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740eb2d6e6b67af9e5c37653dcd82c5fa5ede7e2 | Rfam/rfam-production | scripts/processing/infernal_2_pdb_full_region.py | [
"Apache-2.0"
] | Python | convert_tblout_2_pdb_full_region | null | def convert_tblout_2_pdb_full_region(tblout_file, dest_dir=None):
"""
Converts Infernal's tblout file to pdb_full_region txt dump
for direct import to the rfam_live database
tblout_file: Infernal's tblout file
return: Void
"""
if dest_dir is None:
dest_dir = os.getcwd()
# Rfa... |
Converts Infernal's tblout file to pdb_full_region txt dump
for direct import to the rfam_live database
tblout_file: Infernal's tblout file
return: Void
| Converts Infernal's tblout file to pdb_full_region txt dump
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Infernal's tblout file
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ba4c493dbd6fbdfe1bd312b94b9d65252b0a3894 | Rfam/rfam-production | scripts/export/metagenomics/fasta2metseq.py | [
"Apache-2.0"
] | Python | fasta_to_metseq_dump | null | def fasta_to_metseq_dump(fasta_input, filename=None, dest_dir=None):
"""
Convert UMGS fasta file header accessions to metseq txt dump
fasta_input: A UMGS fasta file or a directory with multiple fasta files
filename: The output filename. If None, uses the UMGS filename by default
dest_dir: The desti... |
Convert UMGS fasta file header accessions to metseq txt dump
fasta_input: A UMGS fasta file or a directory with multiple fasta files
filename: The output filename. If None, uses the UMGS filename by default
dest_dir: The destination directory. If None, uses the input directory by default
returns:... | Convert UMGS fasta file header accessions to metseq txt dump
fasta_input: A UMGS fasta file or a directory with multiple fasta files
filename: The output filename. If None, uses the UMGS filename by default
dest_dir: The destination directory. If None, uses the input directory by default
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_ref_proteomes | <not_specific> | def fetch_ref_proteomes():
"""
This method returns a list of all reference proteome accessions available
from Uniprot
"""
ref_prot_list = []
response = urllib2.urlopen(REF_PROT_LIST_URL)
for ref_prot in response:
ref_prot_list.append(ref_prot.strip())
return ref_prot_list |
This method returns a list of all reference proteome accessions available
from Uniprot
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ref_prot_list = []
response = urllib2.urlopen(REF_PROT_LIST_URL)
for ref_prot in response:
ref_prot_list.append(ref_prot.strip())
return ref_prot_list | [
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | export_gca_accessions | <not_specific> | def export_gca_accessions(upid_gca):
"""
Retrieves reference proteomes ids and their associated gca accessions
as well as the taxonomic rank/domain (eukaryotes, bacteria etc)
upid_gca: Uniprot's tab separated file (UPID_GCA.tsv)
"""
# need to check if the path provided is a valid file
upid... |
Retrieves reference proteomes ids and their associated gca accessions
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upid_gca: Uniprot's tab separated file (UPID_GCA.tsv)
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prot = prot.strip().split('\t')
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} |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | extract_genome_acc | <not_specific> | def extract_genome_acc(prot_rdf):
"""
Extracts and returns the assembly accession from the proteome rdf
which provided as input. Returns -1 if not available
prot_rdf: A Uniprot's proteome rdf url or file path
"""
g = Graph()
response = requests.get(prot_rdf).status_code
if response ==... |
Extracts and returns the assembly accession from the proteome rdf
which provided as input. Returns -1 if not available
prot_rdf: A Uniprot's proteome rdf url or file path
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g.load(prot_rdf)
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | proteome_rdf_scanner | <not_specific> | def proteome_rdf_scanner(proteome):
"""
Scans a Uniprot's reference proteome rdf file and looks for all
available accessions. Returns a dictionary with GCA and WGS accessions
where applicable
prot_rdf: Uniprot's proteome rdf url or file path
"""
# need to do some http error handling here a... |
Scans a Uniprot's reference proteome rdf file and looks for all
available accessions. Returns a dictionary with GCA and WGS accessions
where applicable
prot_rdf: Uniprot's proteome rdf url or file path
| Scans a Uniprot's reference proteome rdf file and looks for all
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | proteome_xml_scanner | <not_specific> | def proteome_xml_scanner(proteome):
"""
Scans a Uniprot's reference proteome rdf file and looks for all
available accessions. Returns a dictionary with GCA and WGS accessions
where applicable
prot_xml: Uniprot's proteome rdf url or file path
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# need to do some http error handling here a... |
Scans a Uniprot's reference proteome rdf file and looks for all
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prot_xml: Uniprot's proteome rdf url or file path
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_ena_file | <not_specific> | def fetch_ena_file(acc, file_format, dest_dir, compressed=True):
"""
Retrieves a file given a valid ENA accession and stores it in the
indicated destination in the selected format
acc: A valid ENA entry accession
format: A valid ENA file format (xml, fasta, txt)
dest_dit: A valid path to destin... |
Retrieves a file given a valid ENA accession and stores it in the
indicated destination in the selected format
acc: A valid ENA entry accession
format: A valid ENA file format (xml, fasta, txt)
dest_dit: A valid path to destination directory
| Retrieves a file given a valid ENA accession and stores it in the
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seq_url = None
file_path = None
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seq_url = ENA_XML_URL % acc
file_path = os.path.join(dest_dir, acc + FORMATS[file_format])
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"# fetching compressed ... | [
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"docstring_toke... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | extract_assembly_accs | <not_specific> | def extract_assembly_accs(accession):
"""
Loads an xml tree from a file or a string (usually an http response),
and returns a list with the genome assembly's chromosomes
accession: A valid ENA GCA accession (without the assembly version)
"""
accessions = []
root = None
assembly_link = ... |
Loads an xml tree from a file or a string (usually an http response),
and returns a list with the genome assembly's chromosomes
accession: A valid ENA GCA accession (without the assembly version)
| Loads an xml tree from a file or a string (usually an http response),
and returns a list with the genome assembly's chromosomes
A valid ENA GCA accession (without the assembly version) | [
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... | def extract_assembly_accs(accession):
accessions = []
root = None
assembly_link = None
assembly = None
assembly_xml = requests.get(ENA_XML_URL % accession).content
if os.path.isfile(assembly_xml):
root = ET.parse(assembly_xml).getroot()
else:
root = ET.fromstring(assembly_xml... | [
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],
"outlier_params": [],
"others": []
} |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | download_genomes | <not_specific> | def download_genomes(gen, dest_dir):
"""
Downloads all chromosome files of a given assembly accession (ENA) in
dest_dir
gen: Single accession (string) or a list of genome accessions (GC*)
dest_dir: The path of the destination directory to export the fasta
files
"""
# need to add loggin... |
Downloads all chromosome files of a given assembly accession (ENA) in
dest_dir
gen: Single accession (string) or a list of genome accessions (GC*)
dest_dir: The path of the destination directory to export the fasta
files
| Downloads all chromosome files of a given assembly accession (ENA) in
dest_dir
Single accession (string) or a list of genome accessions (GC*)
dest_dir: The path of the destination directory to export the fasta
files | [
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accessions = None
if os.path.isfile(gen):
gen_fp = open(gen, 'r')
for gen_acc in gen_fp:
gen_acc = string.strip(gen_acc)
if string.find(gen_acc, '.') != -1:
gen_acc = gen_acc.partition('.')
gen_acc = gen... | [
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"# need to add logging",
"# if no accessio... | [
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] | {
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{
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"docstring_tokens"... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_genome | null | def fetch_genome(gen, dest_dir):
"""
Downloads and parses xml file of the given genome accession (gen), and
downloads all chromosome files in fasta format in destination directory
(dest_dir). The xml file is deleted after completion.
gen: ENA assembly accession (GCA*)
dest_dir: Destination of t... |
Downloads and parses xml file of the given genome accession (gen), and
downloads all chromosome files in fasta format in destination directory
(dest_dir). The xml file is deleted after completion.
gen: ENA assembly accession (GCA*)
dest_dir: Destination of the output directory
| Downloads and parses xml file of the given genome accession (gen), and
downloads all chromosome files in fasta format in destination directory
(dest_dir). The xml file is deleted after completion.
ENA assembly accession (GCA*)
dest_dir: Destination of the output directory | [
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... | def fetch_genome(gen, dest_dir):
gen_dir = os.path.join(dest_dir, gen.partition('.')[0])
try:
os.mkdir(gen_dir)
except:
pass
fetch_ena_file(gen, "xml", gen_dir)
gen_xml = os.path.join(gen_dir, gen + ".xml")
chroms = extract_assembly_accs(gen_xml)
for chrom in chroms:
... | [
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"docstring_tokens"... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | rdf_accession_search | <not_specific> | def rdf_accession_search(ref_prot_acc, sub_str):
"""
Parses rdf url and returns a list of ENA accessions
rdf_url: The url to a Uniprot's reference proteome rdf url
sub_str: A sub string to look for in the rdf file
"""
accessions = []
rdf_graph = Graph()
rdf_url = PROTEOME_URL % ref_pro... |
Parses rdf url and returns a list of ENA accessions
rdf_url: The url to a Uniprot's reference proteome rdf url
sub_str: A sub string to look for in the rdf file
| Parses rdf url and returns a list of ENA accessions
rdf_url: The url to a Uniprot's reference proteome rdf url
sub_str: A sub string to look for in the rdf file | [
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"the... | def rdf_accession_search(ref_prot_acc, sub_str):
accessions = []
rdf_graph = Graph()
rdf_url = PROTEOME_URL % ref_prot_acc
response = requests.get(rdf_url).status_code
if response == httplib.OK:
rdf_graph.load(rdf_url)
for s, p, o in rdf_graph:
if string.find(o, sub_str) ... | [
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rdf_url: The url to a Uniprot's reference proteome rdf url
sub_str: A sub string to look for in the rdf file | [
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] | [
{
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}
] | {
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"docstring... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | assembly_report_parser | <not_specific> | def assembly_report_parser(assembly_report, url=True):
"""
Parses an assembly report file and returns a list of all available
accessions (scaffolds, contigs etc)
report_url: A url provided within an ENA assembly xml file. This is the
text of URL tag under ASSEMBLY/ASSEMBLY_LINKS/ASSEMBLY_LINK.By de... |
Parses an assembly report file and returns a list of all available
accessions (scaffolds, contigs etc)
report_url: A url provided within an ENA assembly xml file. This is the
text of URL tag under ASSEMBLY/ASSEMBLY_LINKS/ASSEMBLY_LINK.By default this
is an ftp request url. Converting to http to fe... | Parses an assembly report file and returns a list of all available
accessions (scaffolds, contigs etc)
A url provided within an ENA assembly xml file. This is the
text of URL tag under ASSEMBLY/ASSEMBLY_LINKS/ASSEMBLY_LINK.By default this
is an ftp request url. Converting to http to fetch assembly accessions. | [
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accessions = []
report_url = None
ass_rep_file = None
if url is True:
report_url = assembly_report.replace("ftp://", "http://")
ass_rep_file = requests.get(report_url).content.split('\n')[1:]
if ass_rep_file[len(ass_rep_file)... | [
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] | {
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{
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"docstring_... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | lsf_cmd_generator | <not_specific> | def lsf_cmd_generator(upid, gca_acc, domain, exec_path, proj_dir):
"""
Generates an lsf job command for downloading a new genome. Returns an
LSF specific bsub command
upid: Uniprot's reference proteome id
gca_acc: ENA's genome accession. -1 if there's no available id
domain: Proteome's taxonomi... |
Generates an lsf job command for downloading a new genome. Returns an
LSF specific bsub command
upid: Uniprot's reference proteome id
gca_acc: ENA's genome accession. -1 if there's no available id
domain: Proteome's taxonomic domain
exec_path: The path to the pipeline executable
proj_dir: ... | Generates an lsf job command for downloading a new genome. Returns an
LSF specific bsub command
Uniprot's reference proteome id
gca_acc: ENA's genome accession. -1 if there's no available id
domain: Proteome's taxonomic domain
exec_path: The path to the pipeline executable
proj_dir: The path to the project directory | [
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... | def lsf_cmd_generator(upid, gca_acc, domain, exec_path, proj_dir):
subdir_idx = upid[8:]
prot_dir = os.path.join(os.path.join(proj_dir, subdir_idx), upid)
cmd = ("bsub -M %s "
"-R \"rusage[mem=%s,tmp=%s]\" "
"-o \"%s\" "
"-e \"%s\" "
"-u \"%s\" "
"-n 4 ... | [
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"docstring_tokens"... |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | genome_script_generator | null | def genome_script_generator(upid, domain, gen_size, out_dir):
"""
Generates a shell script for a proteome with ip upid under out_dir.
Memory is reserved according to genome size
upid: Uniprot's unique proteome id
domain: The domain under which a proteome has been classified
gen_size: The genome... |
Generates a shell script for a proteome with ip upid under out_dir.
Memory is reserved according to genome size
upid: Uniprot's unique proteome id
domain: The domain under which a proteome has been classified
gen_size: The genome's size
out_dir: Destination directory
| Generates a shell script for a proteome with ip upid under out_dir.
Memory is reserved according to genome size
Uniprot's unique proteome id
domain: The domain under which a proteome has been classified
gen_size: The genome's size
out_dir: Destination directory | [
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shell_fp = open(os.path.join(out_dir, upid + ".sh"), 'w')
mem_size = 8000
tmp_size = gen_size * 2
tmp_dir = "/tmp/%s_$LSB_JOBID" % (upid)
prot_dest_dir = os.path.join(
os.path.join(os.path.split(out_dir)[0], domain), upid)
she... | [
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | load_upid_gca_pairs | <not_specific> | def load_upid_gca_pairs():
"""
This is an alternative version to load_upid_gca_file loading the pairs from
Uniprot's REST API. Returns a dictionary of upid, gca accession pairs,
including the species kingdom
"""
id_pairs = {}
response = requests.get(gc.REF_PROT_REST_URL)
if response.st... |
This is an alternative version to load_upid_gca_file loading the pairs from
Uniprot's REST API. Returns a dictionary of upid, gca accession pairs,
including the species kingdom
| This is an alternative version to load_upid_gca_file loading the pairs from
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id_pairs = {}
response = requests.get(gc.REF_PROT_REST_URL)
if response.status_code == 200:
content = response.content
prot_lines = content.split('\n')
prot_lines.pop(0)
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_genome_accessions | <not_specific> | def fetch_genome_accessions(upid, gca_acc):
"""
Fetches and returns a list of all accessions for a specific ref. proteome
upid: Uniprot's ref. proteome id
gca_acc: An ENA GCA accession associated with the upid (if available or -1)
"""
gen_accs = []
gca_acc = str(gca_acc)
# there's a G... |
Fetches and returns a list of all accessions for a specific ref. proteome
upid: Uniprot's ref. proteome id
gca_acc: An ENA GCA accession associated with the upid (if available or -1)
| Fetches and returns a list of all accessions for a specific ref. proteome
upid: Uniprot's ref. proteome id
gca_acc: An ENA GCA accession associated with the upid (if available or -1) | [
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gen_accs = []
gca_acc = str(gca_acc)
if gca_acc != "-1":
gca_acc = gca_acc.split('.')[0]
gen_accs = extract_assembly_accs(gca_acc)
else:
prot_accs = proteome_rdf_scanner(upid)
if prot_accs["GCA"] == -1 and prot_accs["WGS"] == -1... | [
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_wgs_range_accs | <not_specific> | def fetch_wgs_range_accs(wgs_range):
"""
Splits the WGS range into distinct accessions for metadata retrieval
wgs_range: A valid ENA-WGS set range
"""
wgs_accs = []
wgs_end_points = wgs_range.strip().split('-')
wgs_prefix = wgs_end_points[0][0:5]
wgs_start = int(wgs_end_points[0][5:]... |
Splits the WGS range into distinct accessions for metadata retrieval
wgs_range: A valid ENA-WGS set range
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wgs_range: A valid ENA-WGS set range | [
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wgs_accs = []
wgs_end_points = wgs_range.strip().split('-')
wgs_prefix = wgs_end_points[0][0:5]
wgs_start = int(wgs_end_points[0][5:])
wgs_end = int(wgs_end_points[1][5:])
wgs_acc = ''
while wgs_start < wgs_end:
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],
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} |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | genome_download_validator | null | def genome_download_validator(genome_dir):
"""
Loop over Genome Download output directory and report any upids with
erroneous output
genome_dir: The path to Genome Download output directory
"""
erroneous_genomes = {}
# list all kingdom dirs under genome output directory
project_dirs =... |
Loop over Genome Download output directory and report any upids with
erroneous output
genome_dir: The path to Genome Download output directory
| Loop over Genome Download output directory and report any upids with
erroneous output
The path to Genome Download output directory | [
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erroneous_genomes = {}
project_dirs = os.listdir(genome_dir)
kingdom_dirs = [x for x in project_dirs if os.path.isdir(os.path.join(genome_dir, x))]
for kingdom in kingdom_dirs:
erroneous_genomes[kingdom] = []
kingdom_dir_loc = os.path.join(genom... | [
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | download_fasta_from_ncbi | <not_specific> | def download_fasta_from_ncbi(accession, dest_dir):
"""
Download fasta sequences from NCBI. In case of ENA obsolete sequences use
this function to download the relevant files
accession: A genome accession to download
dest_dir: Destination directory to save the file to
return: True on success, o... |
Download fasta sequences from NCBI. In case of ENA obsolete sequences use
this function to download the relevant files
accession: A genome accession to download
dest_dir: Destination directory to save the file to
return: True on success, otherwise False
| Download fasta sequences from NCBI. In case of ENA obsolete sequences use
this function to download the relevant files
A genome accession to download
dest_dir: Destination directory to save the file to
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seq_url = None
file_path = None
seq_url = NCBI_SEQ_URL % (accession)
file_path = os.path.join(dest_dir, accession + '.fa')
urllib.urlretrieve(seq_url, file_path)
if os.path.exists(file_path):
return True
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | download_sequence_report_files | null | def download_sequence_report_files(project_dir, upid_gca_file):
"""
Loads upid_gca_file json file and downloads from ENA all sequence report
files per GCA accession. Skips if no GCA accession available
project_dir: The path to a project directory as generated by Genome
Download pipeline (genome_dow... |
Loads upid_gca_file json file and downloads from ENA all sequence report
files per GCA accession. Skips if no GCA accession available
project_dir: The path to a project directory as generated by Genome
Download pipeline (genome_downloader.py)
upid_gca_file: upid_gca file in json format as generate... | Loads upid_gca_file json file and downloads from ENA all sequence report
files per GCA accession. Skips if no GCA accession available
The path to a project directory as generated by Genome
Download pipeline (genome_downloader.py)
upid_gca_file: upid_gca file in json format as generated by the Genome
download pipeline ... | [
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acc_pairs = json.load(upid_gca_fp)
upid_gca_fp.close()
for upid in acc_pairs.keys():
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | sequence_report_to_json | <not_specific> | def sequence_report_to_json(seq_report_file, dest_dir=None):
"""
Convert a GCA sequence report file (ENA) from .txt to .json format
seq_report_file: The path to a valid GCA related sequence report file
dest_dir: The path to destination directory. If None use the directory
of the input file
ret... |
Convert a GCA sequence report file (ENA) from .txt to .json format
seq_report_file: The path to a valid GCA related sequence report file
dest_dir: The path to destination directory. If None use the directory
of the input file
return: Accession dictionary
| Convert a GCA sequence report file (ENA) from .txt to .json format
seq_report_file: The path to a valid GCA related sequence report file
dest_dir: The path to destination directory. If None use the directory
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Accession dictionary | [
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seq_rep_fp.readline()
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | split_and_download | null | def split_and_download(wgs_range, dest_dir):
"""
Function to split and download smaller segments of large genome assemblies
wgs_range: A WGS assembly sequence accession range from ENA
(e.g. CBTL0100000001-CBTL0111673940)
dest_dir: The path to the destination directory
returns: void
"""
... |
Function to split and download smaller segments of large genome assemblies
wgs_range: A WGS assembly sequence accession range from ENA
(e.g. CBTL0100000001-CBTL0111673940)
dest_dir: The path to the destination directory
returns: void
| Function to split and download smaller segments of large genome assemblies
wgs_range: A WGS assembly sequence accession range from ENA
dest_dir: The path to the destination directory
void | [
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accessions = fetch_wgs_range_accs(wgs_range)
file_no = len(accessions) / MAX_SEQS
remainder = len(accessions) % MAX_SEQS
count = 0
idx1 = 0
idx2 = MAX_SEQS
while count < file_no:
accession = accessions[idx1] + '-' + accessions[idx2]
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | fetch_accessions_from_proteome_xml | <not_specific> | def fetch_accessions_from_proteome_xml(proteome):
"""
Parses Uniprot's proteome xml and extracts all available ENA accessions
proteome: A valid Uniprot's proteome accession
returns: A list of genome accessions
"""
prot_accessions = []
# namespace prefix # or register a namespace in the ET... |
Parses Uniprot's proteome xml and extracts all available ENA accessions
proteome: A valid Uniprot's proteome accession
returns: A list of genome accessions
| Parses Uniprot's proteome xml and extracts all available ENA accessions
proteome: A valid Uniprot's proteome accession
A list of genome accessions | [
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prot_accessions = []
prefix = "{http://uniprot.org/uniprot}%s"
response = requests.get(gc.PROTEOME_XML_URL % proteome)
if response.status_code == 200:
prot_tree_root = ET.fromstring(response.content)
proteome = prot_tree_root.find(prefix ... | [
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} |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | check_accession_availability | <not_specific> | def check_accession_availability(accession):
"""
Check whether a specific accession is available from ENA
accession: sequence accession
return: True if accession is available, False otherwise
"""
# we can expand this by adding a db option (e.g. ena, uniprot, ncbi)
response = requests.get(E... |
Check whether a specific accession is available from ENA
accession: sequence accession
return: True if accession is available, False otherwise
| Check whether a specific accession is available from ENA
accession: sequence accession
return: True if accession is available, False otherwise | [
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response = requests.get(ENA_XML_URL % accession)
if response.status_code == httplib.OK:
xml_root = ET.fromstring(response.content)
entry_node = None
entry_node = xml_root.find("entry")
if entry_node is None:
return False
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} |
8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | copy_wgs_set_from_ftp | null | def copy_wgs_set_from_ftp(wgs_acc, dest_dir):
"""
Copy wgs set sequences from physical location on cluster
wsg_acc: A valid WGS set accession (e.g. AAVU01000000)
dest_dir: Destination directory where the sequences will be copied to
return: void
"""
# build path
wgs_subdir = os.path.jo... |
Copy wgs set sequences from physical location on cluster
wsg_acc: A valid WGS set accession (e.g. AAVU01000000)
dest_dir: Destination directory where the sequences will be copied to
return: void
| Copy wgs set sequences from physical location on cluster
wsg_acc: A valid WGS set accession
dest_dir: Destination directory where the sequences will be copied to
void | [
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wgs_subdir = os.path.join(gc.ENA_FTP_WGS_PUB, wgs_acc[0:2].lower())
wgs_filename = wgs_acc[0:6] + ".fasta.gz"
if os.path.exists(os.path.join(wgs_subdir, wgs_filename)):
shutil.copyfile(os.path.join(wgs_subdir, wgs_filename),
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | proteome_xml_accessions_to_dict | <not_specific> | def proteome_xml_accessions_to_dict(upid):
"""
Parses a valid proteome xml file and returns all accessions in the form of
a dictionary. Component names from proteome xml are used as dictionary keys
upid: A valid Uniprot proteome upid
returns: A dictionary with all proteome associated accessions.
... |
Parses a valid proteome xml file and returns all accessions in the form of
a dictionary. Component names from proteome xml are used as dictionary keys
upid: A valid Uniprot proteome upid
returns: A dictionary with all proteome associated accessions.
| Parses a valid proteome xml file and returns all accessions in the form of
a dictionary. Component names from proteome xml are used as dictionary keys
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proteome_accs = {"GCA": -1, "WGS": -1}
other = {}
prefix = "{http://uniprot.org/uniprot}%s"
response = requests.get(gc.PROTEOME_XML_URL % upid)
if response.status_code == 200:
prot_tree_root = ET.fromstring(response.content)
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | copy_gca_report_file_from_ftp | <not_specific> | def copy_gca_report_file_from_ftp(gca_accession, dest_dir):
"""
Copies the corresponding GCA report file from the ftp
gca_accession: A valid GCA accession
return: True if the file was found, False otherwise
"""
seq_report_file = gca_accession + "_sequence_report.txt"
genomic_regions_file ... |
Copies the corresponding GCA report file from the ftp
gca_accession: A valid GCA accession
return: True if the file was found, False otherwise
| Copies the corresponding GCA report file from the ftp
gca_accession: A valid GCA accession
True if the file was found, False otherwise | [
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seq_report_file = gca_accession + "_sequence_report.txt"
genomic_regions_file = gca_accession + "_regions.txt"
gca_dir = os.path.join(gc.ENA_GCA_SEQ_REPORT, gca_accession[0:7])
gca_dir = os.path.join(gca_dir, gca_accession[0:10])
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | extract_wgs_acc_from_gca_xml | <not_specific> | def extract_wgs_acc_from_gca_xml(gca_accession):
"""
Parses ENA's GCA xml file and extracts the WGS set accession if available
gca_accession: A valid GCA accession
return: A WGS set accesison, None if not found
"""
xml_root = None
wgs_acc = None
assembly_xml = requests.get(ENA_XML_UR... |
Parses ENA's GCA xml file and extracts the WGS set accession if available
gca_accession: A valid GCA accession
return: A WGS set accesison, None if not found
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gca_accession: A valid GCA accession
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wgs_acc = None
assembly_xml = requests.get(ENA_XML_URL % gca_accession).content
if os.path.isfile(assembly_xml):
xml_root = ET.parse(assembly_xml).getroot()
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8a0780c002a6f23c782f35e6cd0023c85eb32c56 | Rfam/rfam-production | scripts/export/genomes/genome_fetch.py | [
"Apache-2.0"
] | Python | download_gca_report_file_from_url | <not_specific> | def download_gca_report_file_from_url(gca_accession, dest_dir):
"""
Loads an xml tree from a file or a string (usually an http response),
and returns a list with the genome assembly's chromosomes
accession: A valid ENA GCA accession (without the assembly version)
"""
accessions = []
root =... |
Loads an xml tree from a file or a string (usually an http response),
and returns a list with the genome assembly's chromosomes
accession: A valid ENA GCA accession (without the assembly version)
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assembly = None
url_links = []
assembly_xml = requests.get(ENA_XML_URL % gca_accession).content
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e1adc3d5a1566283ebe0be575b139f8395d78208 | Rfam/rfam-production | scripts/release/uniprot_file_converter.py | [
"Apache-2.0"
] | Python | convert_proteome_list_to_upid_gca_file | null | def convert_proteome_list_to_upid_gca_file(input_file, filename=None, dest_dir=None):
"""
Converts a proteome list file in tabular format to the upid_gca file format
used with the genome_downloader and genome_search pipelines
input_file: A proteome-all.tab file downloaded from Uniprot's proteomes websi... |
Converts a proteome list file in tabular format to the upid_gca file format
used with the genome_downloader and genome_search pipelines
input_file: A proteome-all.tab file downloaded from Uniprot's proteomes website
filename: A name for the new file to be generated. Defaults to input_file filename
... | Converts a proteome list file in tabular format to the upid_gca file format
used with the genome_downloader and genome_search pipelines
A proteome-all.tab file downloaded from Uniprot's proteomes website
filename: A name for the new file to be generated. Defaults to input_file filename
if None
dest_dir: A path to an o... | [
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input_fp = open(input_file, 'r')
if filename is None:
filename = os.path.basename(input_file).partition('.')[0]
if dest_dir is None:
dest_dir = os.path.split(input_file)[0]
output_fp = open(os.path.join... | [
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e1adc3d5a1566283ebe0be575b139f8395d78208 | Rfam/rfam-production | scripts/release/uniprot_file_converter.py | [
"Apache-2.0"
] | Python | dump_new_upids_to_file | null | def dump_new_upids_to_file(upid_gca_old, upid_gca_new, dest_dir=None):
"""
Compares two upid_gca files from different Uniprot proteome releases
and dumps the new upids in a new upid_gca file all resulting from the
newer version of the proteome file (upid_gca_new). To be used for
downloading a subset... |
Compares two upid_gca files from different Uniprot proteome releases
and dumps the new upids in a new upid_gca file all resulting from the
newer version of the proteome file (upid_gca_new). To be used for
downloading a subset of genomes.
upid_gca_out: A valid upid_gca file in .tsv format of an old... | Compares two upid_gca files from different Uniprot proteome releases
and dumps the new upids in a new upid_gca file all resulting from the
newer version of the proteome file (upid_gca_new). To be used for
downloading a subset of genomes.
A valid upid_gca file in .tsv format of an older reference
proteome release
upid_... | [
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old_upids = {}
upid_gca_old_fp = open(upid_gca_old, 'r')
upid_gca_new_fp = open(upid_gca_new, 'r')
for line in upid_gca_old_fp:
fields = line.strip().split('\t')
if fields[0] not in old_upids:
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | generate_genome_text_file_from_file | null | def generate_genome_text_file_from_file(names_list, release_version, dest_dir):
"""
Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
names_list: A tab delimited file containing mappings of the
assembly name and the genome scientific name e.g... |
Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
names_list: A tab delimited file containing mappings of the
assembly name and the genome scientific name e.g hg38\thomo_sapiens
version: The version of the release
dest_dir: The destinati... | Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
A tab delimited file containing mappings of the
assembly name and the genome scientific name e.g hg38\thomo_sapiens
version: The version of the release
dest_dir: The destination directory where the genome.txt
fil... | [
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trackdb_url = "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/%s/genome_browser_hub/%s/trackDb.txt"
fp_in = open(names_list, 'r')
name_mappings = {}
for line in fp_in:
line = line.strip().split('\t')
if line[0] not i... | [
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | generate_genome_text_file_from_dict | null | def generate_genome_text_file_from_dict(accession_dict, release_version, dest_dir):
"""
Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
names_list: A tab delimited file containing mappings of the
assembly name and the genome scientific name... |
Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
names_list: A tab delimited file containing mappings of the
assembly name and the genome scientific name e.g hg38\thomo_sapiens
version: The version of the release
dest_dir: The destinati... | Generates the genome.txt file for the genome_browser_hup given a list
of assembly-scientific name mappings
A tab delimited file containing mappings of the
assembly name and the genome scientific name e.g hg38\thomo_sapiens
version: The version of the release
dest_dir: The destination directory where the genome.txt
fil... | [
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trackdb_url = "ftp://ftp.ebi.ac.uk/pub/databases/Rfam/%s/genome_browser_hub/%s/trackDb.txt"
fp_out = open(os.path.join(dest_dir, "genomes.txt"), 'w')
for genome in accession_dict.keys():
fp_out.write("genome %s\n" % ... | [
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | generate_hub_txt_file | null | def generate_hub_txt_file(release_version, dest_dir):
"""
Generates the hub.txt file for the new Rfam release
release_version: The Rfam release version
dest_dir:
return: void
"""
# convert to string and chop off the decimals
rel_version_int = str(release_version).partition(".")[0]
... |
Generates the hub.txt file for the new Rfam release
release_version: The Rfam release version
dest_dir:
return: void
| Generates the hub.txt file for the new Rfam release
release_version: The Rfam release version
dest_dir.
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rel_version_int = str(release_version).partition(".")[0]
fp_out = open(os.path.join(dest_dir, "hub.txt"), 'w')
fp_out.write("hub rfam%s\n" % rel_version_int)
fp_out.write("shortLabel rfam%s_ncRNA\n" % rel_version_int)
fp_out.write("longLabel Rfam... | [
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | genome_browser_hub_id_list_parser | <not_specific> | def genome_browser_hub_id_list_parser(genome_id_list):
"""
Parses the input file of genome browser hub and returns
a dictionary with the ids to be used to generate all
related sub directories and files
genome_id_list: A tab delimited file containing the genome upids, assembly names and
scientif... |
Parses the input file of genome browser hub and returns
a dictionary with the ids to be used to generate all
related sub directories and files
genome_id_list: A tab delimited file containing the genome upids, assembly names and
scientific names for each genome
return: A dictionary in the form... | Parses the input file of genome browser hub and returns
a dictionary with the ids to be used to generate all
related sub directories and files
A tab delimited file containing the genome upids, assembly names and
scientific names for each genome
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accession_mapings = {}
fp_in = open(genome_id_list, 'r')
if genome_id_list.endswith(".json"):
accession_mapings = json.load(fp_in)
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for line in fp_in:
line = line.strip().split('\t')
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | generate_trackdb_file | null | def generate_trackdb_file(species, release_version, dest_dir):
"""
Creates a new species trackDb.txt file for a given Rfam release version
species: The name of the species directory
release_version: The version of the Rfam release
dest_dir: The path to the species directory where the trackDb file w... |
Creates a new species trackDb.txt file for a given Rfam release version
species: The name of the species directory
release_version: The version of the Rfam release
dest_dir: The path to the species directory where the trackDb file will
be generated
return: void
| Creates a new species trackDb.txt file for a given Rfam release version
species: The name of the species directory
release_version: The version of the Rfam release
dest_dir: The path to the species directory where the trackDb file will
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void | [
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trackDb_fp = open(os.path.join(dest_dir, "trackDb.txt"), 'w')
trackDb_fp.write("track Rfam\n")
trackDb_fp.write("bigDataUrl ftp://ftp.ebi.ac.uk/pub/databases/Rfam/%s/genome_browser_hub/%s/bigBed\n" %
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3a6a01f1187d5db6c8b60fe8ac62b56dd6b5927b | Rfam/rfam-production | scripts/release/genome_browser_hub_generator.py | [
"Apache-2.0"
] | Python | generate_new_genome_browser_hub_directories | null | def generate_new_genome_browser_hub_directories(genome_id_file, release_version, dest_dir, genome_project_dir):
"""
Generates a new genome_browser_hub directory for an upcoming Rfam release
genome_id_file: A tab delimited file containing the genome upids, assembly names and
scientific names for each ge... |
Generates a new genome_browser_hub directory for an upcoming Rfam release
genome_id_file: A tab delimited file containing the genome upids, assembly names and
scientific names for each genome
release_version: The Rfam version the genome browser hub derives from
dest_dir: A valid path where to gene... | Generates a new genome_browser_hub directory for an upcoming Rfam release
genome_id_file: A tab delimited file containing the genome upids, assembly names and
scientific names for each genome
release_version: The Rfam version the genome browser hub derives from
dest_dir: A valid path where to generate the directories. ... | [
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accession_mapings = genome_browser_hub_id_list_parser(genome_id_file)
if not os.path.exists(dest_dir):
os.mkdir(dest_dir)
bed_files_dir = os.path.join(dest_dir, "bed_files")
os.mkdir(b... | [
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e77e368243c16e3fee537c1b554298218306a70d | Rfam/rfam-production | scripts/support/populate_seed_region_md5.py | [
"Apache-2.0"
] | Python | fetch_sequence | <not_specific> | def fetch_sequence(seq_file, seq_acc, seq_start, seq_end):
"""
Extracts a sequence from sequence file seq_file using rfamseq_acc
and sequence start-end positions (seq_start, seq_end)
seq_file: A sequence file in fasta format to extract a sequence from
seq_acc: The accession of the sequence to extrac... |
Extracts a sequence from sequence file seq_file using rfamseq_acc
and sequence start-end positions (seq_start, seq_end)
seq_file: A sequence file in fasta format to extract a sequence from
seq_acc: The accession of the sequence to extract
seq_start: The starting position of the sequence/subsequence... | Extracts a sequence from sequence file seq_file using rfamseq_acc
and sequence start-end positions (seq_start, seq_end)
seq_file: A sequence file in fasta format to extract a sequence from
seq_acc: The accession of the sequence to extract
seq_start: The starting position of the sequence/subsequence
seq_end: The end pos... | [
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cmd = "%s %s %s/%s-%s" % (ESL_PATH,
seq_file, str(seq_acc),
str(seq_start), str(seq_end))
proc = subprocess.Popen(
cmd, shell=True, stdout=subprocess.PIPE)
seq = proc.communicate... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | fetch_seed_sequence_coordinates | <not_specific> | def fetch_seed_sequence_coordinates(seed_seq, full_seq):
"""
Returns seed sequence start and end coordinates based on the
accession provided as input
accession: A valid GenBank|ENA\RNAcentral accession
return: A tuple with start and end coordinates in this order
"""
start = 0
end = 0
... |
Returns seed sequence start and end coordinates based on the
accession provided as input
accession: A valid GenBank|ENA\RNAcentral accession
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accession provided as input
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start = 0
end = 0
start = full_seq.find(seed_seq)
end = start + len(seed_seq)
if start != -1:
return (start+1, end)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | load_fasta_file_to_dict | <not_specific> | def load_fasta_file_to_dict(fasta):
"""
Loads a fasta file (seqdb) into a dictionary with the sequence
accession used as a key and the sequence as a value
fasta: A valid sequence file in fasta format
return: A python dictionary with accession:sequence pairs
"""
fasta_dict = {}
fasta_... |
Loads a fasta file (seqdb) into a dictionary with the sequence
accession used as a key and the sequence as a value
fasta: A valid sequence file in fasta format
return: A python dictionary with accession:sequence pairs
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fasta_dict = {}
fasta_fp = open(fasta, 'r')
accession = ""
flag_init_seq = 0
for line in fasta_fp:
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elements = line[1:].split(' ')
accession = elements[0]
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} |
4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | stockhom_to_pfam_format | <not_specific> | def stockhom_to_pfam_format(stk_msa, dest_dir=None):
"""
Converts a stockholm MSA to the Pfam format
stk_msa: A valid MSA in strockholm format
dest_dir: The destination directory where the new MSA
will be generated
return: The output MSA in Pfam format, None otherwise
"""
filename = os... |
Converts a stockholm MSA to the Pfam format
stk_msa: A valid MSA in strockholm format
dest_dir: The destination directory where the new MSA
will be generated
return: The output MSA in Pfam format, None otherwise
| Converts a stockholm MSA to the Pfam format
stk_msa: A valid MSA in strockholm format
dest_dir: The destination directory where the new MSA
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filename = os.path.basename(stk_msa).partition('.')[0]
output_pfam_msa = os.path.join(dest_dir, filename + ".pfam")
cmd = "esl-reformat pfam %s > %s" % (stk_msa, output_pfam_msa)
subprocess.call(cmd, shell=True)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | pfam_to_stockholm_format | <not_specific> | def pfam_to_stockholm_format(pfam_msa, dest_dir=None):
"""
Converts a Pfam MSA to the stockholm format
pfam_msa: A valid MSA in Pfam format
dest_dir: The destination directory where the new MSA
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return: The output MSA in Stockholm format, None otherwise
"""
filename =... |
Converts a Pfam MSA to the stockholm format
pfam_msa: A valid MSA in Pfam format
dest_dir: The destination directory where the new MSA
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return: The output MSA in Stockholm format, None otherwise
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output_stk_msa = os.path.join(dest_dir, filename + ".stk")
cmd = "esl-reformat stockholm %s > %s" % (pfam_msa, output_stk_msa)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | relabel_seed_accessions | <not_specific> | def relabel_seed_accessions(seed, accession_coords, dest_dir = None):
"""
Re-writes a seed file with the sequence coordinates appended to the
sequence accessions
seed: A seed file with no star-end sequence coordinates
return: The path to the newly relabelled SEED alignment
"""
if dest_dir... |
Re-writes a seed file with the sequence coordinates appended to the
sequence accessions
seed: A seed file with no star-end sequence coordinates
return: The path to the newly relabelled SEED alignment
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if dest_dir is None:
dest_dir = os.path.split(seed)[0]
sequence_label = 0
new_line = ''
filename = os.path.split(seed)[1].partition('.')[0]
new_seed_loc = os.path.join(dest_dir, filename+'_relabelled')
seed_fp = open(s... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | fetch_RNAcentral_id | <not_specific> | def fetch_RNAcentral_id(sequence):
"""
Looks for a sequence match in RNAcentral based on sequence md5
and fetches the corresponding RNAcentral accession
sequence: A valid DNA/RNA sequence
return: Returns RNAcentral id, otherwise returns None
"""
sequence_md5 = sequence_to_md5(sequence)
... |
Looks for a sequence match in RNAcentral based on sequence md5
and fetches the corresponding RNAcentral accession
sequence: A valid DNA/RNA sequence
return: Returns RNAcentral id, otherwise returns None
| Looks for a sequence match in RNAcentral based on sequence md5
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sequence_md5 = sequence_to_md5(sequence)
rnacentral_url = 'https://rnacentral.org/api/v1/rna'
response = requests.get(rnacentral_url, params={'md5': sequence_md5})
data = response.json()
if data['count'] > 0:
return data['results'][0]['rnacentral_id']
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | generate_seed_id_from_RNAcentral | <not_specific> | def generate_seed_id_from_RNAcentral(sequence):
"""
Generates a seed accession based on a sequence mad5 match in RNAcentral
sequence: A valid DNA/RNA sequence
return: Returns RNAcentral id, otherwise returns None
"""
sequence_md5 = sequence_to_md5(sequence)
rnacentral_url = 'https://rnac... |
Generates a seed accession based on a sequence mad5 match in RNAcentral
sequence: A valid DNA/RNA sequence
return: Returns RNAcentral id, otherwise returns None
| Generates a seed accession based on a sequence mad5 match in RNAcentral
sequence: A valid DNA/RNA sequence
Returns RNAcentral id, otherwise returns None | [
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sequence_md5 = sequence_to_md5(sequence)
rnacentral_url = 'https://rnacentral.org/api/v1/rna'
response = requests.get(rnacentral_url, params={'md5': sequence_md5})
data = response.json()
if data['count'] > 0:
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} |
4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | sequence_to_md5 | <not_specific> | def sequence_to_md5(sequence):
"""
Converts a sequence to an md5 hash after replacing Us with
Ts
sequence: A valid RNA/DNA sequence
return: MD5 hash of the sequence
"""
md5_converter = hashlib.md5()
# convert to DNA
sequence = sequence.replace('U', 'T')
md5_converter.update(se... |
Converts a sequence to an md5 hash after replacing Us with
Ts
sequence: A valid RNA/DNA sequence
return: MD5 hash of the sequence
| Converts a sequence to an md5 hash after replacing Us with
Ts
A valid RNA/DNA sequence
MD5 hash of the sequence | [
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md5_converter = hashlib.md5()
sequence = sequence.replace('U', 'T')
md5_converter.update(sequence.encode('utf-8'))
sequence_md5 = md5_converter.hexdigest()
return sequence_md5 | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | validate_sequences | <not_specific> | def validate_sequences(seed_sequence, extracted_full_seq, rnac=True):
"""
Validates whether the SEED sequence matches the sequence
extracted at specific coordinates
seed_sequence: A DNA/RNA sequecne extracted from the SEED alignment
extracted_full: A DNA/RNA subsequence extracted at specific locati... |
Validates whether the SEED sequence matches the sequence
extracted at specific coordinates
seed_sequence: A DNA/RNA sequecne extracted from the SEED alignment
extracted_full: A DNA/RNA subsequence extracted at specific locations
return: True if the sequences match, False otherwise. Returns False ... | Validates whether the SEED sequence matches the sequence
extracted at specific coordinates
A DNA/RNA sequecne extracted from the SEED alignment
extracted_full: A DNA/RNA subsequence extracted at specific locations
True if the sequences match, False otherwise. Returns False by default | [
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new_seed_sequence = seed_sequence
if rnac is False:
new_seed_sequence = seed_sequence.replace('U', 'T')
if extracted_full_seq.find(new_seed_sequence) != -1:
return True
return False | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | seed_to_fasta | <not_specific> | def seed_to_fasta(seed_msa, dest_dir=None):
"""
Converts a multiple sequence alignment (MSA) to fasta
param seed_msa: A valid Rfam SEED file in stockholm format to convert to fasta
return: Path to updated seed file
"""
filename = ""
path_elements = os.path.split(seed_msa)
if dest_di... |
Converts a multiple sequence alignment (MSA) to fasta
param seed_msa: A valid Rfam SEED file in stockholm format to convert to fasta
return: Path to updated seed file
| Converts a multiple sequence alignment (MSA) to fasta
param seed_msa: A valid Rfam SEED file in stockholm format to convert to fasta
Path to updated seed file | [
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filename = ""
path_elements = os.path.split(seed_msa)
if dest_dir is None:
dest_dir = path_elements[0]
if "." in path_elements[1]:
filename = path_elements[1].partition('.')[0]
else:
filename = path_elements[1]
cmd = "esl-sfetch... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | align_sequences_to_cm | <not_specific> | def align_sequences_to_cm(cmfile, fasta_file, dest_dir=None):
"""
Aligns a fasta to a covariance model using cmalign
cmfile: A valid covariance model
fasta_file: A valid nucleotide fasta file
dest_dir: Destination directory where to generate any output
return: Returns path to the aligned sequ... |
Aligns a fasta to a covariance model using cmalign
cmfile: A valid covariance model
fasta_file: A valid nucleotide fasta file
dest_dir: Destination directory where to generate any output
return: Returns path to the aligned sequences, otherwise
returns None if file does not exist
| Aligns a fasta to a covariance model using cmalign
cmfile: A valid covariance model
fasta_file: A valid nucleotide fasta file
Destination directory where to generate any output
Returns path to the aligned sequences, otherwise
returns None if file does not exist | [
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dest_dir = os.path.split(fasta_file)[0]
out_filename = os.path.basename(fasta_file).partition('.')[0]
out_filename += "_aln.stk"
new_seed = os.path.join(dest_dir, out_filename)
cmd = "cmalign %s %s | grep -Ev ... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | map_rnacentral_urs_wirh_db_accessions | <not_specific> | def map_rnacentral_urs_wirh_db_accessions(db_accession, expert_db):
"""
Maps a database accession with a URS accession assigned by
RNAcentral. The limitation
db_accession: A valid member database accession already imported
to RNAcentral
expert_db: RNAcentral expert database to map the SEED acce... |
Maps a database accession with a URS accession assigned by
RNAcentral. The limitation
db_accession: A valid member database accession already imported
to RNAcentral
expert_db: RNAcentral expert database to map the SEED accessions to
return: The corresponding RNAcentral accession (URS)
| Maps a database accession with a URS accession assigned by
RNAcentral. The limitation
A valid member database accession already imported
to RNAcentral
expert_db: RNAcentral expert database to map the SEED accessions to
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rnacentral_url = "http://www.ebi.ac.uk/ebisearch/ws/rest/rnacentral?query=\"%s\" AND expert_db:\"%s\" AND so_rna_type_name:\"%s\""
response = requests.get(rnacentral_url % (db_accession, expert_db, DB_RNA_TYPES[expert_db.lower()]))
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | fetch_sequence_from_rnacentral | <not_specific> | def fetch_sequence_from_rnacentral(rnacentral_id):
"""
Uses RNAcentral's API to fetch corresponding sequence based on
RNAcentral URS id
rnacentral_id: A valid RNAcentral URS identifier e.g.
return: Corresponding sequence if available, none otherwise
"""
# isolate URS if necessary
if r... |
Uses RNAcentral's API to fetch corresponding sequence based on
RNAcentral URS id
rnacentral_id: A valid RNAcentral URS identifier e.g.
return: Corresponding sequence if available, none otherwise
| Uses RNAcentral's API to fetch corresponding sequence based on
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rnacentral_id = rnacentral_id.partition('_')[0]
rnacentral_url = "https://rnacentral.org/api/v1/rna/%s.fasta"
response = requests.get(rnacentral_url % rnacentral_id)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | relabel_seeds_from_rnacentral_md5_mapping | <not_specific> | def relabel_seeds_from_rnacentral_md5_mapping(seed, dest_dir=None):
"""
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted seed in Pfam format
dest_di... |
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted seed in Pfam format
dest_dir: The path to the destination directory. None by default
return: The ... | Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
A reformatted seed in Pfam format
dest_dir: The path to the destination directory. None by default
The path to the relabelled SEED alignement | [
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if dest_dir is None:
dest_dir = os.path.split(seed)[0]
sequence_label = 0
new_line = ''
filename = os.path.split(seed)[1].partition('.')[0]
new_seed_loc = os.path.join(dest_dir, filename+'_relabelled')
seed_fp = open(see... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | rewrite_seed_with_sscons | <not_specific> | def rewrite_seed_with_sscons(input_seed, ss_cons, dest_dir=None):
"""
Rewrites a SEED alignment in stockholm format with a ss_cons
param input_seed: Initial seed to rewrite and add ss_cons to.
The seed alignment needs to be in stockholm format
param ss_cons: Consensus secondary structure to add to... |
Rewrites a SEED alignment in stockholm format with a ss_cons
param input_seed: Initial seed to rewrite and add ss_cons to.
The seed alignment needs to be in stockholm format
param ss_cons: Consensus secondary structure to add to the alignment
return: The path to the new SEED is successful, other... | Rewrites a SEED alignment in stockholm format with a ss_cons
param input_seed: Initial seed to rewrite and add ss_cons to.
The seed alignment needs to be in stockholm format
param ss_cons: Consensus secondary structure to add to the alignment
The path to the new SEED is successful, otherwise None | [
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if dest_dir is None:
dest_dir = os.path.split(input_seed)[0]
filename = os.path.basename(input_seed).partition('.')[0]
new_seed_loc = os.path.join(dest_dir, filename + "ss_cons.stk")
new_seed_fp = open(new_seed_loc, 'w')
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | merge_seeds | <not_specific> | def merge_seeds(seed1, seed2, filename=None, dest_dir=None):
"""
Merges two alignments into one using esl-alimerge
seed1: The path to SEED alignment 1
seed2: The path to SEED alignment 2
filename: A string specifying the filename of the merged alignment
dest_dir: The path to the destination dir... |
Merges two alignments into one using esl-alimerge
seed1: The path to SEED alignment 1
seed2: The path to SEED alignment 2
filename: A string specifying the filename of the merged alignment
dest_dir: The path to the destination directory. If None uses current
working directory
return: The ... | Merges two alignments into one using esl-alimerge
seed1: The path to SEED alignment 1
seed2: The path to SEED alignment 2
filename: A string specifying the filename of the merged alignment
dest_dir: The path to the destination directory. If None uses current
working directory
The path to the merged SEED if it exists, ... | [
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if dest_dir is None:
dest_dir = os.getcwd()
merged_seed_loc = os.path.join(dest_dir, filename + '_merged.stk')
cmd = "esl-alimerge -o %s %s %s" % (merged_seed_loc, seed1, seed2)
subprocess.call(cmd, shell=True)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | remove_all_gap_columns | <not_specific> | def remove_all_gap_columns(seed, filename, dest_dir=None):
"""
Uses esl-reformat to remove all-gap columns from a SEED
alignment
seed: A valid SEED alignment in stockholm format
filename: A string specifying the modified SEED name
dest_dir: The path to the destination directory where
the ou... |
Uses esl-reformat to remove all-gap columns from a SEED
alignment
seed: A valid SEED alignment in stockholm format
filename: A string specifying the modified SEED name
dest_dir: The path to the destination directory where
the output will be generated
return: Returns the path to the update... | Uses esl-reformat to remove all-gap columns from a SEED
alignment
A valid SEED alignment in stockholm format
filename: A string specifying the modified SEED name
dest_dir: The path to the destination directory where
the output will be generated
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otherwise it returns N... | [
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if dest_dir is None:
dest_dir = os.path.split(os.path.abspath(seed))[0]
new_seed_loc = os.path.join(dest_dir, filename + '_nogaps.stk')
cmd = "esl-reformat -o %s --mingap --wussify stockholm %s" % (new_seed_loc, seed)
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | relabel_seeds_from_rnacentral_urs_mapping | <not_specific> | def relabel_seeds_from_rnacentral_urs_mapping(seed, expert_db=None, dest_dir=None, clean=False):
"""
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted se... |
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted seed in Pfam format
expert_db: An existing RNAcentral expert database
dest_dir: The path to the de... | Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
A reformatted seed in Pfam format
expert_db: An existing RNAcentral expert database
dest_dir: The path to the destination directory. None by de... | [
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if dest_dir is None:
dest_dir = os.path.split(seed)[0]
sequence_label = 0
new_line = ''
write_log = False
filename = os.path.split(seed)[1].partition('.')[0]
new_seed_filename = filename + '_... | [
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | write_fasta_seed_file | <not_specific> | def write_fasta_seed_file(sequence_collection, filename="sequences", dest_dir=None):
"""
Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
sequence_collection: A python dictionary with the candidate
sequ... |
Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
sequence_collection: A python dictionary with the candidate
sequences
filename: A string specifying the sequence file name
dest_dir: Destination dir... | Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
A python dictionary with the candidate
sequences
filename: A string specifying the sequence file name
dest_dir: Destination directory where to generate output
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if dest_dir is None:
sys.exit("\nNo destination directory was provided for fasta generation!\n")
fasta_file = os.path.join(dest_dir, filename + '.fa')
fasta_fp = open(fasta_file, 'w')
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | write_fasta_file | <not_specific> | def write_fasta_file(sequence_collection, filename="sequences", dest_dir=None):
"""
Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
sequence_collection: A python dictionary with the candidate
sequences... |
Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
sequence_collection: A python dictionary with the candidate
sequences
filename: A string specifying the sequence file name
dest_dir: Destination dir... | Writes a fasta file in destination directory based on a
dictionary of sequence_accession : sequence pairs to be
used to generate a fasta file
A python dictionary with the candidate
sequences
filename: A string specifying the sequence file name
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fasta_file = os.path.join(dest_dir, filename + '.fa')
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | map_sequence_segments | <not_specific> | def map_sequence_segments(seed_seq, rnac_seq, no_segments=4):
"""
Splits a seed sequence into smaller segments and maps the
individual segments to the RNAcentral sequence
param seed_seq:
param rnac_seq:
no_segments:
return: RNAcentral subsequence if segments match by 75%, None otherwise
... |
Splits a seed sequence into smaller segments and maps the
individual segments to the RNAcentral sequence
param seed_seq:
param rnac_seq:
no_segments:
return: RNAcentral subsequence if segments match by 75%, None otherwise
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segment_hits = {}
output = {}
seq_match_score = 0
seed_length = len(seed_seq)
reference_start = None
remainder = seed_length % no_segments
segment_size = int((seed_length - remainder) / no_segments)
index = 0
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | build_temporary_cm_from_seed | <not_specific> | def build_temporary_cm_from_seed(seed_file, dest_dir=None):
"""
Build a temporary covariance model based on the seed_file,
which is provided as input using cmbuild.
seed_file: Seed alignment in Stockhold format to be used as
input to cmbuild
dest_dir: Destination directory where the output wil... |
Build a temporary covariance model based on the seed_file,
which is provided as input using cmbuild.
seed_file: Seed alignment in Stockhold format to be used as
input to cmbuild
dest_dir: Destination directory where the output will be
generated
return: True if the covariance model exists... | Build a temporary covariance model based on the seed_file,
which is provided as input using cmbuild.
Seed alignment in Stockhold format to be used as
input to cmbuild
Destination directory where the output will be
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True if the covariance model exists, False otherwise | [
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dest_dir = os.path.split(seed_file)[0]
filename = os.path.basename(seed_file).partition('.')[0]
cm_file = os.path.join(dest_dir, filename+'.cm')
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | fix_coordinates | <not_specific> | def fix_coordinates(seed_file, dest_dir=None):
"""
Replaces 0 starting points with 1s in SEED sequences
seed_file: Seed alignment in Stockhold format
dest_dir: dest_dir: Destination directory where the output will be
generated
return: The path to the updated SEED
"""
filename = os.pa... |
Replaces 0 starting points with 1s in SEED sequences
seed_file: Seed alignment in Stockhold format
dest_dir: dest_dir: Destination directory where the output will be
generated
return: The path to the updated SEED
| Replaces 0 starting points with 1s in SEED sequences
seed_file: Seed alignment in Stockhold format
Destination directory where the output will be
generated
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4128beadfa258555d5cf673fca90d58317708929 | Rfam/rfam-production | scripts/preprocessing/relabel_seed.py | [
"Apache-2.0"
] | Python | parse_arguments | <not_specific> | def parse_arguments():
"""
Basic argument parsing
return: Argparse parser object
"""
parser = argparse.ArgumentParser(description='Script to relabel SEED alignments')
required_arguments = parser.add_argument_group("required arguments")
required_arguments.add_argument("--seed", help="SEED ... |
Basic argument parsing
return: Argparse parser object
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parser = argparse.ArgumentParser(description='Script to relabel SEED alignments')
required_arguments = parser.add_argument_group("required arguments")
required_arguments.add_argument("--seed", help="SEED alignment in stockholm format to relabel", type=str)
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06d0dd1d37c91aad3d6f2136a7f5034a6cf8d62e | Rfam/rfam-production | scripts/support/group_cms.py | [
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] | Python | group_cms | null | def group_cms(cm_dir, no_of_cms=6, dest_dir=None):
"""
Fetch all family accessions from the database and sort in DESC order according to
seed size. Split the cms into multiple files defined by no_of_cms making sure that
we split the large families across the multiple cms
cm_dir: A directory with al... |
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seed size. Split the cms into multiple files defined by no_of_cms making sure that
we split the large families across the multiple cms
cm_dir: A directory with all Rfam single covariance model files
no_of_cms: The nu... | Fetch all family accessions from the database and sort in DESC order according to
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rfam_cms = [x for x in os.listdir(cm_dir) if x.endswith('.cm')]
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dest_dir = cm_dir
idx = 1
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419a83050c522e75a2e51b6eced5d9191af90297 | Rfam/rfam-production | scripts/export/genomes/ncbi_genome_downloader.py | [
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] | Python | gcf_report_parser | <not_specific> | def gcf_report_parser(gcf_report):
"""
Parses a GCF report file from NCBI and returns all the NCBI accessions
gcf_report:
return: a list of wgs accessions listed in the gcf report file
"""
fp = open(gcf_report, 'r')
accessions = [x.strip().split('\t')[4] for x in fp if x[0] != '#']
... |
Parses a GCF report file from NCBI and returns all the NCBI accessions
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419a83050c522e75a2e51b6eced5d9191af90297 | Rfam/rfam-production | scripts/export/genomes/ncbi_genome_downloader.py | [
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"""
Parses a GCF report file from NCBI and returns all the NCBI accessions
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5b775c331a7afca40f8f9830d36f643ed8640fed | Rfam/rfam-production | scripts/support/rnac2rfamseq.py | [
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] | Python | parse_arguments | <not_specific> | def parse_arguments():
"""
Basic argument parsing using python's argparse
return: void
"""
parser = argparse.ArgumentParser(description="Script to convert RNAcentral sequence metadata to Rfamseq")
parser.add_argument("--rnac-csv",
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Basic argument parsing using python's argparse
return: void
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parser = argparse.ArgumentParser(description="Script to convert RNAcentral sequence metadata to Rfamseq")
parser.add_argument("--rnac-csv",
help="A valid csv file with RNAcentral sequence metadata", action="store")
parser.add_argument("--source",
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304d0081eea06482af8dee28bb79f795ae19acb1 | Rfam/rfam-production | scripts/export/rfam_svn_file_export.py | [
"Apache-2.0"
] | Python | export_rfam_family_files | null | def export_rfam_family_files(f_types, out_dir):
"""
Fetches all Rfam family accessions from rfam_live, checks out each
family and copies the files in f_types in their corresponding
directories
f_types: A list of file type keywords we need to
export (e.g. ["SEED", "CM"])
out_dir: Th... |
Fetches all Rfam family accessions from rfam_live, checks out each
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directories
f_types: A list of file type keywords we need to
export (e.g. ["SEED", "CM"])
out_dir: The path to the output directory. If it does not exist it... | Fetches all Rfam family accessions from rfam_live, checks out each
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A list of file type keywords we need to
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out_dir: The path to the output directory. If it does not exist it will
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304d0081eea06482af8dee28bb79f795ae19acb1 | Rfam/rfam-production | scripts/export/rfam_svn_file_export.py | [
"Apache-2.0"
] | Python | usage | null | def usage():
"""
Displays information on how to run rfam_svn_file_export
"""
print "\nUsage:\n------"
print "\npython rfam_svn_file_export.py out_dir"
print "\nout_dir: Path to an output directory"
print "\n-h option for usage\n" |
Displays information on how to run rfam_svn_file_export
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print "\nout_dir: Path to an output directory"
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9a7ee469bb363a323e358f5161f9acab025f7b42 | Rfam/rfam-production | scripts/release/clanin_file_generator.py | [
"Apache-2.0"
] | Python | generate_clanin_file | null | def generate_clanin_file(dest_dir=None):
"""
Creates a clanin file to be used for clan competition during cmscan
dest_dir: The path to destination directory. Using current if no
directory provided
returns: void
"""
# create destination directory or use current if not provided
if dest_... |
Creates a clanin file to be used for clan competition during cmscan
dest_dir: The path to destination directory. Using current if no
directory provided
returns: void
| Creates a clanin file to be used for clan competition during cmscan
dest_dir: The path to destination directory. Using current if no
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if dest_dir is None:
dest_dir = os.getcwd()
else:
if not os.path.exists(dest_dir):
os.mkdir(dest_dir)
clan_members = db.fetch_clanin_data()
fp = open(os.path.join(dest_dir, 'Rfam.clanin'), 'w')
for clan in clan_members.keys():
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8f822a80d47a50a9576d445a86bee522e56d3c8c | Rfam/rfam-production | scripts/support/mirnas/find_family_overlaps.py | [
"Apache-2.0"
] | Python | extract_tax_ids_from_species_file | <not_specific> | def extract_tax_ids_from_species_file(species_file):
"""
Parses family's species file and extracts all distinct tax ids
:param species_file: The path to a family's species file
:return: A dictionary of
"""
tax_ids = {}
seen_ga = False
fp = open(species_file, 'r')
for line in fp:... |
Parses family's species file and extracts all distinct tax ids
:param species_file: The path to a family's species file
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tax_ids = {}
seen_ga = False
fp = open(species_file, 'r')
for line in fp:
if line[0] != '#' and not seen_ga:
line = line.strip().split()
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8f822a80d47a50a9576d445a86bee522e56d3c8c | Rfam/rfam-production | scripts/support/mirnas/find_family_overlaps.py | [
"Apache-2.0"
] | Python | count_total_num_hits | <not_specific> | def count_total_num_hits(outlist_hits):
"""
Counts total number of family hits
:param outlist_hits: A dictionary in the form of {rfamseq_acc: [(s1,e1),...]
:return: Total number of hits found in the dictionary
"""
total_num_hits = 0
for accession in outlist_hits.keys():
total_num... |
Counts total number of family hits
:param outlist_hits: A dictionary in the form of {rfamseq_acc: [(s1,e1),...]
:return: Total number of hits found in the dictionary
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total_num_hits = 0
for accession in outlist_hits.keys():
total_num_hits += len(outlist_hits[accession])
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a89b735f05c5ab647f18d3ecc85c1fd7c879f5be | Rfam/rfam-production | scripts/support/genome_restore_launcher.py | [
"Apache-2.0"
] | Python | bsub_redownload_genome_from_gca_report | null | def bsub_redownload_genome_from_gca_report(updir, gca_report_file):
"""
Launch the genome downloads on LSF
:return:
"""
cmd = "bsub -M 6000 -R \"rusage[mem=6000]\" -o %s -e %s python %s %s %s"
bsub_cmd = cmd % (os.path.join(updir, 'restore.out'),
os.path.join(updir, 'res... |
Launch the genome downloads on LSF
:return:
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cmd = "bsub -M 6000 -R \"rusage[mem=6000]\" -o %s -e %s python %s %s %s"
bsub_cmd = cmd % (os.path.join(updir, 'restore.out'),
os.path.join(updir, 'restore.err'),
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751bd93d19401a7e9df717f717570e90597fd7fe | Rfam/rfam-production | scripts/support/merge_fasta.py | [
"Apache-2.0"
] | Python | merge_genome_files | null | def merge_genome_files(upid_dir):
"""
Merge all sequence files of a genome in a single file
upid_dir: The path to a genome directory
:return:
"""
sequence_dir_loc = os.path.join(upid_dir, "sequences")
seq_dir_contents = os.listdir(sequence_dir_loc)
upid = os.path.split(upid_dir)[1]
... |
Merge all sequence files of a genome in a single file
upid_dir: The path to a genome directory
:return:
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seq_dir_contents = os.listdir(sequence_dir_loc)
upid = os.path.split(upid_dir)[1]
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623b67835bef73fc620a53961b7a4dd1540bf0a0 | Rfam/rfam-production | scripts/validation/validate_miRNA_seqs.py | [
"Apache-2.0"
] | Python | seed_to_dict | <not_specific> | def seed_to_dict(seed):
"""
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted seed in Pfam format
dest_dir: The path to the destination directory. No... |
Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
seed: A reformatted seed in Pfam format
dest_dir: The path to the destination directory. None by default
return: The ... | Relabels the accessions of a SEED alignment using RNAcentral
identifiers. This is done by matching the seed sequences, with
sequences existing in RNAcentral using md5 hashing.
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dest_dir: The path to the destination directory. None by default
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9ad1440865c552d231401d94409993b649602888 | Rfam/rfam-production | scripts/view/job_dequeuer.py | [
"Apache-2.0"
] | Python | job_dequeue_from_file | null | def job_dequeue_from_file(fam_pend_jobs, out_dir):
"""
Calls family_view_process based on a list of family job_uuid pairs as
listed in fam_jobs file
fam_pend_jobs: A list of all pending rfam jobs obtained from
_post_process table export (rfam_acc\tuuid)
out_dir: Path to output di... |
Calls family_view_process based on a list of family job_uuid pairs as
listed in fam_jobs file
fam_pend_jobs: A list of all pending rfam jobs obtained from
_post_process table export (rfam_acc\tuuid)
out_dir: Path to output directory where .err and .out will be generated
... | Calls family_view_process based on a list of family job_uuid pairs as
listed in fam_jobs file
A list of all pending rfam jobs obtained from
_post_process table export (rfam_acc\tuuid)
out_dir: Path to output directory where .err and .out will be generated
upon lsf job completion (to be used for debugging purposes) | [
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fp_out = open(os.path.join(out_dir, "famview_job_ids.txt"), 'w')
jobs_fp = open(fam_pend_jobs, 'r')
os.mkdir(os.path.join(out_dir, "scripts"))
for job in jobs_fp:
job = job.strip().split('\t')
print "job: ", job
filepath = lsf_sc... | [
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9ad1440865c552d231401d94409993b649602888 | Rfam/rfam-production | scripts/view/job_dequeuer.py | [
"Apache-2.0"
] | Python | lsf_script_generator | <not_specific> | def lsf_script_generator(rfam_acc, uuid, out_dir):
"""
Generates a shell script per family to ease re-running family view
process upon failure
rfam_acc: Family specific accession
uuid: Family associated uuid
out_dir: Path to output directory where scripts will be generated
"""
mem = No... |
Generates a shell script per family to ease re-running family view
process upon failure
rfam_acc: Family specific accession
uuid: Family associated uuid
out_dir: Path to output directory where scripts will be generated
| Generates a shell script per family to ease re-running family view
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Family specific accession
uuid: Family associated uuid
out_dir: Path to output directory where scripts will be generated | [
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mem = None
if (rfam_acc in DEM_FAMS):
mem = MEM_D
else:
mem = MEM_R
filepath = os.path.join(os.path.join(out_dir, "scripts"), rfam_acc + ".sh")
fp = open(filepath, 'w')
filename = rfam_acc
fv_cmd = "%s -id %s -f %s family" % ... | [
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9ad1440865c552d231401d94409993b649602888 | Rfam/rfam-production | scripts/view/job_dequeuer.py | [
"Apache-2.0"
] | Python | parse_arguments | <not_specific> | def parse_arguments():
"""
Basic argument parsing
return: Python's argparse parser object
"""
parser = argparse.ArgumentParser(description="View process dequeuer")
parser.add_argument("--view-list", help="A list of rfam_acc\tuuids to run View plugins on", type=str)
parser.add_argument("--... |
Basic argument parsing
return: Python's argparse parser object
| Basic argument parsing
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parser = argparse.ArgumentParser(description="View process dequeuer")
parser.add_argument("--view-list", help="A list of rfam_acc\tuuids to run View plugins on", type=str)
parser.add_argument("--dest-dir", help="An existing destination directory to store logs", type=str)
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} |
8371e4ff61a6c4fdb63bb3c7744f80d9a9f255d9 | Rfam/rfam-production | scripts/support/genome_size_calculator.py | [
"Apache-2.0"
] | Python | calculate_genome_size | <not_specific> | def calculate_genome_size(genome_source):
"""
Calculate the size of a given sequence file (this should be a genome) and return the total
number of nucleotides in the file, or if genome_fasta is a directory, return a dictionary
of genome_ids: size pairs
genome_source: A valid sequence file in fasta ... |
Calculate the size of a given sequence file (this should be a genome) and return the total
number of nucleotides in the file, or if genome_fasta is a directory, return a dictionary
of genome_ids: size pairs
genome_source: A valid sequence file in fasta format or a directory of fasta files
return:... | Calculate the size of a given sequence file (this should be a genome) and return the total
number of nucleotides in the file, or if genome_fasta is a directory, return a dictionary
of genome_ids: size pairs
A valid sequence file in fasta format or a directory of fasta files
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genome_files = []
genome_sizes = {}
if os.path.isdir(genome_source):
genome_files = [x for x in os.listdir(genome_source)
if x.endswith('.fa') or x.endswith('.fasta')]
for seq_file in genome_files:
try:
... | [
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],
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} |
2a087e92601fbf634f7432b8f0081bc5bde2af5d | Rfam/rfam-production | scripts/export/generate_ftp_files.py | [
"Apache-2.0"
] | Python | create_seed_archive | null | def create_seed_archive(destination):
"""
Create a combined Rfam.seed file and compress it.
"""
cwd = os.getcwd()
os.chdir(destination)
cmd = "rm -f Rfam.seed && cat *.seed > Rfam.seed && gzip -c Rfam.seed > Rfam.seed.gz"
status = os.system(cmd.format(destination))
if status:
rai... |
Create a combined Rfam.seed file and compress it.
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cwd = os.getcwd()
os.chdir(destination)
cmd = "rm -f Rfam.seed && cat *.seed > Rfam.seed && gzip -c Rfam.seed > Rfam.seed.gz"
status = os.system(cmd.format(destination))
if status:
raise Exception('There was a problem generating Rfam.seed.gz in {}'.forma... | [
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} |
2a087e92601fbf634f7432b8f0081bc5bde2af5d | Rfam/rfam-production | scripts/export/generate_ftp_files.py | [
"Apache-2.0"
] | Python | create_combined_cm_file | null | def create_combined_cm_file(destination):
"""
Create a combined Rfam.cm file.
"""
cwd = os.getcwd()
os.chdir(destination)
cmd = "rm -f Rfam.cm && cat *.CM > Rfam.cm"
status = os.system(cmd.format(destination))
if status:
raise Exception('There was a problem generating Rfam.cm in ... |
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cwd = os.getcwd()
os.chdir(destination)
cmd = "rm -f Rfam.cm && cat *.CM > Rfam.cm"
status = os.system(cmd.format(destination))
if status:
raise Exception('There was a problem generating Rfam.cm in {}'.format(destination))
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2a087e92601fbf634f7432b8f0081bc5bde2af5d | Rfam/rfam-production | scripts/export/generate_ftp_files.py | [
"Apache-2.0"
] | Python | create_tree_archive | null | def create_tree_archive(destination):
"""
Create a combined Rfam.seed_tree file.
"""
cwd = os.getcwd()
os.chdir(destination)
cmd = "rm -f Rfam.seed_tree && cat *.taxtree > Rfam.seed_tree && gzip -c Rfam.seed_tree > Rfam.seed_tree.gz"
status = os.system(cmd.format(destination))
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Create a combined Rfam.seed_tree file.
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2a087e92601fbf634f7432b8f0081bc5bde2af5d | Rfam/rfam-production | scripts/export/generate_ftp_files.py | [
"Apache-2.0"
] | Python | validate_seed_archive | null | def validate_seed_archive(destination, rfam_accs):
"""
Check that Rfam.seed contains the correct number of entries.
"""
cwd = os.getcwd()
os.chdir(destination)
family_count = 0
with open(os.path.join(destination, 'Rfam.seed')) as f_seed:
for line in f_seed:
if line.starts... |
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cwd = os.getcwd()
os.chdir(destination)
family_count = 0
with open(os.path.join(destination, 'Rfam.seed')) as f_seed:
for line in f_seed:
if line.startswith('# STOCKHOLM 1.0'):
family_count += 1
os.chdir(cwd)
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bd8cfba0084258c6c7168b998885c9007bf1a86b | Rfam/rfam-production | scripts/release/clan_file_generator.py | [
"Apache-2.0"
] | Python | parse_clan_file | <not_specific> | def parse_clan_file(clan_list):
"""
Parses a list of Rfam clan accessions
clan_list: A plain .txt file containing a list of Rfam Clan Accessions
return: A list of clan accessions
"""
fp = open(clan_list, 'r')
clan_accessions = [x.strip() for x in fp]
fp.close()
return clan_acce... |
Parses a list of Rfam clan accessions
clan_list: A plain .txt file containing a list of Rfam Clan Accessions
return: A list of clan accessions
| Parses a list of Rfam clan accessions
clan_list: A plain .txt file containing a list of Rfam Clan Accessions
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fp = open(clan_list, 'r')
clan_accessions = [x.strip() for x in fp]
fp.close()
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bd8cfba0084258c6c7168b998885c9007bf1a86b | Rfam/rfam-production | scripts/release/clan_file_generator.py | [
"Apache-2.0"
] | Python | clan_file_generator | null | def clan_file_generator(output_dir, clan_comp_type='FULL', clan_acc=None):
"""
Generates clan files for clan competition
output_dir: The path to the output directory. It will be created if
it does not exist
clan_comp_type: This can be 'FULL' for clan competition on on full_region_table
or PDB f... |
Generates clan files for clan competition
output_dir: The path to the output directory. It will be created if
it does not exist
clan_comp_type: This can be 'FULL' for clan competition on on full_region_table
or PDB for clan competition on pdb_full_region
returns: void
| Generates clan files for clan competition
output_dir: The path to the output directory. It will be created if
it does not exist
clan_comp_type: This can be 'FULL' for clan competition on on full_region_table
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if os.path.exists(output_dir) is False:
os.mkdir(output_dir)
clans = []
if clan_acc is None:
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bd8cfba0084258c6c7168b998885c9007bf1a86b | Rfam/rfam-production | scripts/release/clan_file_generator.py | [
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] | Python | parse_arguments | <not_specific> | def parse_arguments():
"""
Performs some basic argument parsing
return: parser object
"""
parser = argparse.ArgumentParser(description='Generates required clan competition input files')
mutualy_exclusive = parser.add_mutually_exclusive_group()
parser.add_argument("--dest-dir", help="Desti... |
Performs some basic argument parsing
return: parser object
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parser = argparse.ArgumentParser(description='Generates required clan competition input files')
mutualy_exclusive = parser.add_mutually_exclusive_group()
parser.add_argument("--dest-dir", help="Destination directory where to generate the files",
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
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] | Python | fetch_gca_data | <not_specific> | def fetch_gca_data(upid, assembly_acc, kingdom):
"""
Parses ENA GCA accession xml, and returns the accession's data in the
form of a dictionary
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
assembly_acc: A valid ENA GCA accession
kingdom: The corresponding species k... |
Parses ENA GCA accession xml, and returns the accession's data in the
form of a dictionary
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
assembly_acc: A valid ENA GCA accession
kingdom: The corresponding species kingdom
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kingdom: The corresponding species kingdom | [
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genome_entry = {}
fields = {}
tmp_acc = assembly_acc
response = requests.get(gc.ENA_XML_URL % tmp_acc)
if response.status_code == httplib.OK:
assembly_xml = response.content
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_assembly_accessions | <not_specific> | def fetch_assembly_accessions(upid, gca_acc, acc_ftp_link, reg_ftp_link=None):
"""
Parses assembly report file and exports all assembly accessions in a
dict format to be easily loaded via Django ORM
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
gca_acc: A valid ENA GCA ... |
Parses assembly report file and exports all assembly accessions in a
dict format to be easily loaded via Django ORM
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
gca_acc: A valid ENA GCA accession
acc_ftp_link: Assembly report file ftp url (as retrieved from GCA xml fi... | Parses assembly report file and exports all assembly accessions in a
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A valid Uniprot proteome accession
gca_acc: A valid ENA GCA accession
acc_ftp_link: Assembly report file ftp url (as retrieved from GCA xml file)
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assembly_accs = []
fields = {}
entry = {}
regions = None
if reg_ftp_link is not None:
regions = region_loader(reg_ftp_link)
http_link = acc_ftp_link.replace("ftp://", "http://")
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | region_loader | <not_specific> | def region_loader(reg_ftp_link):
"""
Parses an assembly's region file and builds a dictionary of accessions and
start-end coordinates which are stored in a tuple format
reg_ftp_link: The ftp url of the corresponding region file
"""
region_dict = {}
http_link = reg_ftp_link.replace("ftp://... |
Parses an assembly's region file and builds a dictionary of accessions and
start-end coordinates which are stored in a tuple format
reg_ftp_link: The ftp url of the corresponding region file
| Parses an assembly's region file and builds a dictionary of accessions and
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region_dict = {}
http_link = reg_ftp_link.replace("ftp://", "http://")
response = requests.get(http_link).content
regions = response.strip().split('\n')
regions.pop(0)
for region in regions:
region = region.strip().split('\t')
coords = region[5].s... | [
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_wgs_metadata | <not_specific> | def fetch_wgs_metadata(upid, assembly_acc, domain):
"""
Parses ENA WGS accession xml, and returns the accession's data in the
form of a dictionary
upid: A valid Uniprot's proteome id
assembly_acc: A valid ENA's WGS accession
domain: A string representing the domain a species belongs to (e.g.vir... |
Parses ENA WGS accession xml, and returns the accession's data in the
form of a dictionary
upid: A valid Uniprot's proteome id
assembly_acc: A valid ENA's WGS accession
domain: A string representing the domain a species belongs to (e.g.viruses)
| Parses ENA WGS accession xml, and returns the accession's data in the
form of a dictionary
A valid Uniprot's proteome id
assembly_acc: A valid ENA's WGS accession
domain: A string representing the domain a species belongs to | [
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wgs_entry = {}
fields = {}
response = requests.get(gc.ENA_XML_URL % assembly_acc)
if response.status_code == httplib.OK:
assembly_xml = ET.fromstring(response.content)
entry = assembly_xml.find("entry")
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_wgs_accs_metadata | <not_specific> | def fetch_wgs_accs_metadata(upid, assembly_acc, wgs_range):
"""
This function runs over the wgs range and exports all metadata for every
accession in the provided wgs range
wgs_range: A valid ENA-WGS set range
"""
wgs_entries = []
entry = {}
fields = {}
wgs_accs = gf.fetch_wgs_ran... |
This function runs over the wgs range and exports all metadata for every
accession in the provided wgs range
wgs_range: A valid ENA-WGS set range
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wgs_accs = gf.fetch_wgs_range_accs(wgs_range)
for acc in wgs_accs:
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_wgs_acc_metadata | <not_specific> | def fetch_wgs_acc_metadata(wgs_acc):
"""
Return a fields dictionary
wgs_acc: A valid ENA wgs accession
"""
fields = {}
response = requests.get(gf.ENA_XML_URL % wgs_acc)
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acc_xml = ET.fromstring(response.content)
entry = acc_xml.find("e... |
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wgs_acc: A valid ENA wgs accession
| Return a fields dictionary
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fields = {}
response = requests.get(gf.ENA_XML_URL % wgs_acc)
if response.status_code == httplib.OK:
acc_xml = ET.fromstring(response.content)
entry = acc_xml.find("entry")
if entry is None:
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fields["seq_version"] ... | [
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_assembly_attributes | <not_specific> | def fetch_assembly_attributes(attrs_node):
"""
Runs over the attributes node in the xml file and returns all attribute
tag-value pairs in a dictionary format
attrs_node: GCA xml's attributes node
"""
attribute_values = {}
attributes = attrs_node.findall("ASSEMBLY_ATTRIBUTE")
for attr ... |
Runs over the attributes node in the xml file and returns all attribute
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attrs_node: GCA xml's attributes node
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attribute_values = {}
attributes = attrs_node.findall("ASSEMBLY_ATTRIBUTE")
for attr in attributes:
tag = attr.find("TAG").text
value = attr.find("VALUE").text
attribute_values[tag] = value
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5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_gca_acc_metadata | <not_specific> | def fetch_gca_acc_metadata(accession):
"""
Fetch accession metadata and return a dictionary with ncbi_id, molecule's
type, description and tax id
accession: A valid GCA accession from ENA
"""
metadata = {}
response = requests.get(gc.ENA_XML_URL % accession)
if response.status_code ==... |
Fetch accession metadata and return a dictionary with ncbi_id, molecule's
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accession: A valid GCA accession from ENA
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response = requests.get(gc.ENA_XML_URL % accession)
if response.status_code == httplib.OK:
xml_str = response.content
xml_root = ET.fromstring(xml_str)
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} |
5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | fetch_assembly_links | <not_specific> | def fetch_assembly_links(gca_acc):
"""
Retrieves and returns a dictionary with all ftp links found in the GCA xml
file
gca_acc: A valid GCA accession from ENA
"""
gca_ftp_links = {}
response = requests.get(gc.ENA_XML_URL % gca_acc)
if response.status_code == httplib.OK:
xml_... |
Retrieves and returns a dictionary with all ftp links found in the GCA xml
file
gca_acc: A valid GCA accession from ENA
| Retrieves and returns a dictionary with all ftp links found in the GCA xml
file
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] | def fetch_assembly_links(gca_acc):
gca_ftp_links = {}
response = requests.get(gc.ENA_XML_URL % gca_acc)
if response.status_code == httplib.OK:
xml_tree = ET.fromstring(response.content)
assembly_node = xml_tree.find("ASSEMBLY")
assembly_links = assembly_node.find(
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] | [
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],
"outlier_params": [],
"others": []
} |
5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | extract_uniprot_genome_metadata | <not_specific> | def extract_uniprot_genome_metadata(upid):
"""
Parses a proteome's xml file from Uniprot and converts it to a json
like object which is returned
upid: A valid Uniprot Proteome identifier
returns: A dictionary
"""
proteome_dict = {}
# namespace prefix # or register a namespace in the ... |
Parses a proteome's xml file from Uniprot and converts it to a json
like object which is returned
upid: A valid Uniprot Proteome identifier
returns: A dictionary
| Parses a proteome's xml file from Uniprot and converts it to a json
like object which is returned
A valid Uniprot Proteome identifier
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] | def extract_uniprot_genome_metadata(upid):
proteome_dict = {}
prefix = "{http://uniprot.org/uniprot}%s"
response = requests.get(gc.PROTEOME_XML_URL % upid)
if response.status_code == httplib.OK:
prot_tree_root = ET.fromstring(response.content)
proteome = prot_tree_root.find(prefix % "pro... | [
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],
"outlier_params": [],
"others": []
} |
5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | dump_uniprot_genome_metadata | <not_specific> | def dump_uniprot_genome_metadata(upid, kingdom):
"""
Parses ENA GCA accession xml, and returns the accession's data in the
form of a dictionary
proteome_dict: A proteome dict built from Uniprot's proteome xml files
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
assem... |
Parses ENA GCA accession xml, and returns the accession's data in the
form of a dictionary
proteome_dict: A proteome dict built from Uniprot's proteome xml files
upid: A valid Uniprot proteome accession (e.g. UP000005640 - Homo Sapiens)
assembly_acc: A valid ENA GCA accession
kingdom: The corr... | Parses ENA GCA accession xml, and returns the accession's data in the
form of a dictionary
A proteome dict built from Uniprot's proteome xml files
upid: A valid Uniprot proteome accession
assembly_acc: A valid ENA GCA accession
kingdom: The corresponding species' kingdom | [
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genome_entry = {}
fields = {}
proteome_dict = extract_uniprot_genome_metadata(upid)
if len(proteome_dict.keys()) > 0:
fields["gca_acc"] = None
fields["gca_version"] = None
fields["ensembl_id"] = None
fields["ensembl_source"... | [
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},
{
"identifier": "kingdom",
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"docstring_tokens"... |
5d23a3733de3c0bfee152bd31e7f1292bb87da0f | Rfam/rfam-production | scripts/export/genomes/fetch_gen_metadata.py | [
"Apache-2.0"
] | Python | import_chromosome_names | null | def import_chromosome_names():
"""
Parse GCA accession XML to import chromosome name and chromosome types
into genseq table.
"""
import django
import django
sys.path.append("/Users/ikalvari/RfamWorkspace/Rfam_resource/rfam_schemas")
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "rfam_... |
Parse GCA accession XML to import chromosome name and chromosome types
into genseq table.
| Parse GCA accession XML to import chromosome name and chromosome types
into genseq table. | [
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] | def import_chromosome_names():
import django
import django
sys.path.append("/Users/ikalvari/RfamWorkspace/Rfam_resource/rfam_schemas")
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "rfam_schemas.rfam_schemas.settings")
django.setup()
from rfam_schemas.RfamLive.models import Genome, Genseq
... | [
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] | [] | {
"returns": [],
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"outlier_params": [],
"others": []
} |
6a7c971e4372e2232abdadf289eb250b93829ccf | Rfam/rfam-production | scripts/validation/xml_validator.py | [
"Apache-2.0"
] | Python | validate_xml_dump | <not_specific> | def validate_xml_dump(xml_file):
"""
Validates Rfam XML dumps using xmllint
xml_file: An XML dump used to index Rfam release data
return: True upon success, False for failure
"""
process = Popen(["xmllint", "--schema", "http://www.ebi.ac.uk/ebisearch/XML4dbDumps.xsd", "--noout", xml_file],
... |
Validates Rfam XML dumps using xmllint
xml_file: An XML dump used to index Rfam release data
return: True upon success, False for failure
| Validates Rfam XML dumps using xmllint
xml_file: An XML dump used to index Rfam release data
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] | def validate_xml_dump(xml_file):
process = Popen(["xmllint", "--schema", "http://www.ebi.ac.uk/ebisearch/XML4dbDumps.xsd", "--noout", xml_file],
stdin=PIPE, stdout=PIPE, stderr=PIPE)
output = process.communicate()[1]
if output.find("validates") == -1:
return False
return True | [
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} |
6a7c971e4372e2232abdadf289eb250b93829ccf | Rfam/rfam-production | scripts/validation/xml_validator.py | [
"Apache-2.0"
] | Python | parse_arguments | <not_specific> | def parse_arguments():
"""
Simple argument parsing using python's argparse
return: Python's argparse parser object
"""
parser = argparse.ArgumentParser()
parser.add_argument("--input", help="Single XML file or directory", action="store")
parser.add_argument("--log", help="Generate a log f... |
Simple argument parsing using python's argparse
return: Python's argparse parser object
| Simple argument parsing using python's argparse
return: Python's argparse parser object | [
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] | def parse_arguments():
parser = argparse.ArgumentParser()
parser.add_argument("--input", help="Single XML file or directory", action="store")
parser.add_argument("--log", help="Generate a log file listing all XML files failining validation",
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} |
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