id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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228,500 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc._get_objanno | def _get_objanno(self, assoc_fn):
"""Get an annotation object"""
# Determine annotation file format from filename, if possible
anno_type = get_anno_desc(assoc_fn, None)
# Default annotation file format is id2gos
if anno_type is None:
anno_type = self.args.annofmt if s... | python | def _get_objanno(self, assoc_fn):
"""Get an annotation object"""
# Determine annotation file format from filename, if possible
anno_type = get_anno_desc(assoc_fn, None)
# Default annotation file format is id2gos
if anno_type is None:
anno_type = self.args.annofmt if s... | [
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228,501 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc._init_itemid2name | def _init_itemid2name(self):
"""Print gene symbols instead of gene IDs, if provided."""
if not hasattr(self.args, 'id2sym'):
return None
fin_id2sym = self.args.id2sym
if fin_id2sym is not None and os.path.exists(fin_id2sym):
id2sym = {}
cmpl = re.compi... | python | def _init_itemid2name(self):
"""Print gene symbols instead of gene IDs, if provided."""
if not hasattr(self.args, 'id2sym'):
return None
fin_id2sym = self.args.id2sym
if fin_id2sym is not None and os.path.exists(fin_id2sym):
id2sym = {}
cmpl = re.compi... | [
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228,502 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.prt_results | def prt_results(self, goea_results):
"""Print GOEA results to the screen or to a file."""
# objaart = self.prepgrp.get_objaart(goea_results) if self.prepgrp is not None else None
if self.args.outfile is None:
self._prt_results(goea_results)
else:
# Users can print... | python | def prt_results(self, goea_results):
"""Print GOEA results to the screen or to a file."""
# objaart = self.prepgrp.get_objaart(goea_results) if self.prepgrp is not None else None
if self.args.outfile is None:
self._prt_results(goea_results)
else:
# Users can print... | [
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228,503 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc._prt_results | def _prt_results(self, goea_results):
"""Print GOEA results to the screen."""
min_ratio = self.args.ratio
if min_ratio is not None:
assert 1 <= min_ratio <= 2
self.objgoea.print_date(min_ratio=min_ratio, pval=self.args.pval)
results_adj = self.objgoea.get_adj_records(... | python | def _prt_results(self, goea_results):
"""Print GOEA results to the screen."""
min_ratio = self.args.ratio
if min_ratio is not None:
assert 1 <= min_ratio <= 2
self.objgoea.print_date(min_ratio=min_ratio, pval=self.args.pval)
results_adj = self.objgoea.get_adj_records(... | [
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228,504 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.chk_genes | def chk_genes(self, study, pop, assoc=None):
"""Check gene sets."""
if len(pop) < len(study):
exit("\nERROR: The study file contains more elements than the population file. "
"Please check that the study file is a subset of the population file.\n")
# check the fracti... | python | def chk_genes(self, study, pop, assoc=None):
"""Check gene sets."""
if len(pop) < len(study):
exit("\nERROR: The study file contains more elements than the population file. "
"Please check that the study file is a subset of the population file.\n")
# check the fracti... | [
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228,505 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.get_results_sig | def get_results_sig(self):
"""Get significant results."""
# Only print results when uncorrected p-value < this value.
print("{N:7,} of {M:,} results have uncorrected P-values <= {PVAL}=pval\n".format(
N=sum(1 for r in self.results_all if r.p_uncorrected < self.args.pval),
... | python | def get_results_sig(self):
"""Get significant results."""
# Only print results when uncorrected p-value < this value.
print("{N:7,} of {M:,} results have uncorrected P-values <= {PVAL}=pval\n".format(
N=sum(1 for r in self.results_all if r.p_uncorrected < self.args.pval),
... | [
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228,506 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.get_pval_field | def get_pval_field(self):
"""Get 'p_uncorrected' or the user-specified field for determining significant results."""
pval_fld = self.args.pval_field
# If --pval_field [VAL] was specified
if pval_fld is not None:
if pval_fld[:2] != 'p_':
pval_fld = 'p_' + pval_... | python | def get_pval_field(self):
"""Get 'p_uncorrected' or the user-specified field for determining significant results."""
pval_fld = self.args.pval_field
# If --pval_field [VAL] was specified
if pval_fld is not None:
if pval_fld[:2] != 'p_':
pval_fld = 'p_' + pval_... | [
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228,507 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.rd_files | def rd_files(self, study_fn, pop_fn):
"""Read files and return study and population."""
study, pop = self._read_geneset(study_fn, pop_fn)
print("Study: {0} vs. Population {1}\n".format(len(study), len(pop)))
return study, pop | python | def rd_files(self, study_fn, pop_fn):
"""Read files and return study and population."""
study, pop = self._read_geneset(study_fn, pop_fn)
print("Study: {0} vs. Population {1}\n".format(len(study), len(pop)))
return study, pop | [
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228,508 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc._read_geneset | def _read_geneset(self, study_fn, pop_fn):
"""Open files containing genes. Return study genes and population genes."""
pop = set(_.strip() for _ in open(pop_fn) if _.strip())
study = frozenset(_.strip() for _ in open(study_fn) if _.strip())
if next(iter(pop)).isdigit():
pop =... | python | def _read_geneset(self, study_fn, pop_fn):
"""Open files containing genes. Return study genes and population genes."""
pop = set(_.strip() for _ in open(pop_fn) if _.strip())
study = frozenset(_.strip() for _ in open(study_fn) if _.strip())
if next(iter(pop)).isdigit():
pop =... | [
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228,509 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GroupItems.get_objgrpwr | def get_objgrpwr(self, goea_results):
"""Get a GrpWr object to write grouped GOEA results."""
sortobj = self.get_sortobj(goea_results)
return GrpWr(sortobj, self.pval_fld, ver_list=self.ver_list) | python | def get_objgrpwr(self, goea_results):
"""Get a GrpWr object to write grouped GOEA results."""
sortobj = self.get_sortobj(goea_results)
return GrpWr(sortobj, self.pval_fld, ver_list=self.ver_list) | [
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228,510 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GroupItems.get_sortobj | def get_sortobj(self, goea_results, **kws):
"""Return a Grouper object, given a list of GOEnrichmentRecord."""
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
goids = set(nt.GO for nt in nts_goea)
go2nt = {nt.GO:nt for nt in nts_goea}
grprobj = Grouper("GOEA", goids, ... | python | def get_sortobj(self, goea_results, **kws):
"""Return a Grouper object, given a list of GOEnrichmentRecord."""
nts_goea = MgrNtGOEAs(goea_results).get_goea_nts_prt(**kws)
goids = set(nt.GO for nt in nts_goea)
go2nt = {nt.GO:nt for nt in nts_goea}
grprobj = Grouper("GOEA", goids, ... | [
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228,511 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GroupItems._init_objaartall | def _init_objaartall(self):
"""Get background database info for making ASCII art."""
kws = {
'sortgo':lambda nt: [nt.NS, nt.dcnt],
# fmtgo=('{p_fdr_bh:8.2e} {GO} '
# Formatting for GO terms in grouped GO list
'fmtgo':('{hdr1usr01:2} {NS} {GO} {s_fdr_bh:8} ... | python | def _init_objaartall(self):
"""Get background database info for making ASCII art."""
kws = {
'sortgo':lambda nt: [nt.NS, nt.dcnt],
# fmtgo=('{p_fdr_bh:8.2e} {GO} '
# Formatting for GO terms in grouped GO list
'fmtgo':('{hdr1usr01:2} {NS} {GO} {s_fdr_bh:8} ... | [
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228,512 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.wr_xlsx | def wr_xlsx(self, fout_xlsx):
"""Print grouped GOEA results into an xlsx file."""
objwr = WrXlsxSortedGos("GOEA", self.sortobj)
#### fld2fmt['ratio_in_study'] = '{:>8}'
#### fld2fmt['ratio_in_pop'] = '{:>12}'
#### ntfld2wbfmtdict = {
# ntfld_wbfmt = {
# 'ratio... | python | def wr_xlsx(self, fout_xlsx):
"""Print grouped GOEA results into an xlsx file."""
objwr = WrXlsxSortedGos("GOEA", self.sortobj)
#### fld2fmt['ratio_in_study'] = '{:>8}'
#### fld2fmt['ratio_in_pop'] = '{:>12}'
#### ntfld2wbfmtdict = {
# ntfld_wbfmt = {
# 'ratio... | [
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228,513 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.wr_tsv | def wr_tsv(self, fout_tsv):
"""Print grouped GOEA results into a tab-separated file."""
with open(fout_tsv, 'w') as prt:
kws_tsv = {
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
'prt_flds':self.flds_cur}
prt_tsv_sections(prt, s... | python | def wr_tsv(self, fout_tsv):
"""Print grouped GOEA results into a tab-separated file."""
with open(fout_tsv, 'w') as prt:
kws_tsv = {
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
'prt_flds':self.flds_cur}
prt_tsv_sections(prt, s... | [
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228,514 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.wr_txt | def wr_txt(self, fout_txt):
"""Write to a file GOEA results in an ASCII text format."""
with open(fout_txt, 'w') as prt:
for line in self.ver_list:
prt.write("{LINE}\n".format(LINE=line))
self.prt_txt(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt)) | python | def wr_txt(self, fout_txt):
"""Write to a file GOEA results in an ASCII text format."""
with open(fout_txt, 'w') as prt:
for line in self.ver_list:
prt.write("{LINE}\n".format(LINE=line))
self.prt_txt(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt)) | [
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228,515 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.prt_tsv | def prt_tsv(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
WrSectionsTxt.prt_sections(prt, self.desc2nts['sections'], prtfmt, secspc=True) | python | def prt_tsv(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
WrSectionsTxt.prt_sections(prt, self.desc2nts['sections'], prtfmt, secspc=True) | [
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228,516 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr._init_flds_cur | def _init_flds_cur(self):
"""Choose fields to print from a multitude of available fields."""
flds = []
# ('GO', 'NS', 'enrichment', 'name', 'ratio_in_study', 'ratio_in_pop', 'depth',
# 'p_uncorrected', 'p_bonferroni', 'p_sidak', 'p_holm', 'p_fdr_bh',
# 'pop_n', 'pop_count', 'pop_... | python | def _init_flds_cur(self):
"""Choose fields to print from a multitude of available fields."""
flds = []
# ('GO', 'NS', 'enrichment', 'name', 'ratio_in_study', 'ratio_in_pop', 'depth',
# 'p_uncorrected', 'p_bonferroni', 'p_sidak', 'p_holm', 'p_fdr_bh',
# 'pop_n', 'pop_count', 'pop_... | [
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228,517 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader.do_hdr | def do_hdr(self, line, hdrs_usr):
"""Initialize self.h2i."""
# If there is no header hint, consider the first line the header.
if self.hdr_ex is None:
self._init_hdr(line, hdrs_usr)
return True
# If there is a header hint, examine each beginning line until header ... | python | def do_hdr(self, line, hdrs_usr):
"""Initialize self.h2i."""
# If there is no header hint, consider the first line the header.
if self.hdr_ex is None:
self._init_hdr(line, hdrs_usr)
return True
# If there is a header hint, examine each beginning line until header ... | [
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228,518 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader.hdr_xform | def hdr_xform(self, hdrs):
"""Transform NCBI Gene header fields into valid namedtuple fields."""
xform = []
hdrs = self.replace_nulls(hdrs)
for hdr in hdrs:
hdr = hdr.replace('.', '_')
hdr = hdr.replace(' ', '_')
hdr = hdr.replace('#', 'N')
... | python | def hdr_xform(self, hdrs):
"""Transform NCBI Gene header fields into valid namedtuple fields."""
xform = []
hdrs = self.replace_nulls(hdrs)
for hdr in hdrs:
hdr = hdr.replace('.', '_')
hdr = hdr.replace(' ', '_')
hdr = hdr.replace('#', 'N')
... | [
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228,519 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_nt_hdr | def _init_nt_hdr(self, line):
"""Convert headers into valid namedtuple fields."""
line = line.replace('.', '_')
line = line.replace(' ', '_')
line = line.replace('#', 'N')
line = line.replace('-', '_')
line = line.replace('"', '')
#line = re.sub(r"_$", r"", line)
... | python | def _init_nt_hdr(self, line):
"""Convert headers into valid namedtuple fields."""
line = line.replace('.', '_')
line = line.replace(' ', '_')
line = line.replace('#', 'N')
line = line.replace('-', '_')
line = line.replace('"', '')
#line = re.sub(r"_$", r"", line)
... | [
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228,520 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader.replace_nulls | def replace_nulls(hdrs):
"""Replace '' in hdrs."""
ret = []
idx = 0
for hdr in hdrs:
if hdr == '':
ret.append("no_hdr{}".format(idx))
else:
ret.append(hdr)
return ret | python | def replace_nulls(hdrs):
"""Replace '' in hdrs."""
ret = []
idx = 0
for hdr in hdrs:
if hdr == '':
ret.append("no_hdr{}".format(idx))
else:
ret.append(hdr)
return ret | [
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228,521 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_data_line | def _init_data_line(self, fnc, lnum, line):
"""Process Data line."""
fld = re.split(self.sep, line)
# Lines may contain different numbers of items.
# The line should have all columns requested by the user.
if self.usr_max_idx < len(fld):
self.convert_ints_floats(fld)
... | python | def _init_data_line(self, fnc, lnum, line):
"""Process Data line."""
fld = re.split(self.sep, line)
# Lines may contain different numbers of items.
# The line should have all columns requested by the user.
if self.usr_max_idx < len(fld):
self.convert_ints_floats(fld)
... | [
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228,522 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader.convert_ints_floats | def convert_ints_floats(self, flds):
"""Convert strings to ints and floats, if so specified."""
for idx in self.idxs_float:
flds[idx] = float(flds[idx])
for idx in self.idxs_int:
dig = flds[idx]
#print 'idx={} ({}) {}'.format(idx, flds[idx], flds) # DVK
... | python | def convert_ints_floats(self, flds):
"""Convert strings to ints and floats, if so specified."""
for idx in self.idxs_float:
flds[idx] = float(flds[idx])
for idx in self.idxs_int:
dig = flds[idx]
#print 'idx={} ({}) {}'.format(idx, flds[idx], flds) # DVK
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228,523 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_hdr | def _init_hdr(self, line, hdrs_usr):
"""Initialize self.hdr2idx, self.len, self.idxs_float, and self.idxs_int"""
self.hdr2idx = OrderedDict([(v.strip(), i) for i, v in enumerate(re.split(self.sep, line))])
self.len = len(self.hdr2idx)
# If user is requesting specific data fields...
... | python | def _init_hdr(self, line, hdrs_usr):
"""Initialize self.hdr2idx, self.len, self.idxs_float, and self.idxs_int"""
self.hdr2idx = OrderedDict([(v.strip(), i) for i, v in enumerate(re.split(self.sep, line))])
self.len = len(self.hdr2idx)
# If user is requesting specific data fields...
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228,524 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_float | def _init_idxs_float(self, usr_hdrs):
"""List of indexes whose values will be floats."""
self.idxs_float = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.float_hdrs] | python | def _init_idxs_float(self, usr_hdrs):
"""List of indexes whose values will be floats."""
self.idxs_float = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.float_hdrs] | [
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228,525 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_int | def _init_idxs_int(self, usr_hdrs):
"""List of indexes whose values will be ints."""
self.idxs_int = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.int_hdrs] | python | def _init_idxs_int(self, usr_hdrs):
"""List of indexes whose values will be ints."""
self.idxs_int = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.int_hdrs] | [
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228,526 | tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_strpat | def _init_idxs_strpat(self, usr_hdrs):
"""List of indexes whose values will be strings."""
strpat = self.strpat_hdrs.keys()
self.idxs_strpat = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in strpat] | python | def _init_idxs_strpat(self, usr_hdrs):
"""List of indexes whose values will be strings."""
strpat = self.strpat_hdrs.keys()
self.idxs_strpat = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in strpat] | [
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228,527 | tanghaibao/goatools | goatools/cli/ncbi_gene_results_to_python.py | NCBIgeneToPythonCli._get_geneid2nt | def _get_geneid2nt(nts):
"""Get geneid2nt given a list of namedtuples."""
geneid2nt = {}
for ntd in nts:
geneid = ntd.GeneID
if geneid not in geneid2nt:
geneid2nt[geneid] = ntd
else:
print("DUPLICATE GeneID FOUND {N:9} {SYM}".fo... | python | def _get_geneid2nt(nts):
"""Get geneid2nt given a list of namedtuples."""
geneid2nt = {}
for ntd in nts:
geneid = ntd.GeneID
if geneid not in geneid2nt:
geneid2nt[geneid] = ntd
else:
print("DUPLICATE GeneID FOUND {N:9} {SYM}".fo... | [
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228,528 | tanghaibao/goatools | goatools/cli/ncbi_gene_results_to_python.py | NCBIgeneToPythonCli._wrpy_ncbi_gene_nts | def _wrpy_ncbi_gene_nts(fout_py, geneid2nt, log):
"""Write namedtuples to a dict in a Python module."""
num_genes = len(geneid2nt)
with open(fout_py, 'w') as ofstrm:
docstr = "Data downloaded from NCBI Gene converted into Python namedtuples."
ofstrm.write('"""{PYDOC}"""\n... | python | def _wrpy_ncbi_gene_nts(fout_py, geneid2nt, log):
"""Write namedtuples to a dict in a Python module."""
num_genes = len(geneid2nt)
with open(fout_py, 'w') as ofstrm:
docstr = "Data downloaded from NCBI Gene converted into Python namedtuples."
ofstrm.write('"""{PYDOC}"""\n... | [
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228,529 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | get_goobjs_altgo2goobj | def get_goobjs_altgo2goobj(go2obj):
"""Separate alt GO IDs and key GO IDs."""
goobjs = set()
altgo2goobj = {}
for goid, goobj in go2obj.items():
goobjs.add(goobj)
if goid != goobj.id:
altgo2goobj[goid] = goobj
return goobjs, altgo2goobj | python | def get_goobjs_altgo2goobj(go2obj):
"""Separate alt GO IDs and key GO IDs."""
goobjs = set()
altgo2goobj = {}
for goid, goobj in go2obj.items():
goobjs.add(goobj)
if goid != goobj.id:
altgo2goobj[goid] = goobj
return goobjs, altgo2goobj | [
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228,530 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | add_alt_goids | def add_alt_goids(go2values, altgo2goobj):
"""Add alternate source GO IDs."""
for goobj_key in altgo2goobj.values():
values_curr = go2values[goobj_key.id]
for goid_alt in goobj_key.alt_ids:
go2values[goid_alt] = values_curr
return go2values | python | def add_alt_goids(go2values, altgo2goobj):
"""Add alternate source GO IDs."""
for goobj_key in altgo2goobj.values():
values_curr = go2values[goobj_key.id]
for goid_alt in goobj_key.alt_ids:
go2values[goid_alt] = values_curr
return go2values | [
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228,531 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_main_goids | def fill_main_goids(go2obj, goids):
"""Ensure main GO IDs are included in go2obj."""
# User GO IDs (goids) may be either main GO IDs or alternate GO IDs.
for goid in goids:
goobj = go2obj[goid]
# If a user specified an ALT GO ID and main GO ID not in go2obj:
if goid != goobj.id and g... | python | def fill_main_goids(go2obj, goids):
"""Ensure main GO IDs are included in go2obj."""
# User GO IDs (goids) may be either main GO IDs or alternate GO IDs.
for goid in goids:
goobj = go2obj[goid]
# If a user specified an ALT GO ID and main GO ID not in go2obj:
if goid != goobj.id and g... | [
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228,532 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_altgoids | def fill_altgoids(go2obj):
"""Given a go2obj containing key GO IDs, fill with all alternate GO IDs."""
alt2obj = {altgo:goobj for goobj in go2obj.values() for altgo in goobj.alt_ids}
for goid, goobj in alt2obj.items():
go2obj[goid] = goobj | python | def fill_altgoids(go2obj):
"""Given a go2obj containing key GO IDs, fill with all alternate GO IDs."""
alt2obj = {altgo:goobj for goobj in go2obj.values() for altgo in goobj.alt_ids}
for goid, goobj in alt2obj.items():
go2obj[goid] = goobj | [
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228,533 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_relationshipobjs | def fill_relationshipobjs(go2obj, relationships):
"""Add GO IDs to go2obj that are involved in relationships."""
# Get all GO Term record objects that have relationships
obj = RelationshipFill(go2obj, relationships)
for goobj in go2obj.values():
if goobj.relationship:
obj.fill_relati... | python | def fill_relationshipobjs(go2obj, relationships):
"""Add GO IDs to go2obj that are involved in relationships."""
# Get all GO Term record objects that have relationships
obj = RelationshipFill(go2obj, relationships)
for goobj in go2obj.values():
if goobj.relationship:
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228,534 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_childgoid2obj | def fill_childgoid2obj(childgoid2obj, parent_obj):
"""Fill childgoid2obj with all child key GO IDs and their objects."""
for child_obj in parent_obj.children:
if child_obj.id not in childgoid2obj:
childgoid2obj[child_obj.id] = child_obj
fill_childgoid2obj(childgoid2obj, child_obj... | python | def fill_childgoid2obj(childgoid2obj, parent_obj):
"""Fill childgoid2obj with all child key GO IDs and their objects."""
for child_obj in parent_obj.children:
if child_obj.id not in childgoid2obj:
childgoid2obj[child_obj.id] = child_obj
fill_childgoid2obj(childgoid2obj, child_obj... | [
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228,535 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | get_leaf_children | def get_leaf_children(gos_user, go2obj_arg):
"""Find all the GO descendants under all user GO IDs. Return leaf-level GO IDs."""
childgoid2obj = {}
for goid_usr in gos_user:
goobj_usr = go2obj_arg[goid_usr]
fill_childgoid2obj(childgoid2obj, goobj_usr)
return set(go for go, o in childgoid2... | python | def get_leaf_children(gos_user, go2obj_arg):
"""Find all the GO descendants under all user GO IDs. Return leaf-level GO IDs."""
childgoid2obj = {}
for goid_usr in gos_user:
goobj_usr = go2obj_arg[goid_usr]
fill_childgoid2obj(childgoid2obj, goobj_usr)
return set(go for go, o in childgoid2... | [
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228,536 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | chk_goids | def chk_goids(goids, msg=None, raise_except=True):
"""check that all GO IDs have the proper format."""
for goid in goids:
if not goid_is_valid(goid):
if raise_except:
raise RuntimeError("BAD GO({GO}): {MSG}".format(GO=goid, MSG=msg))
else:
return g... | python | def chk_goids(goids, msg=None, raise_except=True):
"""check that all GO IDs have the proper format."""
for goid in goids:
if not goid_is_valid(goid):
if raise_except:
raise RuntimeError("BAD GO({GO}): {MSG}".format(GO=goid, MSG=msg))
else:
return g... | [
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228,537 | tanghaibao/goatools | goatools/gosubdag/go_tasks.py | TopologicalSortRelationships._get_sorted_relationships | def _get_sorted_relationships(self, goterm):
"""Traverse GO Terms above the current GO Term. Then add current GO Term to sorted."""
if goterm.id in self.goids_seen:
return
self.goids_seen.add(goterm.id)
for goterm_upper in goterm.get_goterms_upper():
self._get_sor... | python | def _get_sorted_relationships(self, goterm):
"""Traverse GO Terms above the current GO Term. Then add current GO Term to sorted."""
if goterm.id in self.goids_seen:
return
self.goids_seen.add(goterm.id)
for goterm_upper in goterm.get_goterms_upper():
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228,538 | tanghaibao/goatools | goatools/grouper/read_goids.py | read_sections | def read_sections(sections_file, exclude_ungrouped=False, prt=sys.stdout):
"""Get sections and GO grouping hdrgos from file, if sections exist."""
if sections_file is None:
return None
assert isinstance(sections_file, str), "BAD SECTIONS FILENAME({S})".format(
S=sections_file)
if os.path... | python | def read_sections(sections_file, exclude_ungrouped=False, prt=sys.stdout):
"""Get sections and GO grouping hdrgos from file, if sections exist."""
if sections_file is None:
return None
assert isinstance(sections_file, str), "BAD SECTIONS FILENAME({S})".format(
S=sections_file)
if os.path... | [
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228,539 | tanghaibao/goatools | goatools/grouper/read_goids.py | ReadGoids.read_py | def read_py(self, fin_txt, get_goids_only, exclude_ungrouped, prt=sys.stdout):
"""Read GO IDs or sections data from a Python file."""
goids_fin = self._read_py(fin_txt, get_goids_only, exclude_ungrouped)
sections = self._read_finish(goids_fin, prt)
# Print summary of GO IDs read
... | python | def read_py(self, fin_txt, get_goids_only, exclude_ungrouped, prt=sys.stdout):
"""Read GO IDs or sections data from a Python file."""
goids_fin = self._read_py(fin_txt, get_goids_only, exclude_ungrouped)
sections = self._read_finish(goids_fin, prt)
# Print summary of GO IDs read
... | [
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228,540 | tanghaibao/goatools | goatools/grouper/read_goids.py | ReadGoids.read_sections | def read_sections(self, sections_file, get_goids_only, exclude_ungrouped):
"""Read sections variable from a text file of from a Python file."""
ext = os.path.splitext(sections_file)[1]
file_contents = None
if ext == '.py':
file_contents = self.read_py(sections_file, get_goids... | python | def read_sections(self, sections_file, get_goids_only, exclude_ungrouped):
"""Read sections variable from a text file of from a Python file."""
ext = os.path.splitext(sections_file)[1]
file_contents = None
if ext == '.py':
file_contents = self.read_py(sections_file, get_goids... | [
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228,541 | tanghaibao/goatools | goatools/grouper/read_goids.py | ReadGoids._rpt_unused_sections | def _rpt_unused_sections(self, prt):
"""Report unused sections."""
sections_unused = set(self.sections_seen).difference(self.section2goids.keys())
for sec in sections_unused:
prt.write(" UNUSED SECTION: {SEC}\n".format(SEC=sec)) | python | def _rpt_unused_sections(self, prt):
"""Report unused sections."""
sections_unused = set(self.sections_seen).difference(self.section2goids.keys())
for sec in sections_unused:
prt.write(" UNUSED SECTION: {SEC}\n".format(SEC=sec)) | [
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228,542 | tanghaibao/goatools | goatools/grouper/read_goids.py | ReadGoids._prt_read_msg | def _prt_read_msg(self, prt, fin_txt, exclude_ungrouped):
"""Print which file was read and the number of GO IDs found."""
if self.sections_seen or exclude_ungrouped:
# dat = Grouper.get_summary_data(self.section2goids.items(), HdrgosSections.secdflt)
dat = SummarySec2dHdrGos().su... | python | def _prt_read_msg(self, prt, fin_txt, exclude_ungrouped):
"""Print which file was read and the number of GO IDs found."""
if self.sections_seen or exclude_ungrouped:
# dat = Grouper.get_summary_data(self.section2goids.items(), HdrgosSections.secdflt)
dat = SummarySec2dHdrGos().su... | [
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228,543 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.rm_gos | def rm_gos(self, rm_goids):
"""Remove any edges that contain user-specified edges."""
self.edges = self._rm_gos_edges(rm_goids, self.edges)
self.edges_rel = self._rm_gos_edges_rel(rm_goids, self.edges_rel) | python | def rm_gos(self, rm_goids):
"""Remove any edges that contain user-specified edges."""
self.edges = self._rm_gos_edges(rm_goids, self.edges)
self.edges_rel = self._rm_gos_edges_rel(rm_goids, self.edges_rel) | [
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228,544 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase._rm_gos_edges_rel | def _rm_gos_edges_rel(self, rm_goids, edges_rel):
"""Remove any relationship that contain user-specified edges."""
edges_ret = {}
for rname, edges_cur in edges_rel.items():
edges_new = self._rm_gos_edges(rm_goids, edges_cur)
if edges_new:
edges_ret[rname] ... | python | def _rm_gos_edges_rel(self, rm_goids, edges_rel):
"""Remove any relationship that contain user-specified edges."""
edges_ret = {}
for rname, edges_cur in edges_rel.items():
edges_new = self._rm_gos_edges(rm_goids, edges_cur)
if edges_new:
edges_ret[rname] ... | [
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228,545 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase._rm_gos_edges | def _rm_gos_edges(rm_goids, edges_all):
"""Remove any is_a edges that contain user-specified edges."""
edges_reduced = []
for goid_child, goid_parent in sorted(edges_all, key=lambda t: t[1]):
if goid_child not in rm_goids and goid_parent not in rm_goids:
edges_reduced... | python | def _rm_gos_edges(rm_goids, edges_all):
"""Remove any is_a edges that contain user-specified edges."""
edges_reduced = []
for goid_child, goid_parent in sorted(edges_all, key=lambda t: t[1]):
if goid_child not in rm_goids and goid_parent not in rm_goids:
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228,546 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.get_all_edge_nodes | def get_all_edge_nodes(self):
"""Return a list of all GO IDs that are connected to edges."""
edge_nodes = set(e for es in self.edges for e in es)
for edges in self.edges_rel.values():
rel_nodes = set(e for es in edges for e in es)
edge_nodes.update(rel_nodes)
retu... | python | def get_all_edge_nodes(self):
"""Return a list of all GO IDs that are connected to edges."""
edge_nodes = set(e for es in self.edges for e in es)
for edges in self.edges_rel.values():
rel_nodes = set(e for es in edges for e in es)
edge_nodes.update(rel_nodes)
retu... | [
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228,547 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.chk_edges | def chk_edges(self):
"""Check that all edge nodes exist in local subset."""
goids = set(self.go2obj)
self.chk_edges_nodes(self.edges, goids, "is_a")
for reltype, edges in self.edges_rel.items():
self.chk_edges_nodes(edges, goids, reltype) | python | def chk_edges(self):
"""Check that all edge nodes exist in local subset."""
goids = set(self.go2obj)
self.chk_edges_nodes(self.edges, goids, "is_a")
for reltype, edges in self.edges_rel.items():
self.chk_edges_nodes(edges, goids, reltype) | [
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228,548 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.chk_edges_nodes | def chk_edges_nodes(edges, nodes, name):
"""Check that user specified edges have a node which exists."""
edge_nodes = set(e for es in edges for e in es)
missing_nodes = edge_nodes.difference(nodes)
assert not missing_nodes, "MISSING: {GOs}\n{NM} EDGES MISSING {N} NODES (OF {T})".format(
... | python | def chk_edges_nodes(edges, nodes, name):
"""Check that user specified edges have a node which exists."""
edge_nodes = set(e for es in edges for e in es)
missing_nodes = edge_nodes.difference(nodes)
assert not missing_nodes, "MISSING: {GOs}\n{NM} EDGES MISSING {N} NODES (OF {T})".format(
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228,549 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.get_c2ps | def get_c2ps(self):
"""Set child2parents dict for all parents used in this set of edges."""
c2ps = defaultdict(set)
for goid_child, goid_parent in self.edges:
c2ps[goid_child].add(goid_parent)
return c2ps | python | def get_c2ps(self):
"""Set child2parents dict for all parents used in this set of edges."""
c2ps = defaultdict(set)
for goid_child, goid_parent in self.edges:
c2ps[goid_child].add(goid_parent)
return c2ps | [
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228,550 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesRelatives._init_edges_relationships | def _init_edges_relationships(rel2src2dsts, rel2dst2srcs):
"""Get the directed edges from GO term to GO term using relationships."""
edge_rel2fromto = {}
relationships = set(rel2src2dsts).union(rel2dst2srcs)
for reltype in relationships:
edge_from_to = []
if relty... | python | def _init_edges_relationships(rel2src2dsts, rel2dst2srcs):
"""Get the directed edges from GO term to GO term using relationships."""
edge_rel2fromto = {}
relationships = set(rel2src2dsts).union(rel2dst2srcs)
for reltype in relationships:
edge_from_to = []
if relty... | [
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228,551 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesRelatives._traverse_relationship_objs | def _traverse_relationship_objs(self, rel2src2dsts, goobj_child, goids_seen):
"""Traverse from source GO up relationships."""
child_id = goobj_child.id
goids_seen.add(child_id)
##A self.go2obj[child_id] = goobj_child
# Update goids_seen and go2obj with child alt_ids
for g... | python | def _traverse_relationship_objs(self, rel2src2dsts, goobj_child, goids_seen):
"""Traverse from source GO up relationships."""
child_id = goobj_child.id
goids_seen.add(child_id)
##A self.go2obj[child_id] = goobj_child
# Update goids_seen and go2obj with child alt_ids
for g... | [
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228,552 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesRelatives._init_rel2dst2srcs | def _init_rel2dst2srcs(self, go_sources, traverse_child):
"""Traverse through reverse relationships."""
if not traverse_child or not self.relationships:
return {}
rel2dst2srcs = {r:defaultdict(set) for r in self.relationships}
goids_seen = set()
go2obj = self.go2obj
... | python | def _init_rel2dst2srcs(self, go_sources, traverse_child):
"""Traverse through reverse relationships."""
if not traverse_child or not self.relationships:
return {}
rel2dst2srcs = {r:defaultdict(set) for r in self.relationships}
goids_seen = set()
go2obj = self.go2obj
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228,553 | tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesRelatives._init_c2ps | def _init_c2ps(self, go_sources, traverse_child):
"""Traverse up children."""
if not traverse_child:
return {}
c2ps = defaultdict(set)
goids_seen = set()
go2obj = self.go2obj
for goid_src in go_sources:
goobj_src = go2obj[goid_src]
if g... | python | def _init_c2ps(self, go_sources, traverse_child):
"""Traverse up children."""
if not traverse_child:
return {}
c2ps = defaultdict(set)
goids_seen = set()
go2obj = self.go2obj
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goobj_src = go2obj[goid_src]
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228,554 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData.chk | def chk(self, annotations, fout_err):
"""Check annotations."""
for idx, ntd in enumerate(annotations):
self._chk_fld(ntd, "Qualifier") # optional 0 or greater
self._chk_fld(ntd, "DB_Reference", 1) # required 1 or greater
self._chk_fld(ntd, "With_From") ... | python | def chk(self, annotations, fout_err):
"""Check annotations."""
for idx, ntd in enumerate(annotations):
self._chk_fld(ntd, "Qualifier") # optional 0 or greater
self._chk_fld(ntd, "DB_Reference", 1) # required 1 or greater
self._chk_fld(ntd, "With_From") ... | [
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228,555 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData.get_gafvals | def get_gafvals(self, line):
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flds = line.split('\t')
flds[3] = self._get_qualifier(flds[3]) # 3 Qualifier
flds[5] = self._get_set(flds[5]) # 5 DB_Reference
flds[7] = self._get_set(flds[7]) #... | python | def get_gafvals(self, line):
"""Convert fields from string to preferred format for GAF ver 2.1 and 2.0."""
flds = line.split('\t')
flds[3] = self._get_qualifier(flds[3]) # 3 Qualifier
flds[5] = self._get_set(flds[5]) # 5 DB_Reference
flds[7] = self._get_set(flds[7]) #... | [
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228,556 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData._get_qualifier | def _get_qualifier(val):
"""Get qualifiers. Correct for inconsistent capitalization in GAF files"""
quals = set()
if val == '':
return quals
for val in val.split('|'):
val = val.lower()
quals.add(val if val != 'not' else 'NOT')
return quals | python | def _get_qualifier(val):
"""Get qualifiers. Correct for inconsistent capitalization in GAF files"""
quals = set()
if val == '':
return quals
for val in val.split('|'):
val = val.lower()
quals.add(val if val != 'not' else 'NOT')
return quals | [
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228,557 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData._chk_fld | def _chk_fld(self, ntd, name, qty_min=0, qty_max=None):
"""Further split a GAF value within a single field."""
vals = getattr(ntd, name)
num_vals = len(vals)
if num_vals < qty_min:
self.illegal_lines['MIN QTY'].append(
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"""Further split a GAF value within a single field."""
vals = getattr(ntd, name)
num_vals = len(vals)
if num_vals < qty_min:
self.illegal_lines['MIN QTY'].append(
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228,558 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData.prt_line_detail | def prt_line_detail(self, prt, line):
"""Print line header and values in a readable format."""
values = line.split('\t')
self._prt_line_detail(prt, values) | python | def prt_line_detail(self, prt, line):
"""Print line header and values in a readable format."""
values = line.split('\t')
self._prt_line_detail(prt, values) | [
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228,559 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData._prt_line_detail | def _prt_line_detail(self, prt, values, lnum=""):
"""Print header and field values in a readable format."""
#### data = zip(self.req_str, self.ntgafobj._fields, values)
data = zip(self.req_str, self.flds, values)
txt = ["{:2}) {:3} {:20} {}".format(i, req, hdr, val) for i, (req, hdr, val... | python | def _prt_line_detail(self, prt, values, lnum=""):
"""Print header and field values in a readable format."""
#### data = zip(self.req_str, self.ntgafobj._fields, values)
data = zip(self.req_str, self.flds, values)
txt = ["{:2}) {:3} {:20} {}".format(i, req, hdr, val) for i, (req, hdr, val... | [
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228,560 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData.prt_error_summary | def prt_error_summary(self, fout_err):
"""Print a summary about the GAF file that was read."""
# Get summary of error types and their counts
errcnts = []
if self.ignored:
errcnts.append(" {N:9,} IGNORED associations\n".format(N=len(self.ignored)))
if self.illegal_lin... | python | def prt_error_summary(self, fout_err):
"""Print a summary about the GAF file that was read."""
# Get summary of error types and their counts
errcnts = []
if self.ignored:
errcnts.append(" {N:9,} IGNORED associations\n".format(N=len(self.ignored)))
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228,561 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData._wrlog_details_illegal_gaf | def _wrlog_details_illegal_gaf(self, fout_err, err_cnts):
"""Print details regarding illegal GAF lines seen to a log file."""
# fout_err = "{}.log".format(fin_gaf)
gaf_base = os.path.basename(fout_err)
with open(fout_err, 'w') as prt:
prt.write("ILLEGAL GAF ERROR SUMMARY:\n\n... | python | def _wrlog_details_illegal_gaf(self, fout_err, err_cnts):
"""Print details regarding illegal GAF lines seen to a log file."""
# fout_err = "{}.log".format(fin_gaf)
gaf_base = os.path.basename(fout_err)
with open(fout_err, 'w') as prt:
prt.write("ILLEGAL GAF ERROR SUMMARY:\n\n... | [
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228,562 | tanghaibao/goatools | goatools/gosubdag/godag_rcnt_init.py | CountRelativesInit.get_relationship_dicts | def get_relationship_dicts(self):
"""Given GO DAG relationships, return summaries per GO ID."""
if not self.relationships:
return None
for goid, goobj in self.go2obj.items():
for reltyp, relset in goobj.relationship.items():
relfwd_goids = set(o.id for o i... | python | def get_relationship_dicts(self):
"""Given GO DAG relationships, return summaries per GO ID."""
if not self.relationships:
return None
for goid, goobj in self.go2obj.items():
for reltyp, relset in goobj.relationship.items():
relfwd_goids = set(o.id for o i... | [
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228,563 | tanghaibao/goatools | goatools/gosubdag/godag_rcnt_init.py | CountRelativesInit.get_goone2ntletter | def get_goone2ntletter(self, go2dcnt, depth2goobjs):
"""Assign letters to depth-01 GO terms ordered using descendants cnt."""
# 1. Group level-01/depth-01 GO terms by namespace
ns2dcntgoobj = cx.defaultdict(list)
for goobj in depth2goobjs[1]:
dcnt = go2dcnt[goobj.id]
... | python | def get_goone2ntletter(self, go2dcnt, depth2goobjs):
"""Assign letters to depth-01 GO terms ordered using descendants cnt."""
# 1. Group level-01/depth-01 GO terms by namespace
ns2dcntgoobj = cx.defaultdict(list)
for goobj in depth2goobjs[1]:
dcnt = go2dcnt[goobj.id]
... | [
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228,564 | tanghaibao/goatools | goatools/grouper/grprdflts.py | GrouperDflts._init_goslims | def _init_goslims(self, dagslim):
"""Get GO IDs in GO slims."""
go2obj_main = self.gosubdag.go2obj
go2obj_slim = {go for go, o in dagslim.items() if go in go2obj_main}
if self.gosubdag.relationships:
return self._get_goslimids_norel(go2obj_slim)
return set(dagslim.key... | python | def _init_goslims(self, dagslim):
"""Get GO IDs in GO slims."""
go2obj_main = self.gosubdag.go2obj
go2obj_slim = {go for go, o in dagslim.items() if go in go2obj_main}
if self.gosubdag.relationships:
return self._get_goslimids_norel(go2obj_slim)
return set(dagslim.key... | [
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228,565 | tanghaibao/goatools | goatools/grouper/grprdflts.py | GrouperDflts._get_goslimids_norel | def _get_goslimids_norel(self, dagslim):
"""Get all GO slim GO IDs that do not have a relationship."""
go_slims = set()
go2obj = self.gosubdag.go2obj
for goid in dagslim:
goobj = go2obj[goid]
if not goobj.relationship:
go_slims.add(goobj.id)
... | python | def _get_goslimids_norel(self, dagslim):
"""Get all GO slim GO IDs that do not have a relationship."""
go_slims = set()
go2obj = self.gosubdag.go2obj
for goid in dagslim:
goobj = go2obj[goid]
if not goobj.relationship:
go_slims.add(goobj.id)
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228,566 | tanghaibao/goatools | goatools/grouper/grprdflts.py | GrouperDflts.get_gosubdag | def get_gosubdag(gosubdag=None):
"""Gets a GoSubDag initialized for use by a Grouper object."""
if gosubdag is not None:
if gosubdag.rcntobj is not None:
return gosubdag
else:
gosubdag.init_auxobjs()
return gosubdag
else:
... | python | def get_gosubdag(gosubdag=None):
"""Gets a GoSubDag initialized for use by a Grouper object."""
if gosubdag is not None:
if gosubdag.rcntobj is not None:
return gosubdag
else:
gosubdag.init_auxobjs()
return gosubdag
else:
... | [
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228,567 | tanghaibao/goatools | goatools/anno/opts.py | AnnoOptions.getfnc_qual_ev | def getfnc_qual_ev(self):
"""Keep annotaion if it passes potentially modified selection."""
fnc_key = (
self.nd_not2desc[(self._keep_nd, self._keep_not)],
self.incexc2num[(
self.include_evcodes is not None,
self.exclude_evcodes is not None)],
... | python | def getfnc_qual_ev(self):
"""Keep annotaion if it passes potentially modified selection."""
fnc_key = (
self.nd_not2desc[(self._keep_nd, self._keep_not)],
self.incexc2num[(
self.include_evcodes is not None,
self.exclude_evcodes is not None)],
... | [
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228,568 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNodeOpts.get_kws | def get_kws(self):
"""Only load keywords if they are specified by the user."""
ret = self.kws['dict'].copy()
act_set = self.kws['set']
if 'shorten' in act_set and 'goobj2fncname' not in ret:
ret['goobj2fncname'] = ShortenText().get_short_plot_name
return ret | python | def get_kws(self):
"""Only load keywords if they are specified by the user."""
ret = self.kws['dict'].copy()
act_set = self.kws['set']
if 'shorten' in act_set and 'goobj2fncname' not in ret:
ret['goobj2fncname'] = ShortenText().get_short_plot_name
return ret | [
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228,569 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNode.get_node | def get_node(self, goid, goobj):
"""Return pydot node."""
# pydot.Node.objdict holds this information. pydot.Node.objdict['name']
return pydot.Node(
self.get_node_text(goid, goobj),
shape="box",
style="rounded, filled",
fillcolor=self.go2color.get(... | python | def get_node(self, goid, goobj):
"""Return pydot node."""
# pydot.Node.objdict holds this information. pydot.Node.objdict['name']
return pydot.Node(
self.get_node_text(goid, goobj),
shape="box",
style="rounded, filled",
fillcolor=self.go2color.get(... | [
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228,570 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNode.str_fmthdr | def str_fmthdr(self, goid, goobj):
"""Return hdr line seen inside a GO Term box."""
# Shorten: Ex: GO:0007608 -> G0007608
go_txt = goid.replace("GO:", "G")
if 'mark_alt_id' in self.present and goid != goobj.id:
go_txt += 'a'
return go_txt | python | def str_fmthdr(self, goid, goobj):
"""Return hdr line seen inside a GO Term box."""
# Shorten: Ex: GO:0007608 -> G0007608
go_txt = goid.replace("GO:", "G")
if 'mark_alt_id' in self.present and goid != goobj.id:
go_txt += 'a'
return go_txt | [
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228,571 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNode._get_prtflds | def _get_prtflds(self):
"""Get print fields for GO header."""
# User-specified print fields
ntflds = self.gosubdag.prt_attr['flds']
prt_flds = self.kws.get('prt_flds')
if prt_flds:
return prt_flds.intersection(ntflds)
exclude = set()
# Default print fi... | python | def _get_prtflds(self):
"""Get print fields for GO header."""
# User-specified print fields
ntflds = self.gosubdag.prt_attr['flds']
prt_flds = self.kws.get('prt_flds')
if prt_flds:
return prt_flds.intersection(ntflds)
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228,572 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNode._get_hdr_childcnt | def _get_hdr_childcnt(self, goobj, ntgo):
"""Get string representing count of children for this GO term."""
if 'childcnt' in self.present:
return "c{N}".format(N=len(goobj.children))
elif self.gosubdag.relationships and not goobj.children and ntgo.dcnt != 0:
return "c0" | python | def _get_hdr_childcnt(self, goobj, ntgo):
"""Get string representing count of children for this GO term."""
if 'childcnt' in self.present:
return "c{N}".format(N=len(goobj.children))
elif self.gosubdag.relationships and not goobj.children and ntgo.dcnt != 0:
return "c0" | [
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228,573 | tanghaibao/goatools | goatools/gosubdag/plot/go_node.py | GoNode._add_parent_cnt | def _add_parent_cnt(self, hdr, goobj, c2ps):
"""Add the parent count to the GO term box for if not all parents are plotted."""
if goobj.id in c2ps:
parents = c2ps[goobj.id]
if 'prt_pcnt' in self.present or parents and len(goobj.parents) != len(parents):
assert len... | python | def _add_parent_cnt(self, hdr, goobj, c2ps):
"""Add the parent count to the GO term box for if not all parents are plotted."""
if goobj.id in c2ps:
parents = c2ps[goobj.id]
if 'prt_pcnt' in self.present or parents and len(goobj.parents) != len(parents):
assert len... | [
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228,574 | tanghaibao/goatools | goatools/anno/idtogos_reader.py | IdToGosReader.prt_summary_anno2ev | def prt_summary_anno2ev(self, prt=sys.stdout):
"""Print a summary of all Evidence Codes seen in annotations"""
prt.write('**NOTE: No evidence codes in associations: {F}\n'.format(F=self.filename)) | python | def prt_summary_anno2ev(self, prt=sys.stdout):
"""Print a summary of all Evidence Codes seen in annotations"""
prt.write('**NOTE: No evidence codes in associations: {F}\n'.format(F=self.filename)) | [
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228,575 | tanghaibao/goatools | goatools/ratio.py | count_terms | def count_terms(geneset, assoc, obo_dag):
"""count the number of terms in the study group
"""
term_cnt = Counter()
for gene in (g for g in geneset if g in assoc):
for goid in assoc[gene]:
if goid in obo_dag:
term_cnt[obo_dag[goid].id] += 1
return term_cnt | python | def count_terms(geneset, assoc, obo_dag):
"""count the number of terms in the study group
"""
term_cnt = Counter()
for gene in (g for g in geneset if g in assoc):
for goid in assoc[gene]:
if goid in obo_dag:
term_cnt[obo_dag[goid].id] += 1
return term_cnt | [
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228,576 | tanghaibao/goatools | goatools/ratio.py | get_terms | def get_terms(desc, geneset, assoc, obo_dag, log):
"""Get the terms in the study group
"""
_chk_gene2go(assoc)
term2itemids = defaultdict(set)
genes = [g for g in geneset if g in assoc]
for gene in genes:
for goid in assoc[gene]:
if goid in obo_dag:
term2itemi... | python | def get_terms(desc, geneset, assoc, obo_dag, log):
"""Get the terms in the study group
"""
_chk_gene2go(assoc)
term2itemids = defaultdict(set)
genes = [g for g in geneset if g in assoc]
for gene in genes:
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228,577 | tanghaibao/goatools | goatools/ratio.py | _chk_gene2go | def _chk_gene2go(assoc):
"""Check that associations is gene2go, not go2gene."""
if not assoc:
raise RuntimeError("NO ITEMS FOUND IN ASSOCIATIONS {A}".format(A=assoc))
for key in assoc:
if isinstance(key, str) and key[:3] == "GO:":
raise Exception("ASSOCIATIONS EXPECTED TO BE gene... | python | def _chk_gene2go(assoc):
"""Check that associations is gene2go, not go2gene."""
if not assoc:
raise RuntimeError("NO ITEMS FOUND IN ASSOCIATIONS {A}".format(A=assoc))
for key in assoc:
if isinstance(key, str) and key[:3] == "GO:":
raise Exception("ASSOCIATIONS EXPECTED TO BE gene... | [
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228,578 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit._init_usrgos | def _init_usrgos(self, goids):
"""Return user GO IDs which have GO Terms."""
usrgos = set()
goids_missing = set()
_go2obj = self.gosubdag.go2obj
for goid in goids:
if goid in _go2obj:
usrgos.add(goid)
else:
goids_missing.add... | python | def _init_usrgos(self, goids):
"""Return user GO IDs which have GO Terms."""
usrgos = set()
goids_missing = set()
_go2obj = self.gosubdag.go2obj
for goid in goids:
if goid in _go2obj:
usrgos.add(goid)
else:
goids_missing.add... | [
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228,579 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit.get_gos_all | def get_gos_all(self):
"""Return a flat list of all GO IDs in grouping object.
All GO IDs:
* header GO IDs that are not user GO IDs
* user GO IDs that are under header GOs
* user GO IDs that are header GOs in groups containing no other user GO IDs
... | python | def get_gos_all(self):
"""Return a flat list of all GO IDs in grouping object.
All GO IDs:
* header GO IDs that are not user GO IDs
* user GO IDs that are under header GOs
* user GO IDs that are header GOs in groups containing no other user GO IDs
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228,580 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit._init_h2us | def _init_h2us(self, fnc_most_specific):
"""Given a set of user GO ids, return GO ids grouped under the "GO high" terms.
Example of a grouped go list:
gos = ['GO:0044464':[ # grp_term: D1 cell part
'GO:0005737', # child: D3 cytoplasm
'GO:... | python | def _init_h2us(self, fnc_most_specific):
"""Given a set of user GO ids, return GO ids grouped under the "GO high" terms.
Example of a grouped go list:
gos = ['GO:0044464':[ # grp_term: D1 cell part
'GO:0005737', # child: D3 cytoplasm
'GO:... | [
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228,581 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit.get_go2nt | def get_go2nt(self, usr_go2nt):
"""Combine user namedtuple fields, GO object fields, and format_txt."""
gos_all = self.get_gos_all()
# Minimum set of namedtuple fields available for use with Sorter on grouped GO IDs
prt_flds_all = get_hdridx_flds() + self.gosubdag.prt_attr['flds']
... | python | def get_go2nt(self, usr_go2nt):
"""Combine user namedtuple fields, GO object fields, and format_txt."""
gos_all = self.get_gos_all()
# Minimum set of namedtuple fields available for use with Sorter on grouped GO IDs
prt_flds_all = get_hdridx_flds() + self.gosubdag.prt_attr['flds']
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228,582 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit._init_go2nt_aug | def _init_go2nt_aug(self, go2nt):
"""Augment go2nt with GO ID key to account for alt GO IDs."""
go2obj = self.gosubdag.go2obj
# Get alt GO IDs
go2nt_aug = {}
# NOW
for goid_usr, nt_usr in go2nt.items():
goobj = go2obj[goid_usr]
if goobj.alt_ids:
... | python | def _init_go2nt_aug(self, go2nt):
"""Augment go2nt with GO ID key to account for alt GO IDs."""
go2obj = self.gosubdag.go2obj
# Get alt GO IDs
go2nt_aug = {}
# NOW
for goid_usr, nt_usr in go2nt.items():
goobj = go2obj[goid_usr]
if goobj.alt_ids:
... | [
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228,583 | tanghaibao/goatools | goatools/grouper/grprobj_init.py | GrouperInit._get_go2nthdridx | def _get_go2nthdridx(self, gos_all):
"""Get GO IDs header index for each user GO ID and corresponding parent GO IDs."""
go2nthdridx = {}
# NtHdrIdx Namedtuple fields:
# * format_txt: Used to determine the format when writing Excel cells
# * hdr_idx: Value printed in an Excel ... | python | def _get_go2nthdridx(self, gos_all):
"""Get GO IDs header index for each user GO ID and corresponding parent GO IDs."""
go2nthdridx = {}
# NtHdrIdx Namedtuple fields:
# * format_txt: Used to determine the format when writing Excel cells
# * hdr_idx: Value printed in an Excel ... | [
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228,584 | tanghaibao/goatools | goatools/godag_obosm.py | OboToGoDagSmall._init_go2obj | def _init_go2obj(self, **kws):
"""Initialize go2obj in small dag for source gos."""
if 'goids' in kws and 'obodag' in kws:
self.godag.go_sources = kws['goids']
obo = kws['obodag']
for goid in self.godag.go_sources:
self.godag.go2obj[goid] = obo[goid]
... | python | def _init_go2obj(self, **kws):
"""Initialize go2obj in small dag for source gos."""
if 'goids' in kws and 'obodag' in kws:
self.godag.go_sources = kws['goids']
obo = kws['obodag']
for goid in self.godag.go_sources:
self.godag.go2obj[goid] = obo[goid]
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228,585 | tanghaibao/goatools | goatools/godag_obosm.py | OboToGoDagSmall._init | def _init(self):
"""Given GO ids and GOTerm objects, create mini GO dag."""
for goid in self.godag.go_sources:
goobj = self.godag.go2obj[goid]
self.godag.go2obj[goid] = goobj
# Traverse up parents
if self.traverse_parent and goid not in self.seen_cids:
... | python | def _init(self):
"""Given GO ids and GOTerm objects, create mini GO dag."""
for goid in self.godag.go_sources:
goobj = self.godag.go2obj[goid]
self.godag.go2obj[goid] = goobj
# Traverse up parents
if self.traverse_parent and goid not in self.seen_cids:
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228,586 | tanghaibao/goatools | goatools/rpt/write_hierarchy_base.py | WrHierPrt.prt_hier_rec | def prt_hier_rec(self, item_id, depth=1):
"""Write hierarchy for a GO Term record and all GO IDs down to the leaf level."""
# Shortens hierarchy report by only printing the hierarchy
# for the sub-set of user-specified GO terms which are connected.
if self.include_only and item_id not in... | python | def prt_hier_rec(self, item_id, depth=1):
"""Write hierarchy for a GO Term record and all GO IDs down to the leaf level."""
# Shortens hierarchy report by only printing the hierarchy
# for the sub-set of user-specified GO terms which are connected.
if self.include_only and item_id not in... | [
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228,587 | tanghaibao/goatools | goatools/rpt/write_hierarchy_base.py | WrHierPrt._init_item_marks | def _init_item_marks(item_marks):
"""Initialize the makred item dict."""
if isinstance(item_marks, dict):
return item_marks
if item_marks:
return {item_id:'>' for item_id in item_marks} | python | def _init_item_marks(item_marks):
"""Initialize the makred item dict."""
if isinstance(item_marks, dict):
return item_marks
if item_marks:
return {item_id:'>' for item_id in item_marks} | [
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228,588 | tanghaibao/goatools | goatools/obo_parser.py | OBOReader._add_to_obj | def _add_to_obj(self, rec_curr, typedef_curr, line):
"""Add information on line to GOTerm or Typedef."""
if rec_curr is not None:
self._add_to_ref(rec_curr, line)
else:
add_to_typedef(typedef_curr, line) | python | def _add_to_obj(self, rec_curr, typedef_curr, line):
"""Add information on line to GOTerm or Typedef."""
if rec_curr is not None:
self._add_to_ref(rec_curr, line)
else:
add_to_typedef(typedef_curr, line) | [
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228,589 | tanghaibao/goatools | goatools/obo_parser.py | OBOReader._init_obo_version | def _init_obo_version(self, line):
"""Save obo version and release."""
if line[0:14] == "format-version":
self.format_version = line[16:-1]
if line[0:12] == "data-version":
self.data_version = line[14:-1] | python | def _init_obo_version(self, line):
"""Save obo version and release."""
if line[0:14] == "format-version":
self.format_version = line[16:-1]
if line[0:12] == "data-version":
self.data_version = line[14:-1] | [
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228,590 | tanghaibao/goatools | goatools/obo_parser.py | OBOReader._init_optional_attrs | def _init_optional_attrs(optional_attrs):
"""Create OboOptionalAttrs or return None."""
if optional_attrs is None:
return None
opts = OboOptionalAttrs.get_optional_attrs(optional_attrs)
if opts:
return OboOptionalAttrs(opts) | python | def _init_optional_attrs(optional_attrs):
"""Create OboOptionalAttrs or return None."""
if optional_attrs is None:
return None
opts = OboOptionalAttrs.get_optional_attrs(optional_attrs)
if opts:
return OboOptionalAttrs(opts) | [
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228,591 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.has_parent | def has_parent(self, term):
"""Return True if this GO object has a parent GO ID."""
for parent in self.parents:
if parent.item_id == term or parent.has_parent(term):
return True
return False | python | def has_parent(self, term):
"""Return True if this GO object has a parent GO ID."""
for parent in self.parents:
if parent.item_id == term or parent.has_parent(term):
return True
return False | [
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228,592 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.has_child | def has_child(self, term):
"""Return True if this GO object has a child GO ID."""
for parent in self.children:
if parent.item_id == term or parent.has_child(term):
return True
return False | python | def has_child(self, term):
"""Return True if this GO object has a child GO ID."""
for parent in self.children:
if parent.item_id == term or parent.has_child(term):
return True
return False | [
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228,593 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_parents | def get_all_parents(self):
"""Return all parent GO IDs."""
all_parents = set()
for parent in self.parents:
all_parents.add(parent.item_id)
all_parents |= parent.get_all_parents()
return all_parents | python | def get_all_parents(self):
"""Return all parent GO IDs."""
all_parents = set()
for parent in self.parents:
all_parents.add(parent.item_id)
all_parents |= parent.get_all_parents()
return all_parents | [
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228,594 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_upper | def get_all_upper(self):
"""Return all parent GO IDs through both 'is_a' and all relationships."""
all_upper = set()
for upper in self.get_goterms_upper():
all_upper.add(upper.item_id)
all_upper |= upper.get_all_upper()
return all_upper | python | def get_all_upper(self):
"""Return all parent GO IDs through both 'is_a' and all relationships."""
all_upper = set()
for upper in self.get_goterms_upper():
all_upper.add(upper.item_id)
all_upper |= upper.get_all_upper()
return all_upper | [
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228,595 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_children | def get_all_children(self):
"""Return all children GO IDs."""
all_children = set()
for parent in self.children:
all_children.add(parent.item_id)
all_children |= parent.get_all_children()
return all_children | python | def get_all_children(self):
"""Return all children GO IDs."""
all_children = set()
for parent in self.children:
all_children.add(parent.item_id)
all_children |= parent.get_all_children()
return all_children | [
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228,596 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_lower | def get_all_lower(self):
"""Return all parent GO IDs through both reverse 'is_a' and all relationships."""
all_lower = set()
for lower in self.get_goterms_lower():
all_lower.add(lower.item_id)
all_lower |= lower.get_all_lower()
return all_lower | python | def get_all_lower(self):
"""Return all parent GO IDs through both reverse 'is_a' and all relationships."""
all_lower = set()
for lower in self.get_goterms_lower():
all_lower.add(lower.item_id)
all_lower |= lower.get_all_lower()
return all_lower | [
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228,597 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_parent_edges | def get_all_parent_edges(self):
"""Return tuples for all parent GO IDs, containing current GO ID and parent GO ID."""
all_parent_edges = set()
for parent in self.parents:
all_parent_edges.add((self.item_id, parent.item_id))
all_parent_edges |= parent.get_all_parent_edges(... | python | def get_all_parent_edges(self):
"""Return tuples for all parent GO IDs, containing current GO ID and parent GO ID."""
all_parent_edges = set()
for parent in self.parents:
all_parent_edges.add((self.item_id, parent.item_id))
all_parent_edges |= parent.get_all_parent_edges(... | [
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228,598 | tanghaibao/goatools | goatools/obo_parser.py | GOTerm.get_all_child_edges | def get_all_child_edges(self):
"""Return tuples for all child GO IDs, containing current GO ID and child GO ID."""
all_child_edges = set()
for parent in self.children:
all_child_edges.add((parent.item_id, self.item_id))
all_child_edges |= parent.get_all_child_edges()
... | python | def get_all_child_edges(self):
"""Return tuples for all child GO IDs, containing current GO ID and child GO ID."""
all_child_edges = set()
for parent in self.children:
all_child_edges.add((parent.item_id, self.item_id))
all_child_edges |= parent.get_all_child_edges()
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228,599 | tanghaibao/goatools | goatools/obo_parser.py | GODag.load_obo_file | def load_obo_file(self, obo_file, optional_attrs, load_obsolete, prt):
"""Read obo file. Store results."""
reader = OBOReader(obo_file, optional_attrs)
# Save alt_ids and their corresponding main GO ID. Add to GODag after populating GO Terms
alt2rec = {}
for rec in reader:
... | python | def load_obo_file(self, obo_file, optional_attrs, load_obsolete, prt):
"""Read obo file. Store results."""
reader = OBOReader(obo_file, optional_attrs)
# Save alt_ids and their corresponding main GO ID. Add to GODag after populating GO Terms
alt2rec = {}
for rec in reader:
... | [
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