAGCTCGTCAGCTAGCTACGTCGATCACGTACGCTGT +>Seq2 with comm +GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT +>Seq3 +GGGGGGGGGGGGGGGGGGGGG +``` + + +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/trim.md",".md","1424","53","--- +layout: default +title: seqfu trim +parent: Core Tools +nav_order: 11 +--- + +# trim + +The `trim` command trims FASTQ sequences from the 3' end when quality drops below a threshold in a sliding window. + +## Usage + +``` +seqfu trim [options] [ ...] +``` + +## Options + +| Option | Description | Default | +|--------|-------------|---------| +| `-w, --window-size INT` | Window size for quality calculation | 5 | +| `-q, --min-avg-qual INT` | Minimum average quality within window | 20 | +| `--offset INT` | Quality offset (33 for Illumina) | 33 | +| `-o, --output FILE` | Output filename | stdout | +| `-v, --verbose` | Verbose output | off | +| `-h, --help` | Show help | | + +## Description + +This command scans the quality scores of FASTQ sequences using a sliding window of the specified size. +When the average quality within the window drops below the specified threshold, it trims the sequence +from that position, discarding all subsequent bases. + +This is useful for removing low-quality regions from the 3' end of sequencing reads, which often +contain more errors as the sequencing reaction progresses. + +## Examples + +Trim sequences when the quality drops below 20 in a window of 5 bases: +```bash +seqfu trim input.fastq -o output.fastq +``` + +Use a more stringent quality threshold: +```bash +seqfu trim -q 25 input.fastq -o output.fastq +``` + +Change the window size: +```bash +seqfu trim -w 10 -q 20 input.fastq -o output.fastq +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/count.md",".md","3039","91","--- +layout: default +title: seqfu count +parent: Core Tools +--- + + +# seqfu count + +*count* (or *cnt*) is one of the core subprograms of *SeqFu*. +It's used to count the sequences in FASTA/FASTQ files, and it's _paired-end_ aware so +it will print the count of both files in a single line, but checking that both +files have the same number of sequences. + +In version 1.5 the program has been redesigned to parse multiple files simultaneously. + +```text +Usage: count [options] [ ...] + +Options: + -a, --abs-path Print absolute paths + -b, --basename Print only filenames + -u, --unpair Print separate records for paired end files + -f, --for-tag R1 Forward tag [default: auto] + -r, --rev-tag R2 Reverse tag [default: auto] + -t, --threads INT Working threads [default: 4] + -v, --verbose Verbose output + -h, --help Show this help +``` + +### Streaming + +Input from stream is supported. + +### Example output + +Output is a TSV text with three columns: sample name, number of reads and type (""SE"" for Single End, ""Paired"" for Paired End) + +```text +data/test.fastq 3 SE +data/comments.fastq 5 SE +data/test2.fastq 3 SE +data/qualities.fq 5 SE +data/illumina_1.fq.gz 7 Paired +``` + +In case of errors will print a warning: + +```text +ERROR: Different counts in data/longerone_R1.fq.gz and data/longerone_R2.fq.gz +# data/longerone_R1.fq.gz: 7 +# data/longerone_R2.fq.gz: 2 +``` + +### Multithreading + +Performance improvement measured on the _MiSeq SOP_ dataset from [mothur](https://mothur.org): + +| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu count ../mothur-sop/*.fastq -t 4` | 142.5 ± 5.8 | 127.3 | 152.3 | 1.00 | +| `seqfu count ../mothur-sop/*.fastq -t 1` | 416.5 ± 15.2 | 397.8 | 440.9 | 2.92 ± 0.16 | +| `seqfu count-legacy ../mothur-sop/*.fastq` | 539.2 ± 16.6 | 519.6 | 577.4 | 3.78 ± 0.19 | + +## Legacy algorithm + +```text +Usage: count-legacy [options] [ ...] + +Options: + -a, --abs-path Print absolute paths + -b, --basename Print only filenames + -u, --unpair Print separate records for paired end files + -f, --for-tag R1 Forward string, like _R1 [default: auto] + -r, --rev-tag R2 Reverse string, like _R2 [default: auto] + -m, --multiqc FILE Save report in MultiQC format + -v, --verbose Verbose output + -h, --help Show this help +``` + +### MultiQC output + +Using the `--multiqc OUTPUTFILE` option it's possible to save a MultiQC compatible file (we recommend to use the *projectname_mqc.tsv* filename format). +After coolecting all the MultiQC files in a directory, using `multiqc -f .` will generate the MultiQC report. +MultiQC itself can be installed via Bioconda with `conda install -y -c bioconda multiqc`. + +To understand how to use MultiQC, if you never did so, check their excellent [documentation](https://multiqc.info). + +### Screenshot + +![Screenshot of ""seqfu count""]({{site.baseurl}}/img/screenshot-count.svg ""SeqFu cat"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/metadata.md",".md","5122","138","--- +layout: default +title: seqfu metadata +parent: Core Tools +--- + +# seqfu metadata + +Given one (or more) directories containing sequencing reads, this tool produces a metadata file by extracting the ID from the filename and optionally adding file paths or read counts. + +## Usage +``` +Usage: + metadata [options] [...] + metadata formats + +Prepare mapping files from directory containing FASTQ files + +Options: + -1, --for-tag STR String found in filename of forward reads [default: _R1] + -2, --rev-tag STR String found in filename of forward reads [default: _R2] + -s, --split STR Separator used in filename to identify the sample ID [default: _] + --pos INT... Which part of the filename is the Sample ID [default: 1] + + -f, --format TYPE Output format: dadaist, irida, manifest,... list to list [default: manifest] + -p, --add-path Add the reads absolute path as column + -c, --counts Add the number of reads as a property column (experimental) + -t, --threads INT Number of simultaneously opened files (legacy: ignored) + --pe Enforce paired-end reads (not supported) + --ont Long reads (Oxford Nanopore) [default: false] + + GLOBAL OPTIONS + --abs Force absolute path + --basename Use basename instead of full path + --force-tsv Force '\t' separator, otherwise selected by the format + --force-csv Force ',' separator, otherwise selected by the format + -R, --rand-meta INT Add a random metadata column with INT categories + + FORMAT SPECIFIC OPTIONS + -P, --project INT Project ID (only for irida) + --meta-split STR Separator in the SampleID to extract metadata, used in MetaPhage [default: _] + --meta-part INT Which part of the SampleID to extract metadata, used in MetaPhage [default: 1] + --meta-default STR Default value for metadata, used in MetaPhage [default: Cond] + + -v, --verbose Verbose output + --debug Debug output + -h, --help Show this help + +``` + +## Output formats + +SeqFu metadata now supports the following output formats: + +1. **manifest**: Used as import manifest for [Qiime2](https://qiime2.org/) artifacts. +2. **qiime1**: Forward-compatible [Qiime1](http://qiime.org/) mapping file. +3. **qiime2**: [Qiime2](https://qiime2.org/) metadata file. +4. **dadaist**: [Dadaist2](https://quadram-institute-bioscience.github.io/dadaist2) compatible metadata. +5. **lotus**: [Lotus](http://lotus2.earlham.ac.uk/) mapping file (tested with Lotus1). +6. **irida**: [IRIDA uploader](https://github.com/phac-nml/irida-uploader) sample sheet. Requires `-P PROJECTID`. +7. **metaphage**: [MetaPhage](https://mattiapandolfovr.github.io/MetaPhage) metadata file. Use `--meta-split`, `--meta-part`, and `--meta-default` to customize a Treatment column. +8. **ampliseq**: [nf-core/ampliseq](https://nf-co.re/ampliseq) metadata file. +9. **rnaseq**: [nf-core/rnaseq](https://nf-co.re/rnaseq) metadata file. +10. **bactopia**: [Bactopia](https://bactopia.github.io/) FOFN (File of File Names) file. +11. **mag**: [nf-core/mag](https://nf-co.re/mag) metadata file. + +## New Features + +- Support for `--format bactopia` to generate Bactopia FOFN files. +- Added `--ont` option for long reads (Oxford Nanopore Technology). +- Enhanced support for various bioinformatics pipelines (ampliseq, rnaseq, mag). + +## Examples + +### Manifest (default) + +```bash +seqfu metadata ./MiSeq_SOP/ +``` + +Output: +``` +sample-id forward-absolute-filepath reverse-absolute-filepath +F3D0 /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D0_S188_L001_R2_001.fastq.gz +F3D1 /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R1_001.fastq.gz /Users/telatin/MiSeq_SOP/F3D1_S189_L001_R2_001.fastq.gz +... +``` + +### Qiime1 mapping file + +```bash +seqfu metadata MiSeq_SOP -f qiime1 --add-path --counts +``` + +Output: +``` +#SampleID Counts Paths +F3D0 7793 F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz +F3D1 5869 F3D1_S189_L001_R1_001.fastq.gz,F3D1_S189_L001_R2_001.fastq.gz +... +``` + +### IRIDA uploader + +```bash +seqfu metadata -f irida -P 123 data/pe/ +``` + +Output: +``` +Sample_Name,Project_ID,File_Forward,File_Reverse +sample1,123,sample1_R1.fq.gz,sample1_R2.fq.gz +sample2,123,sample2_R1.fq.gz,sample2_R2.fq.gz +``` + +### Bactopia FOFN + +```bash +seqfu metadata -f bactopia data/pe/ +``` + +For ONT data, add `--ont` + +Output: +``` +sample runtype r1 r2 +sample1 paired-end /path/to/data/pe/sample1_R1.fq.gz /path/to/data/pe/sample1_R2.fq.gz +sample2 paired-end /path/to/data/pe/sample2_R1.fq.gz /path/to/data/pe/sample2_R2.fq.gz +``` + +## Notes + +- Use `--add-path` to include full file paths in the output (when supported by the format). +- The `--counts` option adds read counts to the output (experimental feature, not supported by all formats). +- Format-specific options (like `--project` for IRIDA) are required for certain output types. +- Use `--verbose` for detailed processing information and `--debug` for troubleshooting. + +For more information on each format and its specific options, please refer to the respective tool's documentation.","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/lanes.md",".md","2363","87","--- +layout: default +title: seqfu lanes +parent: Core Tools +--- + + +# seqfu lanes + +```note +This function was called `merge` in a pre-release. +``` + +*lanes* is one of the core subprograms of *SeqFu*, that allows +to quickly and easily merge Illumina lanes. + +```text +Usage: lanes [options] -o + +A program to merge Illumina lanes for a whole directory. + +Options: + -o, --outdir DIR Output directory + -e, --extension STR File extension [default: .fastq] + -s, --file-separator STR Field separator in filenames [default: _] + --comment-separator STR String separating sequence name and its comment [default: TAB] + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Input + +A directory containing files in the standard Illumina naming scheme, like: +``` +ID1_S99_L001_R1_001.fastq.gz +ID1_S99_L001_R2_001.fastq.gz +ID1_S99_L002_R1_001.fastq.gz +ID1_S99_L002_R2_001.fastq.gz +ID1_S99_L003_R1_001.fastq.gz +ID1_S99_L003_R2_001.fastq.gz +ID1_S99_L004_R1_001.fastq.gz +ID1_S99_L004_R2_001.fastq.gz +ID2_S99_L001_R1_001.fastq.gz +ID2_S99_L001_R2_001.fastq.gz +ID2_S99_L002_R1_001.fastq.gz +ID2_S99_L002_R2_001.fastq.gz +ID2_S99_L003_R1_001.fastq.gz +ID2_S99_L003_R2_001.fastq.gz +ID2_S99_L004_R1_001.fastq.gz +ID2_S99_L004_R2_001.fastq.gz +ID3_S99_L001_R1_001.fastq.gz +ID3_S99_L001_R2_001.fastq.gz +ID3_S99_L002_R1_001.fastq.gz +ID3_S99_L002_R2_001.fastq.gz +ID3_S99_L003_R1_001.fastq.gz +ID3_S99_L003_R2_001.fastq.gz +ID3_S99_L004_R1_001.fastq.gz +ID3_S99_L004_R2_001.fastq.gz +``` + +## Performance + +If compared with an efficient Bash implementation +(as described [here](https://github.com/stephenturner/mergelanes#an-easier-way)), +*SeqFu* is >10X faster. + +| Command | Mean [ms] | Min [ms] | Max [ms] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu merge -o /tmp/ data/lane` | 2.6 ± 0.9 | 1.6 | 10.4 | 1.00 | +| `merge_lanes.sh data/lane/` | 31.8 ± 4.0 | 25.4 | 49.5 | 12.42 ± 4.46 | + +The _merge\_lanes.sh_ script is as follows: +```bash +DIR=$PWD +cd $1 +ls *R1* | cut -d _ -f 1 | sort | uniq \ + | while read id; do \ + cat $id*R1*.fastq.gz > $id.R1.fastq.gz; + cat $id*R2*.fastq.gz > $id.R2.fastq.gz; + done + +cd $DIR/ +rm $1/*.R{1,2}.* +``` + +and the test was performed against the `/data/lane` directory of SeqFu repository +using the [hyperfine](https://github.com/sharkdp/hyperfine) program.","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/grep.md",".md","2793","92","--- +layout: default +title: seqfu grep +parent: Core Tools +--- + + +# seqfu grep + +*grep* is one of the core subprograms of *SeqFu*. + +It can be used to select sequences by their name, comments or +sequence using IUPAC degenerate oligo as query. + +```text +Usage: grep [options] [ ...] + +Print sequences selected if they match patterns or contain oligonucleotides + +Options: + -n, --name STRING String required in the sequence name + -r, --regex PATTERN Pattern to be matched in sequence name + -c, --comment Also search -n and -r in the comment + -f, --full The string or pattern covers the whole name + (mainly used without -c) + -w, --word The string or pattern is a whole word + (only effective with -c, as names do not contain spaces) + -i, --ignore-case Ignore case when matching names (is already enabled with regexes) + -o, --oligo IUPAC Oligonucleotide required in the sequence, + using ambiguous bases and reverse complement + -A, --append-pos Append matching positions to the sequence comment + --max-mismatches INT Maximum mismatches allowed [default: 0] + --min-matches INT Minimum number of matches [default: oligo-length] + -v, --verbose Verbose output + --help Show this help +``` + + +## Get sequences by name + +In a sequence the name, or id, is the string before the first white space +character, while we define as comment all the rest: +```text +>Seq_Name_Here after the name or ID, everything else is the comment +ATTACAAACAGTCGATCGTAGCTAGCTAGCTGATC +``` + + +To extract all the sequences containing ""Here"" in the name: +``` +seqfu grep -n Here file.fasta +``` + +If we also want to extend the search to comments we need to add the `-c` (or `--comment`) switch: +``` +seqfu grep -c -n extend file.fasta +``` + +Finally, [regular expressions](https://www.regular-expressions.info/) +are supported only enabling `-r` (or `--regex`): +``` +seqfu grep -r -n Seq_N..._ file.fasta +``` + + +## Matching patterns in DNA sequences + +A simple text search (even with regular expressions) cannot be +a handy way to identify matches in a DNA/RNA sequence. + +Using the `-o` (`--oligo`) parameter, we scan the sequence for matches +of oligonucleotides supporting [IUPAC degenerate bases](https://www.bioinformatics.org/sms/iupac.html), +supporting **reverse complement** matches and partial matches. + +```text +>Example +CAGATAAAA +``` + +if we scan for `TTTT` we will match the sequence, as it's in the reverse complement strand: +``` +seqfu -o TTTT file.fasta +``` + +We can also use IUPAC bases (N for any base, B for C, G or A...): +``` +seqfu -o TTTTNT file.fasta +``` + +## Screenshot + +![Screenshot of ""seqfu grep""]({{site.baseurl}}/img/screenshot-grep.svg ""SeqFu grep"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/head.md",".md","1943","61","--- +layout: default +title: seqfu head +parent: Core Tools +--- + + +# seqfu head + +*head* is one of the core subprograms of *SeqFu*. + +It will print the first sequences of a FASTX file (like GNU head), but +can be instructed to skip a number of sequences between each printed one. + +```text +Usage: head [options] [ ...] + +Select a number of sequences from the beginning of a file, allowing +to select a fraction of the reads (for example to print 100 reads, +selecting one every 10). + +Options: + -n, --num NUM Print the first NUM sequences [default: 10] + -k, --skip SKIP Print one sequence every SKIP [default: 0] + -p, --prefix STRING Rename sequences with prefix + incremental number + -s, --strip-comments Remove comments + -b, --basename prepend basename to sequence name + -v, --verbose Verbose output + --quiet Don't print warnings + --help Show this help + +Output: + --fasta Force FASTA output + --fastq Force FASTQ output + --sep STRING Sequence name fields separator [default: _] + -q, --fastq-qual INT FASTQ default quality [default: 33]``` +``` + +## Example + +By default the program prints the first 10 sequences of a file (the number +can be changed with `-n` or `--num`). + +Sometimes to have a preview of a file we can add the `--skip` (or `-k` for short) +parameter to take a sequence every _N_. + +The following examples shows the output of `seqfu head -n 10`, and `seqfu head -n 5 -k 4`): + +![Example]({{site.baseurl}}/img/seqfu-head.png) + +## Input and output + +`seqfu head` takes as input one ore _more_ FASTA/FASTQ files (or reads from +the standard input if no filenames are provided, or `-` is added to the list). +The output will be in the same format as the input, unless `--fasta` or `--fastq` +are specified to force a different output. + + +## Screenshot + +![Screenshot of ""seqfu head""](img/screenshot-head.svg ""SeqFu head"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/qual.md",".md","3627","104","--- +layout: default +title: seqfu qual +parent: Core Tools +--- + + +# seqfu qual + +*qual* allows to detect the range of qualities of a FASTQ file, returning the possible encodings. +Can be used to detect the last qualified position (). + + +```text +Usage: qual [options] [...] + +Quickly check the quality of input files returning the detected encoding +and the profile of quality scores. +To read from STDIN, use - as filename. + + -m, --max INT Check the first INT reads [default: 5000] + -l, --maxlen INT Maximum read length [default: 1000] + -k, --skip INT Print one sequence every INT [default: 1] + +Qualified position: + -w, --wnd INT Sliding window size [default: 4] + -q, --wnd-qual FLOAT Minimum quality in the sliding window [default: 30.0] + -z, --min-qual FLOAT Stop the sliding windows when quality is below [default: 18.0] + +Additional output: + --gc Print GC content as extra column + -p, --profile Quality profile per position (will comment the summary lines) + -c, --colorbars Print graphical average quality profile + +Other options: + -v, --verbose Verbose output + -O, --offset INT Quality encoding offset [default: 33] + --help Show this help +``` + +## Example + +Check if a set of files is likely in Illumina 1.8 encoding: + +``` +seqfu qual data/primers/* + +data/primers/16S_R1.fq.gz 7.0 38.0 Sanger;Illumina-1.8; 33.42+/-8.47 249 +data/primers/16S_R2.fq.gz 2.0 38.0 Sanger;Illumina-1.8; 31.96+/-9.53 205 +data/primers/16Snano_R1.fq.gz 7.0 38.0 Sanger;Illumina-1.8; 33.37+/-8.63 246 +data/primers/16Snano_R2.fq.gz 2.0 38.0 Sanger;Illumina-1.8; 32.05+/-9.54 220 +data/primers/art_R1.fq.gz 40.0 40.0 Illumina-1.3;Sanger;Illumina-1.5;Solexa;Illumina-1.8; 40.00+/-0.00 95 +data/primers/art_R2.fq.gz 40.0 40.0 Illumina-1.3;Sanger;Illumina-1.5;Solexa;Illumina-1.8; 40.00+/-0.00 93 +``` + +The artifical datasets (`art*`) were designed to be compatible with most encodings, +while the `16S*` files are real Illumina 1.8 sequences. + +## Output + +For each file a tab separated record is printed: +1. Filename +2. Minimum quality value +3. Maximum quality value +4. Possible encoding (semicolon separated list) +5. Mean, StDev of the quality value +6. Last qualified position +7. GC content (5 decimal positions) if enabled via `--gc` + +## Per base statistics + +With the `--profile` option tabular overview of the quality scores per +nucleotide position of the read is printed: + +```text +#data/primers/16Snano_R1.fq.gz 40.0 71.0 Sanger;Illumina-1.8; 66.37+/-8.63 +#Pos Min Max Mean StDev Skewness +0 27.0 34.0 33.95 0.50 -12.36 +1 27.0 34.0 33.97 0.46 -14.78 +2 11.0 34.0 33.73 2.28 -9.08 +3 23.0 34.0 33.92 0.76 -13.09 +4 31.0 34.0 33.99 0.20 -15.20 +5 28.0 38.0 37.76 0.86 -7.20 +6 10.0 38.0 36.26 3.98 -4.89 +... +298 7.0 37.0 26.34 10.34 -0.58 +299 7.0 37.0 25.62 11.23 -0.55 +300 7.0 37.0 21.29 9.26 -0.09 +``` + +## Graphical summary + +With the `--colorbar` option a graphical (Unicode) colored histogram of the _average_ +quality _per base position_ is printed after each file. + +![View]({{site.baseurl}}/img/qual.png) + + +## Use with DADA2 + +The last column of the tabular report (_last qualified position_), can be used to +automatically detect the truncating position when using [DADA2](https://benjjneb.github.io/dada2/tutorial_1_8.html). +[Dadaist](https://quadram-institute-bioscience.github.io/dadaist2/) +uses *SeqFu* to automatically detect the qualified region.","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/derep.md",".md","4936","75","--- +layout: default +title: seqfu derep +parent: Core Tools +--- + + +# seqfu derep + +*derep* is one of the core subprograms of *SeqFu*, that allows the dereplication of FASTA and FASTQ files. +Dereplication, in R. C. Edgard [words](https://drive5.com/usearch/manual/dereplication.html) is *A rather obscure name for finding the set of unique sequences. Or, equivalently, the process of finding duplicated (replicate) sequences.* + +In simple words, given a FASTA file, only unique sequences will be printed in the output. A core feature is printing the number of identical sequences found in the original dataset. + +Dereplication is a step commonly used in NGS sequencing of amplicons, to reduce the computational time dedicated to the analysis of each representative sequence, and some tools will require dereplicated sequences as input +(e.g. [USEARCH](https://rcedgar.github.io/usearch12_documentation/)). + + + +```text +Usage: derep [options] [ ...] + +Options: + -k, --keep-name Do not rename sequence, but use the first sequence name + -i, --ignore-size Do not count 'size=INT;' annotations (they will be stripped in any case) + -m, --min-size=MIN_SIZE Print clusters with size equal or bigger than INT sequences [default: 0] + -p, --prefix=PREFIX Sequence name prefix [default: seq] + -5, --md5 Use MD5 as sequence name (overrides other parameters) + -j, --json=JSON_FILE Save dereplication metadata to JSON file + -s, --separator=SEPARATOR Sequence name separator [default: .] + -w, --line-width=LINE_WIDTH FASTA line width (0: unlimited) [default: 0] + -l, --min-length=MIN_LENGTH Discard sequences shorter than MIN_LEN [default: 0] + -x, --max-length=MAX_LENGTH Discard sequences longer than MAX_LEN [default: 0] + -c, --size-as-comment Print cluster size as comment, not in sequence name + --add-len Add length to sequence + -v, --verbose Print verbose messages + -h, --help Show this help +``` + +## Size values + +By default the program will add the number of identical sequences found to the sequence name, as USEARCH does: +For example, if a sequence is found 18.335 times in the input file, the output will contain a sequence with "";size=18335"" in the name (unless `--ignore-size` is passed). The term ""size"" can be confusing, but it was adopted for compatibility with USEARCH/VSERACH. + +``` +>seq.1;size=18335 +CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC +>seq.2;size=4085 +CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC +>seq.3;size=2453 +CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC +``` + +To keep the size separate from the sequence name it's possible to used `-c` (`--size-as-comment`): +``` +>seq.1 size=18335 +CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTACAGTATTCTTTTTGCCAGCGCTTAATTGCGCGGCGAAAAAACCTTACACACAGTGTTTTTTGTTATTACAAGAACTTTTGCTTTGGTCTGGACTAGAAATAGTTTGGGCCAGAGGTTTACTGAACTAAACTTCAATATTTATATTGAATTGTTATTTATTTAATTGTCAATTTGTTGATTAAATTCAAAAAATCTTCAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGC +>seq.2 size=4085 +CTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTGAAGTTTAACTCAGAGGGTTGTAGCTGGCTCCTCCAAGAGCATGTGCACGCCCTTTGTCTTTACTCTTTTCCACCTGTGCACCTTTTGTAGACCATGAGTGAACTCTCGAGAGCGTTGGCAACGACGTGATCGGTTTGGGGATTTGCGTTCAGCTTTCCCTGTAGCTCGTGGTTTATGTCTTATAAACTCTATAGTCTGTTTTGAATGTCTTATGGGTTTTGCGCTGTAATGGTGCGACCTTTATAAACTATACAACTTTTAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGC +>seq.3 size=2453 +CTTGGTCATTTAGAGGAAGTAAGAGAGAAATGTATAAACTCATAATTGACGAATGATAATTGTTATTGAAGTTTTTGTAAAGGGGCTTCTTTATGAATAAGGGATACACGTTTGACGATATGATTAATACCATGATGCCCCTGGCCCTTTGACGGCTCGGCAAAGGGTGAAGGAATTTACTGCACGGTCAGGCCCTCGTCGCATCGATGAAGAACGCAGC +``` + +## Summing dereplicated outputs + +If the input files were already dereplicated printing the ""size"" of the cluster, `derep` will sum the +size values. + +This is a feature that to our knowledge is only available in SeqFu and allows to process in parallel multiple samples +and generating a single ""dereplicated file"" at the end, propagating the correct cluster sizes. + + +## Screenshot + +![Screenshot of ""seqfu derep""]({{site.baseurl}}/img/screenshot-derep.svg ""SeqFu derep"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/merge.md",".md","1828","57","--- +layout: default +title: seqfu merge +parent: Core Tools +--- + + +# seqfu merge + +```note +Function under development: APIs and default parameters are likely going to change. + +This is why you don't see it listed in the main screen of SeqFu (yet). +``` + +A tool to naively merge paired end reads preserving the quality of the forward read. + +``` +Usage: merge [options] -1 File_R1 + + Options: + -1, --R1 FILE First paired-end file + -2, --R2 FILE Second paired-end file, can be automatically inferred + -i, --minid FLOAT Minimum identity [default: 0.80] + -m, --minlen INT Minimum overlap [default: 20] + --accepted-identity FLOAT Accept fusion when identity is above FLOAT [default: 0.96] + -v, --verbose Print verbose messages + -h, --help Show this help +``` + +## Merging reads + +There are several tools to merge overlapping reads, and some are better than others. +In particular if we use tools that correcly interpret the _Phred quality scores_, then +tools like USEARCH and VSEARCH are correcly recalibrating the quality of the overlapping +bases. + +Some tools, however, are expeting quality scores that are more likely produced by a +sequencing tool. This experimental module of SeqFu joins the reads in a different way: +takes the forward read _as is_, and extends it with the (reverse complemented) missing +part taken from the R2. + +## Potential uses + +This tool can be used to estimate the overlapping size or the ""mergeability"" of reads +before using the tools of choice. + +For example: +``` +seqfu merge -1 reads_R1.fq | seqfu head -n 200 | seqfu stats -n +``` + +## Output +The merged reads are printed to the standard output. + +Also this is somehow unusual compared with most mergin tools, but allows streaming which +is a core feature in SeqFu tools.","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/tabulate.md",".md","2849","99","--- +layout: default +title: seqfu tabulate +parent: Core Tools +--- + + +# seqfu tabulate + +```note +This tool has been introduced with seqfu 1.2.2 +``` + +This program converts a sequence file (FASTA or FASTQ) to a tabular file, +and vice versa. + +Several Unix tools can process a stream of information line-by-line, and +tabular file can be easily modified and filtered piping serveral programs. + +This tool will allow to **tabulate** (convert to TSV) and +**detabulate** (convert to FASTX) sequences. + +``` +Usage: tabulate [options] [] + +Convert FASTQ to TSV and viceversa. Single end is a 4 columns table (name, comment, seq, qual), +paired end have 4 columns for the R1 and 4 columns for the R2. +Paired end reads need to be supplied as interleaved. + + +Options: + -i, --interleaved Input is interleaved (paired-end) + -d, --detabulate Convert TSV to FASTQ (if reading from file is autodetected) + -c, --comment-sep CHAR Separator between name and comment (default: tab) + -s, --field-sep CHAR Field separator (default: tab) + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Tabular format + +The conversion works as follows: +* FASTA files are converted to a 3 columns table: name, comments and sequence +* Single-End FASTQ files are converted to a 4 columns table: name, comments, sequence and quality +* Paired-End FASTQ (interleaved) files are converted to 8 colums table: R1 name, comments, sequence and quality and R2 name, comments, sequence and quality + +To allow an efficient use of streams, paired-end datasets need to be interleaved (see: _seqfu interleave_). + +To make an example this FASTQ file: +``` +@read_1 tag=A +ATTACAATTACAATTACAA ++ +EAFFFFFABBBAAAAAAAC +@read_2 tag=B +GGACAGAATTACAATTTTT ++ +FFFFFFFFABBBAAAAAAA +``` +will become: +``` +read_1 tag=A ATTACAATTACAATTACAA EAFFFFFABBBAAAAAAAC +read_2 tag=B GGACAGAATTACAATTTTT FFFFFFFFABBBAAAAAAA +``` + + +## Conversions + + +### Sequence to table +A single file can be converted to tabular format. + +*NOTE*: If the file is automatically detected as interleaved (the first and second read +have the same name) you can omit `-i` (or `--interleave`), but we recommend to use it to make the command clearer. + +``` +seqfu tabulate file.fastq | gzip -c > tabular.tab.gz +``` + + +### Table to sequences +When a file is provided, the input format is automatically detected. Otherwise specify `-d` (or `--detabulate` to convert from table to FASTX). + +``` +seqfu tabulate file.tab > sequences.fq +``` +or, via _stream_: +``` +cat file.tab.gz | seqfu tabulate --detabulate > sequences.fq +``` + +### Pipeline + +We designed the tool to provide a simple way to make ad hoc modifications via tabular lines, so a full workflow could be: + +``` +seqfu interleave ... | seqfu tabulate | CUSTOM_STEP | seqfu tabulate --detabulate | seqfu deinterleave -o basename - +``` +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/check.md",".md","5231","139","--- +layout: default +title: seqfu check +parent: Core Tools +--- + +# seqfu check + +```note +**EXPERIMENTAL**: Introduced in SeqFu 1.15, updated with --deep in 1.18 (see below). +In SeqFu 2.0 a strict behaviour will be used by default, see **fu-pecheck** and **fu-secheck**. +``` + +Evaluates the integrity of DNA FASTQ files. + +```text +Usage: seqfu check [options] [] + seqfu check [options] --dir + + Check the integrity of FASTQ files, returns non zero + if an error occurs. Will print a table with a report. + + Input is a single dataset: + the forward read file + the reverse read file + or a directory of FASTQ files (--dir): + the directory containing the FASTQ files + + Options: + -d, --deep Perform a deep check of the file and will not + lsupport multiline Sanger FASTQ [default: false] + -n, --no-paired Disable autodetection of second pair + -s, --safe-exit Exit with 0 even if errors are found + -q, --quiet Do not print infos, just exit status + -v, --verbose Verbose output + -t, --thousands Print numbers with thousands separator + --debug Debug output + -h, --help Show this help +``` + +### Integrity check + +:warning: If not using `--deep`, the file is considered valid if `seqfu cat $INPUT > $OUTPUT` would produce a valid file (i.e. if an error is detected at the 100-th sequence, the file +would be considered valid reporting 99 as total sequences) + +A single FASTQ file is considered valid if: + +* each record has the same sequence and quality length +* only A,C,G,T,N characters are present in the sequence + +A paired-end set of FASTQ files is considered valid if: + +* each file is individually valid +* the two files have the same number of sequences +* the first and last sequence of both files has the same name (the last three characters are ignored if the remaining sequence name is greater than 4 characters) +* the first and last sequence of the two files are not identical (R1 != R2) + +### Deep check + +If you are parsing NGS files, i.e. FASTQ files, with four lines per record and you expect them to be accepted by any program, use `--deep`. + +### Usage + +To test a single file: + +```bash +seqfu check test_file.fq.gz +``` + +To test a pair of files: + +```bash +seqfu check test_R1.fq.gz [test_R2.fq.gz] +``` + +Note that if supplying a single file but a matching pair is detected (e.g. `test_R1.fq.gz` is supplied and `test_R2.fq.gz` is found), the check will be performed on both files. + +To test all files in a directory: + +```bash +seqfu check --dir test_dir +``` + +#### Other options + +* `--no-paired` disables the autodetection of the second pair (i.e. force single end check) +* `--thousands` will add a thousands separator to the output +* `--quiet` will not print data, but only the exit status will be used +* `--verbose` will print more information (including processing speed) +* `--debug` will print debug information +* `--safe-exit` will always exit with 0, even if errors are found (useful in pipelines) + +### Exit status + +If an error is identified in at least one file, the program will exit with non zero status, +unless the `--safe-exit` option is used. + +### Output + +The output is a table with the following columns: + +1. Status (`OK` or `ERR`) +2. Library type (`SE` or `PE`) +3. Filename (the path to the first pair, if `PE`) +4. Number of sequences counted (if `PE`: number of sequences in **both** files) or `-` if the dataset is not valid +5. Number of bases (if `PE`: total number of bases in **both** files) or `-` if the dataset is not valid +6. Number of errors +7. List of detected errors (if any) + +#### Example + +Example of output for a directory containing 3 Paired End datasets: + +```text +OK PE /tmp/data/16S_R1.fq.gz 12274 3694474 0 +OK PE /tmp/data/16Snano_R1.fq.gz 468 140868 0 +OK PE /tmp/data/illumina_1.fq.gz 14 1260 0 +``` + +Example of errors (can be reproduced using the *data* directory of the repository) + +```bash +seqfu check --dir data/primers +``` + +```text +OK SE data/primers/16S_merge.fq.gz 6137 2596981 0 +OK SE data/primers/16S_vsearch_merge.fq.gz 3935 1818111 0 +ERR SE data/primers/artificial.fq.gz - - 2 Invalid character in sequence: < > in R2.REV+.middle; +OK SE data/primers/its-merge.fq.gz 7299 1504898 0 +OK SE data/primers/se.fq.gz 234 70434 0 +OK SE data/primers/small.fq 4 360 0 +OK PE data/primers/16S_R1.fq.gz 12274 3694474 0 +OK PE data/primers/16Snano_R1.fq.gz 468 140868 0 +ERR PE data/primers/art_R1.fq.gz 7 - 5 R2=Invalid character in sequence: < > in R2.REV+.middle;;First sequence names do not match (R1.startFOR+, R2.startREV+);Last sequence names do not match (R1.FOR1+.start-middle, ); +OK PE data/primers/its_R1.fq.gz 16000 3387804 0 +OK PE data/primers/itsfilt_R1.fq.gz 15618 3272396 0 +OK PE data/primers/pico_R1.fq.gz 24 7224 0 +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/tofasta.md",".md","4466","144","# seqfu tofasta + +Converts various sequence file formats to FASTA format. + +```note +Introduced in SeqFu 1.23.0 +``` + +A versatile format converter supporting multiple bioinformatics file formats including +sequence alignments, genome annotations, and assembly graphs. The tool automatically +detects the input format and converts sequences to standard FASTA format. + +Replicates the approach of [any2fasta](https://github.com/tseeman/any2fasta), but it's faster. + +```text +Usage: tofasta [options] ... + +Convert various sequence formats to FASTA format. + +Options: + -n, --replace-iupac Replace non-IUPAC characters with 'N' + -l, --to-lowercase Convert sequences to lowercase + -u, --to-uppercase Convert sequences to uppercase + -o, --output FILE Write output to FILE (default: stdout) + Note: checks for duplicate IDs across all files + -v, --verbose Print progress information to stderr + -h, --help Show this help +``` + +## Supported Formats + +`seqfu tofasta` automatically detects and converts the following formats: + +| Format | Description | Notes | +|--------|-------------|-------| +| FASTA | Standard FASTA format | Pass-through with optional transformations | +| FASTQ | Sanger, Illumina, Solexa | Quality scores are discarded | +| GenBank | NCBI GenBank flat file | Extracts sequences from ORIGIN section | +| EMBL | EMBL-Bank format | Extracts sequences from SQ section | +| GFF | Generic Feature Format | Extracts sequences after `##FASTA` directive | +| GFA | Graphical Fragment Assembly | Extracts sequences from S (segment) lines | +| Clustal | Clustal W alignment | Preserves gaps in sequences | +| Stockholm | Stockholm alignment | Converts '.' gaps to '-' | + +## Options + + +**`-n, --replace-iupac`** +Replaces non-standard IUPAC characters with 'N'. Standard IUPAC codes (A, T, G, C, N) +are preserved, while ambiguous codes (R, Y, W, S, K, M, etc.) are replaced with 'N'. + +**`-l, --to-lowercase`** +Converts all sequence characters to lowercase. Useful for soft-masking or +compatibility with tools that expect lowercase input. + +**`-u, --to-uppercase`** +Converts all sequence characters to uppercase. Takes precedence over `-l` if both +are specified. + +**`-o, --output FILE`** +Writes all sequences to a single output file instead of stdout. When using this option, +the tool performs duplicate ID checking across all input files and will exit with an +error if duplicate sequence IDs are found. + +**`-v, --verbose`** +Prints progress information to stder + +## Examples + +### Basic Format Conversion + +Convert a GenBank file to FASTA: + +```bash +seqfu tofasta genome.gbk > genome.fasta +``` + +Convert a FASTQ file (quality scores are discarded): + +```bash +seqfu tofasta reads.fastq.gz > reads.fasta +``` + +### Multiple Files + +Process multiple files and combine into one FASTA file: + +```bash +seqfu tofasta -o combined.fasta file1.gbk file2.gff file3.fastq.gz +``` + +Replace ambiguous IUPAC codes with N: + +```bash +seqfu tofasta -n -u sequences.fasta > clean.fasta +``` + + +### Input Handling + +- **Gzip Support**: All input files can be gzip-compressed (`.gz` extension) +- **No STDIN**: Currently, `tofasta` requires file arguments and does not support reading from standard input +- **Format Detection**: File format is automatically detected from content, not file extension +- **Error Handling**: The tool is strict and will exit with an error on unknown or malformed formats + +### Duplicate ID Detection + +When using `-o/--output`, the tool checks for duplicate sequence IDs across all input files: + +```bash +# This will fail if seq1.gbk and seq2.gbk contain sequences with the same ID +seqfu tofasta -o combined.fasta seq1.gbk seq2.gbk +``` + +Error message example: +``` +ERROR: Duplicate sequence ID found: NZ_12345 + First occurrence in a previous file + Second occurrence in: seq2.gbk +``` + +### Format-Specific Behavior + +**GenBank/EMBL**: +- Extracts accession number as sequence ID +- Extracts sequence from ORIGIN/SQ section +- Handles multiple records in a single file + +**GFF**: +- Only processes sequences after `##FASTA` directive +- Ignores feature annotations +- Preserves sequence IDs from FASTA headers + +**Clustal/Stockholm**: +- Preserves alignment gaps in output +- Concatenates sequence fragments if alignment spans multiple blocks +- Stockholm '.' gaps are converted to '-' + +**GFA**: +- Only processes S (segment) lines +- Uses segment name as sequence ID +- Ignores paths, links, and other graph elements + +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/stats.md",".md","6692","161","--- +layout: default +title: seqfu stats +parent: Core Tools +--- + + +# seqfu stats + +*stats* is one of the core subprograms of *SeqFu*. + +```note +Version prior to v1.22.1 were calculatin auN incorrectly +``` + +```text +Usage: stats [options] [ ...] + +Options: + -a, --abs-path Print absolute paths + -b, --basename Print only filenames + -n, --nice Print nice terminal table + -j, --json Print json (EXPERIMENTAL) + -s, --sort-by KEY Sort by KEY from: filename, counts, n50, tot, avg, min, max + descending for values, ascending for filenames [default: none] + -r, --reverse Reverse sort order + -t, --thousands Add thousands separator (only tabbed/nice output) + --csv Separate output by commas instead of tabs + --gc Also print %GC + --multiqc FILE Saves a MultiQC report to FILE (suggested: name_mqc.txt) + --precision INT Number of decimal places to round to [default: 2] + --noheader Do not print header + -v, --verbose Verbose output + -h, --help Show this help +``` + +### Sorting + +```note +Sorting added in SeqFu 1.11. +``` + +To sort by filename (ascending alphabetical order) add `--sort filename`. +Numerical values are sorted from the largest (descending), supported values are: +* *n50*, *n75* or *N90* +* *count* or *counts* (number of reads) +* *sum* or *tot* (total bases) +* *min* or *minimum* (minimum length) +* *max* or *maximum* (maximum length) +* *avg* or *mean* (average length) +* *aun* (area under the Nx curve) + +**NOTE** Specifying an invalid key will result in unsorted results with a warning, +but in future releases this might throw an error. + +### Example output + +Output is a TSV text with three columns (or CSV using `--csv`): + +```text +File,#Seq,Sum,Avg,N50,N75,N90,Min,Max +data/filt.fa.gz,78730,24299931,308.6,316,316,220,180,485 +``` + +### Screen friendly output + +When using `-n` (`--nice`) output: + +```text +seqfu stats data/filt.fa.gz -n +┌─────────────────┬───────┬──────────┬───────┬─────┬─────┬─────┬───────┬─────┬─────┐ +│ File │ #Seq │ Total bp │ Avg │ N50 │ N75 │ N90 │ auN │ Min │ Max │ +├─────────────────┼───────┼──────────┼───────┼─────┼─────┼─────┼───────┼─────┼─────┤ +│ data/filt.fa.gz │ 78730 │ 24299931 │ 308.6 │ 316 │ 316 │ 220 │ 0.385 │ 180 │ 485 │ +└─────────────────┴───────┴──────────┴───────┴─────┴─────┴─────┴───────┴─────┴─────┘ +``` + + +## MultiQC output + +Using the `--multiqc OUTPUTFILE` option it's possible to save a MultiQC compatible file (we recommend to use the *projectname_mqc.tsv* filename format). +After coolecting all the MultiQC files in a directory, using `multiqc -f .` will generate the MultiQC report. +MultiQC itself can be installed via Bioconda with `conda install -y -c bioconda multiqc`. + +To understand how to use MultiQC, if you never did so, check their excellent [documentation](https://multiqc.info). + +## Legacy + +The pre 1.11 version of the statistics has been made available via `seqfu oldstats`. +There are no breaking changes at the moment, and an expanded set of tests ensures +the compatibility not only of the metrics (unchanged) but also of the output (now +supporting sorting options). + + +## Benchmark + +A similar functionality is provided by `SeqKit`, so we compared the performance of +SeqFu with +[SeqKit](https://bioinf.shenwei.me/seqkit/) and +[n50](https://metacpan.org/pod/release/PROCH/Proch-N50-1.3.0/bin/n50), +both available from bioconda. +We used a Linux Virtual Machine running Ubuntu 18.04, with 8 cores and 64 Gb of RAM for the test, +with Miniconda (4.9.2) to install the required tools. + +:warning: SeqKit, by default, omits N50 calculation, that is a core feature (always enabled) in SeqFu. +The correct comparison is thus between `seqfu stats` and `seqkit stats --all`. + +Speed evaluate with +[hyperfine](https://github.com/sharkdp/hyperfine), +peak memory usage with this +[bash script](https://gist.github.com/MattForshaw/86b82b6c09bdbfce5ff5ee570e8a8bef). + +As dataset we used the Human Genome (see [this benchmark page](https://bioinf.shenwei.me/seqkit/benchmark/)), +which contains few large sequences, and the reference genome of the gastrointestinal tract, which is composed by many +short sequences instead. + +The test can be replicated with these commands: +```bash +# Download tools (can be done in a new environment) +conda install -c conda-forge -c bioconda hyperfine n50=1.3.0 seqkit=0.16.0 seqfu=0.9.6 + +# Download datasets: many short sequences and few large sequences +wget http://downloads.hmpdacc.org/data/reference_genomes/body_sites/Gastrointestinal_tract.nuc.fsa +wget ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz + +# Compare execution times +FILE1=Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz +FILE2=Gastrointestinal_tract.nuc.fsa + +for FILE in $FILE1 $FILE2; do + hyperfine --export-markdown stat_$(basename $FILE | cut -f1 -d.).md --warmup 1 --min-runs 3 \ + ""seqfu stats $FILE"" \ + ""seqkit stats $FILE"" \ + ""seqkit stats --all $FILE"" \ + ""n50 -x $FILE"" +done +``` + +The result, for the **Human Genome** (few large sequences), has been: + +| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu stats $FILE` | 27.420 ± 0.349 | 27.090 | 27.785 | 1.00 | +| `seqkit stats $FILE` :warning: | 116.693 ± 0.236 | 116.512 | 116.960 | 4.26 ± 0.05 | +| `seqkit stats --all $FILE` | 120.435 ± 0.434 | 120.054 | 120.907 | 4.39 ± 0.06 | +| `n50 -x $FILE` | 34.888 ± 0.628 | 34.167 | 35.316 | 1.27 ± 0.03 | + +For the **Gastrointestinal reference genomes** (many short sequences): + +| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu stats $FILE` | 6.885 ± 0.307 | 6.602 | 7.211 | 1.82 ± 0.09 | +| `seqkit stats $FILE` :warning: | 3.793 ± 0.082 | 3.699 | 3.854 | 1.00 | +| `seqkit stats --all $FILE` | 7.667 ± 0.081 | 7.583 | 7.746 | 2.02 ± 0.05 | +| `n50 -x $FILE` | 76.377 ± 1.990 | 74.891 | 78.638 | 20.14 ± 0.68 | + + +## Screenshot + +![Screenshot of ""seqfu stats""]({{site.baseurl}}/img/screenshot-stats.svg ""SeqFu stats"") +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/view.md",".md","3116","92","--- +layout: default +title: seqfu view +parent: Core Tools +--- + + +# seqfu view + +*view* is one of the core subprograms of *SeqFu*. + +It can be used to visually inspect a FASTQ file printing +colored bars for quality scores and highlighting oligonucleotide +matches. + +```text +Usage: view [options] [] + +View a FASTA/FASTQ file for manual inspection, allowing to search for +an oligonucleotide. + +Options: + -o, --oligo1 OLIGO Match oligo, with ambiguous IUPAC chars allowed + (rev. compl. search is performed), color blue + -r, --oligo2 OLIGO Second oligo to be scanned for, color red + -q, --qual-scale STR Quality thresholds, seven values + separated by columns [default: 3:15:25:28:30:35:40] + + --match-ths FLOAT Oligo matching threshold [default: 0.75] + --min-matches INT Oligo minimum matches [default: 5] + --max-mismatches INT Oligo maxmimum mismataches [default: 2] + --ascii Use simple ASCII chars instead of UNICODE to + render the quality values + -Q, --qual-chars Show quality characters instead of bars + -n, --nocolor Disable colored output + --verbose Show extra information + -h, --help Show this help +``` + +## Example output + +The quality scores are rendered as colored bars (grey, red, yellow, green) of different heights. +Matching oligos are rendered as blue arrows (forward) or red arrows (reverse). + +![Screenshot of ""seqfu view, action""]({{site.baseurl}}/img/screenshot-view-example.svg ""SeqFu view example"") + + +## Important hints + +### Disabling wordwrap + +_SeqFu view_ is designed for a manual inspection, and thus it's very convenient to pipe the output to +`less` to avoid being misled by word-wraps: + +```bash +seqfu view sequence.fq | less -SR +``` + +(in `less`: `-S` prevents word-wrap, and `-R` will preserve the colored output) + +### Encoding of ""graphical"" bars + +The _graphical_ rendering of the quality values is done using Unicode characters (UTF-8 encoding), +thus requiring both the host system and the terminal emulator to support UTF-8. A simple test +to check if your terminal supports Unicode is to type: + +```bash +echo -e '\xe2\x82\xac' +``` + +If you see the Euro character (€) then your terminal fully supports UTF-8. If not, you can use +`--ascii` or `--qual-chars`. + +The following screenshot shows how quality scores are rendered using the different options: + +* Default view with quality scale + +![Screenshot: Quality scale""]({{site.baseurl}}/img/screenshot-view-qual.svg ""SeqFu view: quality scale"") + +* Graphical representation of the quality with ASCII characters + +![Screenshot: Quality scale in ASCII]({{site.baseurl}}/img/screenshot-view-qual-ascii.svg ""Qualities in ASCII chars"") + +* Quality encoded as in the FASTQ file, but colored + +![Screenshot: Quality scale as in FASTQ]({{site.baseurl}}/img/screenshot-view-qual-raw.svg ""Qualities as encoded in FASTQ"") + +## Screenshot + +![Screenshot of ""seqfu view, help""]({{site.baseurl}}/img/screenshot-view.svg ""SeqFu view"") + +","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/deinterleave.md",".md","3401","88","--- +layout: default +title: seqfu deinterleave +parent: Core Tools +--- + + +# seqfu deinterleave + +*deinterleave* (or *dei*) is one of the core subprograms of *SeqFu*. +It's used to produce two separate FASTQ files from an interleaved file. + +```text +ilv: interleave FASTQ files + + Usage: dei [options] -o basename + + -o --output-basename ""str"" save output to output_R1.fq and output_R2.fq + -f --for-ext ""R1"" extension for R1 file [default: _R1.fq] + -r --rev-ext ""R2"" extension for R2 file [default: _R2.fq] + -c --check enable careful mode (check sequence names and numbers) + -v --verbose print verbose output + + -s --strip-comments skip comments + -p --prefix ""string"" rename sequences (append a progressive number) + +notes: + use ""-"" as input filename to read from STDIN + +example: + + dei -o newfile file.fq +``` + + +### Streaming + +If a program produce an interleaved output, `seqfu deinterleave` can be used in a pipe (specifying ""-"" as input): + +```bash +fu-primers -1 file_R1.fq -2 file_R2.fq | seqfu deinterleave -o fileNoPrimers - +``` + + +## What are interleaved files? + +[Paired end sequences](https://www.illumina.com/science/technology/next-generation-sequencing/plan-experiments/paired-end-vs-single-read.html) can be stored in two separate files +(usually denoted with the **_R1** and **_R2** strings) or in a single sequence where each sequence pair is +stored as two subsequent sequences. + +A simple example is depicted below: + +```text +======================================================================= +File_R1.fq File_R2.fq Interleaved.fq +======================================================================= + + +@seq1 @seq1 @seq1 +TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG ++ + + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII +@seq2 @seq2 @seq1 +GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC ++ + + +IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII +@seq3 @seq3 @seq2 +AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA ++ + + +IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII + @seq2 + TTTTTTTTTTTTTTTTTTT + + + IIIIIIIIIIIIIIIIIII + @seq3 + AGAGTGTCTGATAGCA + + + IIIIIIIIIIIIIIII + @seq3 + GATAGCAG + + + IIIIIIII +``` + + +## Screenshot + +![Screenshot of ""seqfu deinterleave""]({{site.baseurl}}/img/screenshot-deinterleave.svg ""SeqFu deinterleave"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/sort.md",".md","618","28","--- +layout: default +title: seqfu sort +parent: Core Tools +--- + + +# seqfu sort + +*sort* is one of the core subprograms of *SeqFu*, that allows +sorting a FASTA/FASTQ file by sequence size. + +```text +Usage: sort [options] [ ...] + + Sort sequences by size printing only unique sequences + +Options: + -p, --prefix STRING Sequence prefix + -s, --strip-comments Remove sequence comments + --asc Ascending order + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Screenshot + +![Screenshot of ""seqfu sort""]({{site.baseurl}}/img/screenshot-sort.svg ""SeqFu sort"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/tools/rotate.md",".md","1767","92","--- +layout: default +title: seqfu rotate +parent: Core Tools +--- + + + +# seqfu rotate + +Rotate a sequence setting a new starting position, using +a new position or an oligonucleotide. + +Introduced with SeqFu 1.8.6. + +```text +sage: + fu-rotate [options] -i POS [...] + fu-rotate [options] -m STR [...] + + Rotate the sequences of one or more sequence files using + coordinates or motifs. + + Position based: + -i, --start-pos POS Restart from base POS, where 1 is the first base [default: 1] + + Motif based: + -m, --motif STR Rotate sequences using motif STR as the new start, + where STR is a string of bases + -s, --skip-unmached If a motif is provided, skip sequences that do not + match the motif + -r, --revcomp Also scan for reverse complemented motif + + Other options: + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Examples + +Given an input file with a single sequence: + +```text +>polyA +ACACGTACTACTGAAAAAAAAAACTGCTACTA +``` + +### Rotate by new position + +```bash +seqfu rotate -i 14 data/homopolymer.fa +``` + +Output: + +```text +>polyA +AAAAAAAAAACTGCTACTAACACGTACTACTG +``` + +### Rotate by oligonucleotide + +:warning: rotation by oligo will only produce an output if the match is unique + +```bash +seqfu rotate -m AAAAAAAAAA data/homopolymer.fa +``` + +Output: + +```text +>polyA +AAAAAAAAAACTGCTACTAACACGTACTACTG +``` + + +### Rotate by oligonucleotide (also in reverse) + +```bash +seqfu rotate -r -m GTTTTTTTTTT data/homopolymer.fa +``` + +Output: + +```text +>polyA +GTTTTTTTTTTCAGTAGTACGTGTTAGTAGCA +``` + +## Screenshot + +![Screenshot of ""seqfu rotate""]({{site.baseurl}}/img/screenshot-rotate.svg ""SeqFu rotate"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-primers.md",".md","1367","34","--- +layout: default +title: fu-primers +parent: Utilities +--- + + +# fu-primers + +A program to remove primers from the raw output (FASTQ) +of amplicons, +allowing IUPAC degenerate bases and checking for +multiple occurrences (dimers/concatamers). + +```text +Usage: fu-primers [options] -1 [-2 ] + + This program currently only supports paired-end Illumina reads. + + Options: + -1 --first-pair First sequence in pair + -2 --second-pair Second sequence in pair (can be guessed) + -f --primer-for FOR Sequence of the forward primer [default: CCTACGGGNGGCWGCAG] + -r --primer-rev REV Sequence of the reverse primer [default: GGACTACHVGGGTATCTAATCC] + -m --min-len INT Minimum sequence length after trimming [default: 50] + --primer-thrs FLOAT Minimum amount of matches over total length [default: 0.8] + --primer-mismatches INT Maximum number of missmatches allowed [default: 2] + --primer-min-matches INT Minimum numer of matches required [default: 8] + --primer-pos-margin INT Number of bases from the extremity of the sequence allowed [default: 2] + --pattern-R1 Tag in first pairs filenames [default: auto] + --pattern-R2 Tag in second pairs filenames [default: auto] + -v --verbose Verbose output + -h --help Show this help +``` ","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-shred.md",".md","4492","112","--- +layout: default +title: fu-shred +parent: Utilities +--- + + +# fu-shred + + +```note +Since 1.18 paired end support was enabled +``` + +A program to systematically shotgun a reference +(i.e. this does **not** simulate +a random shotgun library preparation, but produce +reads of length _L_ sliding +over the reference chromosomes at a step _S_). + +This tool is to test the effect of read size alone on +alignment and classification +methods, and was introduced in SeqFu 1.4. + +```text +Usage: fu-shred [options] [...] + + Systematically produce a ""shotgun"" of input sequences. Can read from standard input. + + Options: + -l, --length INT Segment length [default: 100] + -s, --step INT Distance from one segment start to the following [default: 10] + -q, --quality INT Quality (constant) for the segment, if -1 is + provided will be printed in FASTA [default: 40] + -r, --add-rc Print every other read in reverse complement + -b, --basename Prepend the file basename to the read name + --split-basename STRING Split the file basename at this character [default: .] + --prefix-separator STRING Join the basename with the rest of the read name with this [default: _] + -f, --frag-len INT Total fragment length [default: 500] + -o, --out-prefix STR If specified, will run in paired end mode, and will output two files + with this prefix, one for each end. If not specified, will output + to STDOUT in single end mode. + + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Input + +One or more FASTA or FASTQ files. By default will read from STDIN. + +## Parameters + +Main parameters: + +* the desired sequence length with `--length INT` +* the distance between the starting site of each read, with `--step INT` +* the quality value of each base, with `--quality INT` (if you supply **-1**, the output will be in FASTA format) + +If processing multiple files, it can be convenient to prepend the file basename with `--basename`. The basename +will be split at the first `.`, but this can be changed with `--split-basename STR/CHAR`. + +If a mix of forward and reverse reads is required, `--add-rc` will reverse complement every other read. If you +want to test every read and its reverse complement, run the program _without_ `--add-rc` and make a reverse +complement of the whole dataset with `seqfu rc`. + +## Paired end mode + +If you specify `--out-prefix STR`, the program will run in paired end mode, and will output two files with this +prefix, one for each end. The fist step is to generate a ""read"" as long as the fragment (`--frag-len`) and then +the first bases (`--read-len`) will be used as the first read, and the last bases as the second read. The second +read is reverse complemented + +## Output + +The generated sequences will be printed to the standard output (STDOUT). Each read has a progressive +name generated like this: + +* file basename (if `--basename` is specified) +* a string separator (if `--basename` is specified) +* the chromosome name +* a string separator +* a progressive number + +```text +@k141_1_1 +GTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGGCATCAAGTCGAAGGATATGTTCCTGCCCGACTGCTTCGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@k141_1_2 +TCGGGCAGGAACATATCCTTCGACTTGATGCCGAACTCCTTTTTATAAAACTCCTGTGCAAGCAGGATGTTGCGGATAAACGACTCCGACGACGGCATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@k141_1_3 +AACGACCCGAACATGCCGTCGTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGGCATCAAGTCGAAGGATATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@k141_1_4 +CGACTTGATGCCGAACTCCTTTTTATAAAACTCCTGTGCAAGCAGGATGTTGCGGATAAACGACTCCGACGACGGCATGTTCGGGTCGTTGGCCTCGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@k141_1_5 +CGGGGGCTTCGTTCGAGGCCAACGACCCGAACATGCCGTCGTCGGAGTCGTTTATCCGCAACATCCTGCTTGCACAGGAGTTTTATAAAAAGGAGTTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +``` + +## Shotgun simulation + +If you need to simulate a whole genome shotun, you will need alternative software like +[ART](https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm). +","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-orf.md",".md","4340","132","--- +layout: default +title: fu-orf +parent: Utilities +--- + + + +# fu-orf + +Extraction of ORFs from raw reads datasets (and other +sequence files). +Open reading frames are defined as a stretch of aminoacids +not interrupted by stop codons: +this program does not perform any _gene finding_ procedure +and merely extracts ORFs (under the assumption that, running +on raw reads, fragments are expected). + +A major update was introduced with version **1.8.4**, with +improved reporting (strand and reding frame in the output), +improved tests and `--scan-reverse` option (previously +enabled by default). + +```text +fu-orf + +Extract ORFs from Paired-End reads. + + Usage: + fu-orf [options] + fu-orf [options] -1 File_R1.fq + fu-orf [options] -1 File_R1.fq -2 File_R2.fq + fu-orf --help | --codes + + Input files: + -1, --R1 FILE First paired end file + -2, --R2 FILE Second paired end file + + ORF Finding and Output options: + -m, --min-size INT Minimum ORF size (aa) [default: 25] + -p, --prefix STRING Rename reads using this prefix + -r, --scan-reverse Also scan reverse complemented sequences + -c, --code INT NCBI Genetic code to use [default: 1] + -l, --min-read-len INT Minimum read length to process [default: 25] + + Paired-end optoins: + -j, --join Attempt Paired-End joining + --min-overlap INT Minimum PE overlap [default: 12] + --max-overlap INT Maximum PE overlap [default: 200] + --min-identity FLOAT Minimum sequence identity in overlap [default: 0.80] + + Other options: + --codes Print NCBI genetic codes and exit + --pool-size INT Size of the sequences array to be processed + by each working thread [default: 250] + --verbose Print verbose log + --debug Print debug log + --help Show help +``` + +## Example usage + +Single input file (FASTA or FASTQ): + +```bash +fu-orf --min-size 500 data/orf.fa.gz +``` + +Paired-end Illumina reads: + +```bash +fu-orf --min-size 29 -1 data/illumina_1.fq.gz -2 data/illumina_2.fq.gz +``` + +will produce a FASTA output reporting, as comment, +the frame and the total ORFs printed for each sequence: + +```text +>filt.1_1 frame=+0 tot=5 +RNLIILKMDFFFENFALVGLLYGACQRLNSTKFYLMSTDYLIVKTFNNGSLGSRIDEERS +>filt.1_2 frame=+2 tot=5 +WSFRGSKSRNKVSVGEPAEGSLKKFNNFENGFFF +>filt.1_3 frame=+2 tot=5 +KLCFGRPSIWGLPEVKLNQILFNVNRLFNSQNFQQRISWFSHR +>filt.1_4 frame=-1 tot=5 +NLVEFNLWQAPYRRPTKAKFSKKKSIFKIIKFL +>filt.1_5 frame=-2 tot=5 +LLNNRLTLNKIWLSLTSGRPHIEGLPKQSFQKKNPFSKLLNFFNDPSAGSPTETLLRLLLPLNDQ +>filt.2_1 frame=+0 tot=5 +TYNQFFINLSHQIITNSQNFQQRISWFSHRNA +>filt.2_2 frame=+1 tot=5 +NKLALAVGPACRQRSKLTTNFLSTCHTRLLLIVKTFNNGSLGSRIETQ +>filt.2_3 frame=+2 tot=5 +WSFRGSKSRNKVSVGEPAEGSLLICLIAPHVFFFETNLLWRWAQPAARGLNLQPIFYQLVTPDYY +>filt.2_4 frame=-1 tot=5 +KIGCKFRPLAAGWAHRQSKFVSKKNTCGAIKQISNDPSAGSPTETLLRLLLPLNDQ +>filt.2_5 frame=-2 tot=5 +QVDKKLVVSLDLWRQAGPTAKASLFQRKTHVVQLSKSVMILPQVHLRKPCYDFYFL +``` + + +## Genetic codes + +Genetic codes can be changed using [NCBI Genetic Codes](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). + +Type `fu-orf --codes` to print the following list. + + * `1`: The Standard Code + * `2`: The Vertebrate Mitochondrial Code + * `3`: The Yeast Mitochondrial Code + * `4`: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code + * `5`: The Invertebrate Mitochondrial Code + * `6`: The Ciliate, Dasycladacean and Hexamita Nuclear Code + * `9`: The Echinoderm and Flatworm Mitochondrial Code + * `10`: The Euplotid Nuclear Code + * `11`: The Bacterial, Archaeal and Plant Plastid Code + * `12`: The Alternative Yeast Nuclear Code + * `13`: The Ascidian Mitochondrial Code + * `14`: The Alternative Flatworm Mitochondrial Code + * `16`: Chlorophycean Mitochondrial Code + * `21`: Trematode Mitochondrial Code + * `22`: Scenedesmus obliquus Mitochondrial Code + * `23`: Thraustochytrium Mitochondrial Code + * `24`: Rhabdopleuridae Mitochondrial Code + * `25`: Candidate Division SR1 and Gracilibacteria Code + * `26`: Pachysolen tannophilus Nuclear Code + * `27`: Karyorelict Nuclear Code + * `28`: Condylostoma Nuclear Code + * `29`: Mesodinium Nuclear Code + * `30`: Peritrich Nuclear Code + * `31`: Blastocrithidia Nuclear Code + * `33`: Cephalodiscidae Mitochondrial UAA-Tyr Code","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-sw.md",".md","2475","75","--- +layout: default +title: fu-sw +parent: Utilities +--- + + +# fu-sw + +Simple implementation of the _Smith-Waterman_ alignment: + +```text +Usage: fu-sw [options] -q QUERY -t TARGET + + Options: + -q --query File with the sequence(s) to align against target + -t --target File with the target sequence(s) + -i --id ID Align only against the sequence named `ID` in the target file + -s --showaln Show graphical alignment + + Smith-Waterman options: + --score-match INT Score for a match [default: 10] + --score-mismatch INT Score for a mismatch [default: -5] + --score-gap INT Score for a gap [default: -10] + --min-score INT Minimum alignment score [default: 80] + --pct-id FLOAT Minimum percentage of identity [default: 85] + + Other options: + --pool-size INT Number of sequences/pairs to process per thread [default: 20] + -v --verbose Verbose output + -h --help Show this help +``` + +## Input files + +Input files can be in FASTA or FASTQ format, and both query and +target can hold multiple sequences even if the common application +is to have a single sequence in the target file. + +If the target file contains multiple sequences but only one is +the intended target, the target can be specified with `--id` +parameter. + +## Example output + +The output will print the alignment score and coordinates in a +single line after `QUERY` and `TARGET`. +If `--showaln` is specified, a graphical summary of the local +alignment is provided. + +```text +# QUERY: not_in_target +## TARGET: ecoli + +# QUERY: 16S_1_for_ins +## TARGET: ecoli +Score: 406 (97.18%) Length: 69 Strand: + Query: 0-71 Target: 21-90 + GCTCAGATTGAACGCTccGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGC + |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| + GCTCAGATTGAACGCT--GGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGC + +# QUERY: 16S_2_rev +## TARGET: ecoli +Score: 312 (100.00%) Length: 52 Strand: - Query: 0-52 Target: 175-227 + CGCATAATGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGG + |||||||||||||||||||||||||||||||||||||||||||||||||||| + CGCATAATGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGG +``` + +## Release note + +From 1.19.0 the algorithm has been rewritten using only standard libraries, +while the initial implementation used the neo library for storing matrices. +This resulted in a 2X speedup. +","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-tabcheck.md",".md","1597","69","--- +layout: default +title: fu-tabcheck +parent: Utilities +--- + + +# fu-tabcheck + +An utility to parse CSV/TSV files to check that all the +records have the same size. +Multiline records are supported using double quotes as +field delimiter. +Gzipped files are also supported. + +``` +fu-tabcheck + + A program inspect TSV and CSV files, that must contain more + than 1 column. + Double quotes are considered field delimiters, if present. + Gzipped files are supported natively. + + Usage: + fu-tabcheck [options] ... + + Options: + -s --separator CHAR Character separating the values, 'tab' for tab and 'auto' + to try tab or commas [default: auto] + -c --comment CHAR Comment/Header char [default: #] + --verbose Enable verbose mode + +``` + +## Output + +Tabular output has these columns: + +* File name +* Pass/Error +* Columns number +* Records number +* Separator (when using _auto_ both tabs and commas are tested) + +Example: + +``` +data/tab.txt.gz Pass 8 7 separator= +data/tab.txt Pass 4 3 separator= +data/tab-multi.tsv Pass 2 4 separator= +data/table.csv Pass 3 3 separator=, +data/table.tsv Pass 3 4 separator= +data/table2.tsv Error +data/tablegz.tsv.gz Pass 3 4 separator= +``` + +:bulb: Multiline records are supported using double quotes, like: + +```text +#ID Description +R01 ""this is a cell with a tab inside!"" +R02 ""this is a +multi-line description"" +R03 Last Record +``` + +## Exit code + +A single file is not a valid table will lead to non-zero exit status.","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-index.md",".md","1105","48","--- +layout: default +title: fu-index +parent: Utilities +--- + + +# fu-index + +Extracts the index (barcode) from Illumina demultiplexed files. + +```text +Fastx utility + + A program to print the Illumina INDEX of a set of FASTQ files + + Usage: + fu-index [options] ... + + Options: + + -m, --max-reads INT Evaluate INT number of reads, 0 for unlimited [default: 8000] + -r, --min-ratio FLOAT Minimum ratio of matches of the top index [default: 0.90] + -h, --header Add header to output + --verbose Print verbose log + --help Show help +``` + +## Input files + +FASTQ files demultiplexed by CASAVA (Illumina). + +## Example output + +A tabular output contains: + +* filename +* extracted tag +* fraction of the top tag (accounts for errors) +* PASS (""PASS"" or ""--"") if the top tags is >= min-ratio +* Instrument code (from 1.12) +* Run number (from 1.12) +* Flowcell ID (from 1.12) + +``` +data/illumina_1.fq.gz TACGCTGC+CTATTAAG 1.00 PASS A00709 43 HYG25DSXX +data/illumina_2.fq.gz TACGCTGC+CTATTAAG 1.00 PASS A00709 43 HYG25DSXX +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-virfilter.md",".md","1987","59","--- +layout: default +title: fu-virfilter +parent: Utilities +--- + + +# fu-virfilter + +Filter sequences from VirFinder predictions CSV file. + +```text + + Usage: fu-virfilter [options] + + Files: + VirFinder output file (csv format) + FASTA file to filter + + Options: + -p, --max-pvalue FLOAT Maximum p-value to keep [default: 0.05] + -s, --min-score FLOAT Minimum score [default: 0.90] + --min-len INT Minimum length [default: 100] + --max-len INT Maximum length [default: 1000000] + + Other options: + --sep CHAR Separator [default: ,] + -v, --verbose Verbose output + -h, --help Show this help +``` + + +## Example input and output + +Virfinder output: + +``` +"""",""name"",""length"",""score"",""pvalue"" +""1"",""k141_48132 flag=1 multi=2.0000 len=317"",317,0.805265057231112,0.003813306852036 +""2"",""k141_58828 flag=1 multi=1.0000 len=302"",302,0.386511266211445,0.27648460774578 +""3"",""k141_80217 flag=1 multi=2.0000 len=310"",310,0.245554967660862,0.424905660377358 +``` + +While the FASTA file is: + +``` +>k141_74870 flag=1 multi=2.0000 len=369 +AAAGGCGTGTGTGCCTTGAGCCTTAGACCATGTGAATTGTAAATCAGTGTATAGCCGGCGATACCGGTTTTCTTGTTCA +TCGCACGGCAGAAGCCTCCATCTATCACAAACAGCTTGCCATTGGCCCTGACAGGGTTCTCTCCCTCTATTGCGTGAAC +GGTGTATGTCCATTTATGATATGCGCATCATCATCATACAGCCCGAACTCGTGCAGTATCTGACAGCAGAAGCTCTTAT +CGTAATACCTGCTGTAATATGGGTTAGAAGGCTCTTCCCACATGCTCTTGTCTGTAACATATTCCATCTCAAAGGTCTT +AAGCCTTCTGCCGCACAGCGGTGATTTTTCTCCTCCCCACAAAAACCACATA +>k141_106952 flag=1 multi=2.0000 len=384 +GCGGGCGTTACCCCGGAAGCGGCATGGAGGGCCTGGGAGAAACCGTCCCACAGGCTGCGGCTGCAGCGGCAGTCCGCGA +GGGAGACCGGATACCAGCGGACCAGGGGGTCGGCCGCGACGCGCCGCCCGGTCCCGCCGGTGAGGATGCGCAGCCCCCC +GGATTCTGCGGGCAGGCGGACCTCCAGATCTTCCGTGACCGGGGTCTGACAGGCCAGGACCGAGACCCATTCCTCCCCG +CGGCGGAGCGCCACACGGCACTTTCCGCAGGTCCCATTCCCGCCGCAGGGGCTGTCCAGCCAGAGACCGGCCGCACGGC +AGGCCTCCATCAGCGTGCTTCCCAGGGGGACGGAGCAGCGCACGTCCGCCGGGAGAAAGCGTACCTGT +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-homocomp.md",".md","704","41","--- +layout: default +title: fu-homocom +parent: Utilities +--- + + +# fu-homocom + +Remove all the homopolymers from FASTA and FASTQ files. +The output format is the same of +the input. + +```text +Usage: fu-homocompress [options] [...] + + Other options: + --pool-size INT Number of sequences to process per thread [default: 50] + --max-threads INT Maxiumum number of threads to use [default: 4] + -v, --verbose Verbose output + -h, --help Show this help +``` + + +## Example input and output + +``` +@polya +ACGTACACGTGACGAAAAAAAAAAAAAACGT ++ +IIIIIIIIIIIIIII!!!!!!!!!!!!!III +``` + +will be printed as + +``` +@polya +ACGTACACGTGACGACGT ++ +IIIIIIIIIIIIIIIIII +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-16Sregion.md",".md","3655","124","--- +layout: default +title: fu-16Sregion +parent: Utilities +--- + + +# fu-16Sregion + +```note +This utility is still in development, but feedback is welcome. +``` + +Align paired-end, or single-end, reads against a 16S +reference sequence to determine +the hypervariable regions sequences via local alignment. + +Can read one FASTA/FASTQ file or data from standard input. + +```text +Usage: fu-16Sregion [options] [] + + Options: + -r --reference FILE FASTA file with a reference sequence, E. coli 16S by default + -j --regions FILE Regions names in JSON format, E. coli variable regions by default + -m --min-fraction FLOAT Minimum fraction of reads classified to report a region as detected [default: 0.5] + --min-score INT Minimum alignment score (approx. %id * readlen * matchScore) [default: 2000] + --max-reads INT Parse up to INT reads then quit [default: 500] + + Smith-Waterman: + --score-match INT Score for a match [default: 10] + --score-mismatch INT Score for a mismatch [default: -5] + --score-gap INT Score for a gap [default: -10] + + Other options: + --pool-size INT Number of sequences/pairs to process per thread [default: 25] + -v --verbose Verbose output + --debug Enable diagnostics + -h --help Show this help +``` + + +## Example output + +A tabular report, per read, is provided with the following columns + +* Read name +* Primary target region +* Alignment score +* Region of the reference sequence covered (coordinates) + +The **main** output is given as two columns: + +* regions detected in the same read (e.g. ""V3,V4"") +* fraction of reads with the combination + +Example: + +```text +V3-V4 0.83 +``` + +This is only reported when the number of reads / total reads is above `--min-fraction`. + +When activating the `--verbose` switch, some more information will be +printed to the standard error, but also a **read by read output** will +be printed (read name, score, target region covered, detected regions and Pass/Fail): + + +```text +M05517:39:000000000-CNNWR:1:1105:7840:22808 score:2955 alignment:340..805 regions:V3,V4 Pass +M05517:39:000000000-CNNWR:1:1105:24801:23102 score:3480 alignment:340..805 regions:V3,V4 Pass +M05517:39:000000000-CNNWR:1:1105:9773:23284 score:2835 alignment:340..805 regions:V3,V4 Pass +M05517:39:000000000-CNNWR:1:1105:9791:23288 score:2835 alignment:340..805 regions:V3,V4 Pass +M05517:39:000000000-CNNWR:1:1105:11642:23566 score:1650 alignment:NA regions: Fail +M05517:39:000000000-CNNWR:1:1105:13198:23694 score:1535 alignment:NA regions: Fail +M05517:39:000000000-CNNWR:1:1105:15837:23728 score:2240 alignment:340..641 regions:V3,V4 Pass +M05517:39:000000000-CNNWR:1:1105:14501:23779 score:2225 alignment:340..641 regions:V3,V4 Pass +``` + + +## Example use with paired-reads + +To check paired-end reads, they can be processed independently or merged (if they overlap) before. +SeqFu merge can be used for this purpose: + +``` +seqfu merge -1 read_R1.fq -2 read_R2.fq | fu-16region +``` + +## Region names + +By default the following regions are used, but a new set can be fed in JSON format (each region +should contain the `start` and `end` values as show in the example) + +```json +{ + ""V1"": { + ""start"": 68, + ""end"": 99 + }, ""V2"": { + ""start"": 136, + ""end"": 242 + }, ""V3"": { + ""start"": 338, + ""end"": 533 + }, ""V4"": { + ""start"": 576, + ""end"": 682 + }, ""V5"": { + ""start"": 821, + ""end"": 879 + }, ""V6"": { + ""start"": 970, + ""end"": 1046 + }, ""V7"": { + ""start"": 1117, + ""end"": 1294 + }, ""V8"": { + ""start"": 1435, + ""end"": 1465 + } +} +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-cov.md",".md","1737","59","--- +layout: default +title: fu-cov +parent: Utilities +--- + + +# fu-cov + +A program to filter the output of assembly programs using the +coverage information they print +in the sequence names. + +```text +Extract contig by sequence length and coverage, if provided in the sequence name. + +Usage: + fu-cov [options] [inputfile ...] + +Arguments: + [inputfile ...] + +Options: + -h, --help + -v, --verbose Print verbose messages + -s, --sort Store contigs in memory, and sort them by descending coverage + -c, --min-cov=MIN_COV Minimum coverage (default: 0.0) + -l, --min-len=MIN_LEN Minimum length (default: 0) + -x, --max-cov=MAX_COV Maximum coverage (default: 0.0) + -y, --max-len=MAX_LEN Maximum length (default: 0) + -t, --top=TOP Print the first TOP sequences (passing filters) when using --sort (default: 10) + +``` + +## Input + +The FASTA output of an assembly program (currently tested with SPAdes, MegaHit, Unicycler, Shovill), +as the _length_ of the sequences is clearly checked from the FASTA file itself, while the coverage +is found in the sequence description: + +Example of contig name from _Shovill_: + +``` +>contig00001 len=596929 cov=9.9 corr=0 origname=NODE_1_length_596929_cov_9.873201_pilon sw=shovill-spades/1.0.4 date=20181128 +ACCCGGTAGAATACCGGACTGAGTATCAAAAAGCCGGTTAACTGAAACTGTCCAGGTTTTGGGGTTCAGTTCATGCCGCATCTTATCCGACCTTGTATTATCCCTCCAGTGCAGAGAAAATC +... +``` + +## Output + +A set of filtered contigs in FASTA file. +Will print to STDERR a summary like: + +```` +1/1 sequences printed (1 with coverage info) from 1 files. +Skipped: 0 too short, 0 too long, then 0 low coverage, 0 high coverage, . +Average length: 180.00 bp, [180.0 - 180.0] +Average coverage: 9.90X, [9.9-9.9] +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-msa.md",".md","3841","125","--- +layout: default +title: fu-msa +parent: Utilities +--- + + + +# fu-msa + +```note +Preliminary version +``` + +Interactive **multiple sequence alignment** viewer from the Command Line. + +![Multiple sequence aligner]({{site.baseurl}}/img/msa.png) + +```text +Usage: + full [options] + + Keys: + Scroll Horizontally Left and Right arrow + By 10 bases L, K + By 100 bases ShiftL, ShiftK + To the beginning 1 + To middle parts 2..9 + To the end 0 + + Scroll Vertically A, Up Arrow/ Z, Down Arrow + Jump to top ShiftA, PageUp + Jump to bottom ShiftZ, PageDown + + Rotate color scheme Tab + Refresh screen F5 + Resize seq labels -,+ + Search / (seqname, "":INT"", ""#SEQ"") + Quit Q, CtrlC + + Options: + -m, --mouse Enable mouse + -n, --norefresh Disable autorefresh + -j, --jumpsize INT Jump size (big jump is 10X) [default: 10] + + Visualization settings: + -i, --seqindex INT Start visualization at this sequence [default: 0] + -p, --seqpos INT Start visualization at this nucleotide [default: 0] + -w, --label-width INT Sequence label width [default: 20] + -s, --setting-string STR Settings string (overrrides all other settings) is in the + format Seq:{seqindex}:{seqpos}:{labelwidth} and is the + return value of the program when it is closed. + + More documentation online at https://telatin.github.io/seqfu2/ +``` + +## Keyboard + +#### Horizontal scrolling + +* :arrow_left:, :arrow_up: : scroll by one nucleotide +* `K`, `L`: scroll left and right respectively, by 10 nucleotides +* `Shift + K`, `Shift + L`: scroll left and right respectively, by 100 nucleotides +* `End`: Move to sequence end +* `Home`: Move to the beginning of the sequence +* `1`: Move to the first base +* `2`..`9`: Move to 20% .. 90% of the sequence +* `0`: Move to the last base + +#### Vertical scrolling + +* `A`, `Z` and :arrow_up:, :arrow_down: : Move up and down by one sequence +* `Shift + A`, `Shift + Z`: Move to top and move to bottom + +#### Search + +* `/` Trigger search, then: + * Type the query + * Hit `Enter` to submit or `Esc` to abort + +* The query can be: + * part of a sequence name + * `:` followed by a sequence index (eg: `:0` to go to the first sequence) + * `#` followed by a sequence (eg: `#ATTAC` to jump to the position of the first occurrence of ATTAC) + +#### Visualization + +* `Space`: toggle consensus sequence from ""Consensus"" (show bases identical across all the sequences) to ""Majority"" (show bases shared by 50% of the sequences or more) +* `Tab`: toggle color scheme +* `-`,`+`: Decrease and increase by one the sequence label width +* `F5`, `R`: refresh +* `F6`: toggle autorefresh on/off +* `H`: toggle help screen (only major keys are reported) + +#### Mouse + +* `M`: toggle mouse on/off +* When mouse is on: + * Click in a nucleotide to set that position as first (scroll right) + * Click to the sequence name area (left) to scroll left + +### Resuming session + +When pressing quit (`Q`) the program will print a configuration string like: `Seq:0:6:20` +that can be used to resume the session at the same position with: + +```bash +fu-msa {input_file} --setting-string Seq:0:6:20 +``` + +The settings string is in the format `Seq:{seqindex}:{seqpos}:{labelwidth}` + +### Colors + +* DNA: `A` (red), `C` (cyan), `G` (green), `T` (yellow) +* Protein: [""Lesk"" scheme](https://www.bioinformatics.nl/~berndb/aacolour.html): + * Hydrophobic, green + * Small non polar, yellow (should be orange) + * Polar, magenta + * Negative charge, red + * Positive charge, cyan (should be blue) + +### Screenshot + +![Screenshot of ""seqfu MSA view""]({{site.baseurl}}/img/screenshot-fu-msa.svg ""SeqFu MSA view"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-nanotags.md",".md","3685","93","--- +layout: default +title: fu-nanotags +parent: Utilities +--- + +# fu-nanotags + +```note +Experimental utility. Feedback for this tool is welcome. +``` + +Search for tags (one or more sequences) in long reads using _Smith-Waterman_ +alignment. +The tag has to be at the beginning of the read (specifying the region to scan +with `--cut INT`) or at the end (revserse complemented). If `--cut=0` the search +is in the full read. + +```text +Usage: fu-nanotags [options] -q QUERY [...] + + Options: + -q, --query TAGSEQ Sequence string OR file with the sequence(s) to align against reads + -s, --showaln Show graphical alignment + -c, --cut INT Cut input reads at INT position [default: 300] + -x, --disable-rev-comp Do not scan reverse complemented reads + + Alignment options: + -i, --pct-id FLOAT Percentage of identity in the aligned region [default: 80.0] + -m, --min-score INT Minimum alignment score (0 for auto) [default: 0] + + Smith-Waterman parameters: + -M, --weight-match INT Match [default: 5] + -X, --weight-mismatch INT Mismatch penalty [default: -3] + -G, --weight-gap INT Gap penalty [default: -5] + + Other options: + --pool-size INT Number of sequences/pairs to process per thread [default: 25] + -v, --verbose Verbose output + -h, --help Show this help +``` + +## Output + +The program will print to the **standard output** the reasd containing the tag, +under the specified alignment criteria. +A comment will be added to the reads specifying which tag was found (e.g. `tags=tag1;tag4`). + +The program will print to the **standard error** the number of passing reads per file processed, +and the grand total. + +Example: + +```text +tradis/fastq_1.fq 60.00% (18/30) sequences printed, of which 8 in reverse strand. +tradis/fastq_2.fq.gz 53.75% (2150/4000) sequences printed, of which 949 in reverse strand. +Total 53.80% (2168/4030) sequences printed, of which 957 in reverse strand. +``` + +## Optimisation + +If the tag is 100 bp long and we expect to be at the very beginning (or end) of the read, +it's advisable to reduce the `--cut INT` parameter accordingly to speedup the alingment +step (for example, to 110, to account for a small variation). + +The current version of the program is single threaded, but a multithreading application +will be released. + +## Example + +```bash +fu-nanotags -q tag.fa fastq-reads.fq.gz > passed.fq +``` + +To inspect the parameters, add `--verbose --showaln`, +possibly redirecting the output to `less -S` for a preliminary inspection: + +```bash +fu-nanotags -q tag.fa reads.fq.gz --verbose --showaln 2>&1 | less -S +``` + +A fraction of the output is like the following: + +``` +# a564e10b-c82e-4e59-98a4-fdc6f1b31acb:test-tag strand=-;score=167;pctid=94.57% + < AATGATA-TGCGACCACTGAGATCTACACCTCTCTATACACTC-TT-CCTACACGACGCTCTTCCGATCTTTCGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTG + < ||||||| |||||||| ||||||||||||||||||||||||| || |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + < AATGATACGGCGACCACCGAGATCTACACCTCTCTATACACTCTTTCCCTACACGACGCTCTTCCGATC--TCGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAACTG +# 132518b1-1522-45ed-9a77-94a3c981ac20:test-tag strand=+;score=531;pctid=90.55% + > AATGATACGGCGACCACCGAGATCTACACTATCCCTCTACACTCTTTCCCTACACGACGCTCTTCCGATCTACGTACGTGAGTTTAAATGT-GTTAGCTAAGGTGTATAT-AGCTTCCGACTTCAGC + > ||||||||||||||||||||||||||||| || || |||||||||||||||||||||||||||||||||| ||||||||||||||||||| || |||||||||||| | | |||||||||||| | + > AATGATACGGCGACCACCGAGATCTACAC-CTCTCTATACACTCTTTCCCTACACGACGCTCTTCCGATCT-CGTACGTGAGTTTAAATGTATTTGGCTAAGGTGTATGTAAACTTCCGACTTCAAC +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/utilities/fu-multirelabel.md",".md","1166","39","--- +layout: default +title: fu-multirelabel +parent: Utilities +--- + + +# fu-multirelabel + +A program to rename sequences from multiple files +(adding the filename, and or numerical postfix). +Will fail if multiple sequence receive the same name. + +```text +Usage: + fu-multirelabel [options] FILE... + + Options: + -b, --basename Prepend file basename to sequence + -r, --rename NAME Replace original name with NAME + -n, --numeric-postfix Add progressive number (reset at each new basename) + -t, --total-postfix Add progressive number (without resetting at each new input file) + -d, --split-basename CHAR Remove the final part of basename after CHAR [default: .] + -s, --separator STRING Separator between prefix, name, suffix [default: _] + --no-comments Strip out comments + --comment-separator CHAR Separate comment from name with CHAR [default: TAB] +``` + +## Description + +A list of files (can be specified with wild chars) that +can contain sequences with the same name. +The program allows to prepend the filename as prefix. + +## Example usage + +```bash +fu-multirelabel -b *.fasta > relabeled.fasta +```","Markdown" +"Bioengineering","telatin/seqfu2","docs/releases/history.md",".md","5508","199","--- +layout: default +title: History +parent: Releases +--- + +## Release history + +### version 1.22 + +* Added `seqfu cat --anvio` +* Added layouts to `seqfu metadata`, now supporting nf-core/rnaseq and nf-core/ampliseq +* Improved `seqfu derep` + +### version 1.20 + +* Improved `seqfu interleave/deinterleave` +* Migration to Nim 2.0 +* Added `--translate` to `fu-orf` +* Faster smith-waterman `fu-sw` + +### version 1.18 + +* Added paired end support to `fu-shred` + +### version 1.17 + +* Bugfixes and removal of thread library + +### version 1.16 + +* Added amino-acid color scheme for `fu-msa` +* Bugfixes in `seqfu check` and `seqfu bases` + +### version 1.15.0 + +* New SeqFu check program to validate the integrity of FASTQ datasets +* Bug fix in seqfu qual that was printing debug information in non-debug runs + +#### 1.15.3 + +* Added SeqFu bases to evaluate the composition of FASTX files + +### version 1.14.0 + +* **Seqfu grep** will die if fed with non existing files (to ensure no wrong parameters were passed) +* **Seqfu grep** will match oligos case insensitive by default +* Addedd invert match `-v` to `seqfu grep` +* Improved `fu-tabcheck`, notably added `--inspect` option to print columns info +* `fu-split` now can use a different SeqFu than specified in path, setting `$SEQFU_BIN` or `--bin` option +* `fu-split` version check fixed +* :warning: Bugfix in `seqfu tab`: was not working with FASTA files + +### version 1.13.0 + +* `seqfu cat` now can skip a set of initial sequences (`--skip-first INT`) or start from a specific sequence (`--jump-to`) +* Minor updates in the test suite, github actions (including rich_codex) and documentation updates + +#### 1.13.1 + +* added `fu-split` (experimental) + +#### 1.13.2 + +* added `--print-last` option to **seqfu cat** and **seqfu heda** +* updated `fu-split`, with support for paired end reads, improved performance thanks to `--print-last`, new tests + +### version 1.12.0 + +* Expanded ""fu-index"": also reports run infos, not only indexes +* Minor bugfix + +### version 1.11.0 + +* Improved seqfu stats: added sorting option and JSON output, added GC content, improved test suite. +* bugfix Seqfu tabulate -d (detabulate) was too stringent in requiring forward and reverse reads to have the same length 🤦 + +### version 1.10.0 +* Added support for MetaPhage to seqfu metadata +* Added --header to fu-tabcheck +* Minor fixes + +### version 1.9.3 + +* bugfix: seqfu cat controls the length of operations (truncate, trim) +* improved: seqfu cat improved renaming options (basename and strip-name will now add a progressive number automatically) + +### version 1.9.2 + +* Bugfix on Seqfu Detabulate + +### version 1.9.1 + +* Fixes #8 +* This is a re-release finally with all the necessary commits + +### version 1.9.0 + +* seqfu grep now has -w (word) and -f (full) match options. default behaviour unchanged. +* seqfu cat now has a filter for Ns (--max-ns INT) +* seqfu cat now has a filter for the total expected errors (--max-ee FLOAT), and can report --add-ee and --add-initial-ee +* Added header line in seqfu metadata when using ""irida"" formats + + +### version 1.8.6 + +* Enabled **seqfu rotate** + + +### version 1.8.4 + +* **fu-orf** + * Fixed bug in `fu-orf` to allow for single sequences + * Introduced `-r`, `--scan-reverse` to include reverse complement in the ORF finder + * `fu-orf` also prints frame in the sequence comment +* Expanded test suite + + +### version 1.8.3 + +* Markdown documentation improvements +* Splashscreen for *fu-virfilter* fixed +* Argument parser for _fu-cov_ improved +* Now `seqfu --version` and `seqfu version` will print the version number and exit +* Added test for _fu-cov_ +* Added citation in main command and repository + + +### version 1.8.2 + +* Added `fu-virfilter` to filter VirFinder results +* Bugfix in `seqfu cat --basename`: the last update made it working only when prefix was also specified + + +### version 1.8.1 + +* introduced `fu-homocomp` to compress homopolymers + + +### version 1.8.0 + +* added `seqfu list` to extract sequences via a list + + +### version 1.7.2 + +* `seqfu grep` supports for comments + + +### version 1.7.1 + +* **Bugfix release**: `seqfu cat` with no parameters was stripping the reads name + + +### version 1.7.0 + +* Default primer character for oligo matches in seqfu view was Unicode, now Ascii +* Updated `seqfu cat` with improved sequence id renaming handling +* Updated `seqfu grep` to report the _oligo_ matches in the output as sequence comments + + +### version 1.6.3 + +* Removed ambiguity on `-q` in `seqfu head` +* Minor documentation updates + +### version 1.6.0 + +* Improved STDIN messages, that can be disabled by `$SEQFU_QUIET=1` +* Added `--format irida` in `seqfu metadata` (for [IRIDA uploader](https://github.com/phac-nml/irida-uploader)) +* Added `--gc` in `seqfu qual`: will print an additional column with the GC content +* Minor improvements on `seqfu cat` + + +### version 1.5.4 + +* Improved STDIN messages, that can be disabled by `$SEQFU_QUIET=1` +* Minor improvements on `seqfu cat` + +### version 1.5.2 + +* **seqfu cat** has new options to manipulate the sequence name (like `--append STRING`) and to add comments (like `--add-len`, `--add-gc`) + +### version 1.5.0 + +* **seqfu count** now multithreading and redesigned. The output format is identical but the order of the records is not protected (use **seqfu count-legacy** if needed) +* **seqfu cat** can print a list of sequences matching the criteria (`--list`) + +### version 1.4.0 + +* Added **fu-shred** +* Added `--reverse-read` to *fu-nanotags* + +# version 1.3.6 + +* Automatic release system +* Documentation updates +* Minor updates +","Markdown" +"Bioengineering","telatin/seqfu2","docs/scripts/fu-pecheck.md",".md","959","41","--- +layout: default +title: fu-pecheck +parent: Helper Utilities +--- + + +# fu-pecheck + +```note +Preliminary version +``` + +A program to check the integrity of Paired End FASTQ files. + +```text +usage: fu-pecheck [-h] [--for-tag FOR_TAG] [--rev-tag REV_TAG] [--verbose] [--version] DIR + +Validate FASTQ files + +positional arguments: + DIR Input directory + +optional arguments: + -h, --help show this help message and exit + --for-tag FOR_TAG Tag to use for the forward reads output (default: _R1) + --rev-tag REV_TAG Tag to use for the forward reads output (default: _R2) + --verbose Verbose output + --version show program's version number and exit +``` + +This script runs `fu-secheck` twice and compare the results, +and will print a five column table with the following columns: + +1. Sample basename +2. Status (`OK` or `ERR`) +3. Number of reads or ""None"" if the file is corrupt +4. Name of the first read +5. Name of the last read + +","Markdown" +"Bioengineering","telatin/seqfu2","docs/scripts/fu-split.md",".md","3185","79","--- +layout: default +title: fu-split +parent: Helper Utilities +--- + + +# fu-split + +```note +Preliminary version +``` + +Split a FASTQ or FASTA files into multiple files, by: +* Number of desired output files (`--num-files INT`) +* Number of (max) sequences per file (`--num-seqs INT`) +* Number of (max) bases per file (`--num-bases INT`) + +An important component to configure the program is the ""output file"" string, see below. + +```text +usage: fu-split [-h] -i INPUT [-I INPUT_REV] -o OUTPUT [--for-tag FOR_TAG] [--rev-tag REV_TAG] + (-n NUM_FILES | -s NUM_SEQS | -b NUM_BASES) [--threads THREADS] [--number-char NUMBER_CHAR] [--compress] + [--verbose] [--debug] [--version] + +Split FASTA/FASTQ files into multiple files + +optional arguments: + -h, --help show this help message and exit + -i INPUT, --input INPUT + Input file + -I INPUT_REV, --input-rev INPUT_REV + Second input file (reverse pair) + -o OUTPUT, --output OUTPUT + Output file (add a stretch of 3+ zeroes to specify the progressive number), compression will be detected. + Example: parz_0000.fq.gz + --for-tag FOR_TAG Tag to use for the forward reads output (default: _R1 + --rev-tag REV_TAG Tag to use for the forward reads output (default: _R2 + -n NUM_FILES, --num-files NUM_FILES + Number of desired files + -s NUM_SEQS, --num-seqs NUM_SEQS + Number of sequences per file + -b NUM_BASES, --num-bases NUM_BASES + Number of bases per file + --version show program's version number and exit + +Other options: + --threads THREADS Number of threads (-n only) [default: 8 + --number-char NUMBER_CHAR + Character used to represent the progressive number in output string [default: 0 + --compress Force compression of the output files + --verbose Verbose mode + --debug Debug mode +``` + +## Output file string + +The ideal way to use `fu-split` is to use the `--output` option to specify the output file format +with this apprach: *prefix*, *progressive number*, *suffix*, where *progressive number* is a stretch +of zeroes as long as you would like the progressive number (zeroes can be changed with `--number-char`). + +Example: + +* `--output parz_0000.fq.gz`: forces output in FASTQ format, compressed with Gzip, with four digits of progressive number. +* `--output parz_000.fa`: forces output in FASTA format, uncompressed, with three digits of progressive number. +* `--output parz`: missing the *progressive number* part, this will be used as prefix, with a four digits progressive number (not recommended, behaviour can change in the future) + +## Paired end + +Specify both `--input` and `--input-rev` to split a paired end FASTQ file. The output file will be differentiated +with the `--for-tag` and `--rev-tag` options (default: `_R1` and `_R2`). + +## Binary + +Export `$SEQFU_BIN` to specify the path to SeqFu, otherwise will default to `seqfu` (as in `$PATH`). + +## Splashscreen + +![Screenshot of ""seqfu split""]({{site.baseurl}}/img/screenshot-fu-split.svg ""SeqFu split"")","Markdown" +"Bioengineering","telatin/seqfu2","docs/_scripts/add_frontmatter.py",".py","2632","95","#!/usr/bin/env python3 +"""""" +Add front matter to markdown files for Jekyll navigation. +This script adds proper front matter to child pages in the tools, utilities, and scripts directories. +"""""" + +import os +import re +from pathlib import Path + +# Configuration +BASE_DIR = Path(__file__).parent.parent +SECTIONS = { + 'tools': 'Core Tools', + 'utilities': 'Utilities', + 'scripts': 'Helper Utilities', + 'releases': 'Releases' +} + +def has_frontmatter(content): + """"""Check if file already has front matter."""""" + return content.strip().startswith('---') + +def extract_title_from_content(content): + """"""Extract title from the first # heading in the content."""""" + lines = content.split('\n') + for line in lines: + if line.strip().startswith('# '): + return line.strip()[2:].strip() + return None + +def create_frontmatter(title, parent): + """"""Create front matter block."""""" + return f""""""--- +layout: default +title: {title} +parent: {parent} +--- + +"""""" + +def process_file(filepath, parent_name): + """"""Add front matter to a single file."""""" + with open(filepath, 'r', encoding='utf-8') as f: + content = f.read() + + # Skip if already has front matter + if has_frontmatter(content): + print(f""Skipping {filepath} (already has front matter)"") + return False + + # Extract title from content + title = extract_title_from_content(content) + if not title: + print(f""Warning: Could not find title in {filepath}"") + # Use filename as fallback + title = filepath.stem.replace('-', ' ').replace('_', ' ').title() + + # Create new content with front matter + frontmatter = create_frontmatter(title, parent_name) + new_content = frontmatter + content + + # Write back to file + with open(filepath, 'w', encoding='utf-8') as f: + f.write(new_content) + + print(f""Added front matter to {filepath}"") + return True + +def main(): + """"""Process all markdown files in the specified sections."""""" + processed = 0 + + for section_dir, parent_name in SECTIONS.items(): + section_path = BASE_DIR / section_dir + + if not section_path.exists(): + print(f""Warning: Directory {section_path} does not exist"") + continue + + print(f""\nProcessing {section_dir}/ (parent: {parent_name})"") + + # Process all .md files except README.md + for md_file in section_path.glob('*.md'): + if md_file.name.upper() == 'README.MD': + continue + + if process_file(md_file, parent_name): + processed += 1 + + print(f""\n\nTotal files processed: {processed}"") + +if __name__ == '__main__': + main() +","Python" +"Bioengineering","telatin/seqfu2","scripts/makeFileFeatures.py",".py","491","19","#!/usr/bin/env python +"""""" +A Python 3.6+ compatible script to generate FASTA or FASTQ files, randomly or using a template. +"""""" + +import argparse +import random +import string +import sys + +def main(): + args = argparse.ArgumentParser(description=__doc__) + args.add_argument('output', help='Output file') + args.add_argument('count', type=int, help='Number of sequences to generate') + args.add_argument('--template', help='Template file') + + +if __name__ == '__main__': + exit(main())","Python" +"Bioengineering","telatin/seqfu2","bench/bash-deinterleave.sh",".sh","233","10","#!/bin/bash + +if [[ $# != 3 ]] +then +echo ""USAGE: $0 interleaved.fastq deinterleaved.R1.fastq deinterleaved.R2.fastq"" +exit 1 +fi + +paste - - - - - - - - < ""$1"" | tee >(cut -f 1-4 | tr '\t' '\n' > ""$2"") | cut -f 5-8 | tr '\t' '\n' > ""$3"" +","Shell" +"Bioengineering","telatin/seqfu2","bench/interleave.md",".md","411","6","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `./bin/seqfu interleave -1 R1.fq -2 R2.fq` | 4.229 ± 0.032 | 4.201 | 4.310 | 1.01 ± 0.02 | +| `seqfu interleave -1 R1.fq -2 R2.fq` | 4.202 ± 0.056 | 4.168 | 4.355 | 1.00 | +| `paste R1.fq R2.fq \| paste - - - - \| awk -v OFS='\n' -v FS='\t' '{print($1,$3,$5,$7,$2,$4,$6,$8)}'` | 4.699 ± 0.033 | 4.670 | 4.786 | 1.12 ± 0.02 | +","Markdown" +"Bioengineering","telatin/seqfu2","bench/bash-interleave.sh",".sh","176","9","#!/bin/bash +if [[ $# != 2 ]] +then +echo ""USAGE: $0 R1.fastq R2.fastq"" +exit 1 +fi + +paste ""$1"" ""$2"" | paste - - - - | awk -v OFS='\n' -v FS='\t' '{print($1,$3,$5,$7,$2,$4,$6,$8)}' +","Shell" +"Bioengineering","telatin/seqfu2","bench/interleave_benchmarks.md",".md","262","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu interleave -1 R1.fq -2 R2.fq` | 4.706 ± 0.139 | 4.507 | 4.939 | 1.00 | +| `taskset 1 ./bash_interleave.sh R1.fq R2.fq` | 11.440 ± 0.068 | 11.349 | 11.595 | 2.43 ± 0.07 | +","Markdown" +"Bioengineering","telatin/seqfu2","bench/deinterleave_benchmarks.md",".md","290","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu deinterleave -o de interleaved.fq` | 3.926 ± 0.080 | 3.831 | 4.075 | 1.00 | +| `taskset 1 ./bash_deinterleave.sh interleaved.fq de_R1.fq de_R2.fq` | 12.819 ± 0.098 | 12.659 | 12.952 | 3.26 ± 0.07 | +","Markdown" +"Bioengineering","telatin/seqfu2","bench/run-benchmarks.md",".md","1522","56","# Benchmark script + + +```bash +#!/bin/bash +# RUN BENCHMARKS +# requires hyperfine +if [[ $# != 2 ]] +then +echo ""USAGE: $0 R1.fastq.gz R2.fastq.gz"" +exit 1 +fi + +R1=""$1"" +R2=""$2"" + +################# +# PREPARE FILES # +################# +echo Decompress test files +zcat ""$R1"" > R1.fq +zcat ""$R2"" > R2.fq +seqfu interleave -1 R1.fq -2 R2.fq > interleaved.fq + + +hyperfine --warmup 1 --export-markdown interleave_benchmarks.md --export-csv interleave_benchmarks.csv ""seqfu interleave -1 R1.fq -2 R2.fq"" ""taskset 1 ./bash_interleave.sh R1.fq R2.fq"" + +hyperfine --warmup 1 --export-markdown deinterleave_benchmarks.md --export-csv deinterleave_benchmarks.csv ""seqfu deinterleave -o de interleaved.fq"" ""taskset 1 ./bash_deinterleave.sh interleaved.fq de_R1.fq de_R2.fq"" + + +#for i in {1..3} +#do time sleep 0.1 > /dev/null +#done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' + +# TIME TEST WITH DEINTERLEAVE +( +echo ""Testing SeqFu deinterleave:"" +echo -e ""TEST\tREAL\tUSER\tSYS"" +for i in {1..11} +do time seqfu deinterleave -o deinterleaved interleaved.fq +done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' +echo ""Testing BASH deinterleave:"" +echo -e ""TEST\tREAL\tUSER\tSYS"" +for i in {1..11} +do time paste - - - - - - - - < interleaved.fq | tee >(cut -f 1-4 | tr '\t' '\n' > deinterleaved.R1.fq) | cut -f 5-8 | tr '\t' '\n' > deinterleaved.R2.fq +done 2>&1 | paste - - - - | awk -v OFS='\t' '{print NR,$2,$4,$6}' +) > deinterleave.time.txt + + +############ +# CLEAN UP # +############ +rm -f R[12].fq interleaved.fq de_R[12].fq + + +```","Markdown" +"Bioengineering","telatin/seqfu2","bench/deinterleave.md",".md","383","5","| Command | Mean [s] | Min [s] | Max [s] | Relative | +|:---|---:|---:|---:|---:| +| `seqfu deinterleave -o deinterleaved. interleaved.fq` | 4.194 ± 0.060 | 4.086 | 4.311 | 1.00 | +| `paste - - - - - - - - < interleaved.fq \| tee >(cut -f 1-4 \| tr '\t' '\n' > R1.deinterleaved.fq) \| cut -f 5-8 \| tr '\t' '\n' > R2.deinterleaved.fq` | 5.106 ± 0.057 | 5.007 | 5.196 | 1.22 ± 0.02 | +","Markdown"