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 51 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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242,300 | tanghaibao/goatools | goatools/go_search.py | GoSearch._search_vals | def _search_vals(self, compiled_pattern, fld_val):
"""Search for user-regex in scalar or iterable data values."""
matches = []
if isinstance(fld_val, set):
for val in fld_val:
self._search_val(matches, compiled_pattern, val)
elif isinstance(fld_val, str):
self._search_val(matches, compiled_pattern, fld_val)
return matches | python | def _search_vals(self, compiled_pattern, fld_val):
matches = []
if isinstance(fld_val, set):
for val in fld_val:
self._search_val(matches, compiled_pattern, val)
elif isinstance(fld_val, str):
self._search_val(matches, compiled_pattern, fld_val)
return matches | [
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242,301 | tanghaibao/goatools | goatools/go_search.py | GoSearch._search_val | def _search_val(matches, compiled_pattern, fld_val):
"""Search for user-regex in scalar data values."""
mtch = compiled_pattern.search(fld_val)
if mtch:
matches.append(fld_val) | python | def _search_val(matches, compiled_pattern, fld_val):
mtch = compiled_pattern.search(fld_val)
if mtch:
matches.append(fld_val) | [
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242,302 | tanghaibao/goatools | goatools/go_search.py | GoSearch.add_children_gos | def add_children_gos(self, gos):
"""Return children of input gos plus input gos."""
lst = []
obo_dag = self.obo_dag
get_children = lambda go_obj: list(go_obj.get_all_children()) + [go_obj.id]
for go_id in gos:
go_obj = obo_dag[go_id]
lst.extend(get_children(go_obj))
return set(lst) | python | def add_children_gos(self, gos):
lst = []
obo_dag = self.obo_dag
get_children = lambda go_obj: list(go_obj.get_all_children()) + [go_obj.id]
for go_id in gos:
go_obj = obo_dag[go_id]
lst.extend(get_children(go_obj))
return set(lst) | [
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242,303 | tanghaibao/goatools | goatools/go_search.py | GoSearch.get_items | def get_items(self, gos):
"""Given GO terms, return genes or gene products for the GOs."""
items = []
for go_id in gos:
items.extend(self.go2items.get(go_id, []))
return set(items) | python | def get_items(self, gos):
items = []
for go_id in gos:
items.extend(self.go2items.get(go_id, []))
return set(items) | [
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242,304 | tanghaibao/goatools | goatools/gosubdag/plot/goea_results.py | GoeaResults.prt_summary | def prt_summary(self, prt=sys.stdout):
"""Print summary of GOEA plotting object."""
desc = "NtGoeaResults" if self.is_goterm else "namedtuple"
prt.write("{N} GOEA results from {O}. P-values stored in {P}.\n".format(
N=len(self.go2res), O=desc, P=self.pval_name)) | python | def prt_summary(self, prt=sys.stdout):
desc = "NtGoeaResults" if self.is_goterm else "namedtuple"
prt.write("{N} GOEA results from {O}. P-values stored in {P}.\n".format(
N=len(self.go2res), O=desc, P=self.pval_name)) | [
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242,305 | tanghaibao/goatools | goatools/gosubdag/plot/goea_results.py | GoeaResults.set_goid2color_pval | def set_goid2color_pval(self, goid2color):
"""Fill missing colors based on p-value of an enriched GO term."""
alpha2col = self.alpha2col
if self.pval_name is not None:
pval_name = self.pval_name
for goid, res in self.go2res.items():
pval = getattr(res, pval_name, None)
if pval is not None:
for alpha, color in alpha2col.items():
if pval <= alpha and res.study_count != 0:
if goid not in goid2color:
goid2color[goid] = color | python | def set_goid2color_pval(self, goid2color):
alpha2col = self.alpha2col
if self.pval_name is not None:
pval_name = self.pval_name
for goid, res in self.go2res.items():
pval = getattr(res, pval_name, None)
if pval is not None:
for alpha, color in alpha2col.items():
if pval <= alpha and res.study_count != 0:
if goid not in goid2color:
goid2color[goid] = color | [
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242,306 | tanghaibao/goatools | goatools/gosubdag/plot/goea_results.py | GoeaResults.get_goid2color_pval | def get_goid2color_pval(self):
"""Return a go2color dict containing GO colors determined by P-value."""
go2color = {}
self.set_goid2color_pval(go2color)
color_dflt = self.alpha2col[1.000]
for goid in self.go2res:
if goid not in go2color:
go2color[goid] = color_dflt
return go2color | python | def get_goid2color_pval(self):
go2color = {}
self.set_goid2color_pval(go2color)
color_dflt = self.alpha2col[1.000]
for goid in self.go2res:
if goid not in go2color:
go2color[goid] = color_dflt
return go2color | [
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242,307 | tanghaibao/goatools | goatools/rpt/rpt_lev_depth.py | RptLevDepth.prttex_summary_cnts_all | def prttex_summary_cnts_all(self, prt=sys.stdout):
"""Print LaTeX format summary of level and depth counts for all active GO Terms."""
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
self._prttex_summary_cnts(prt, cnts) | python | def prttex_summary_cnts_all(self, prt=sys.stdout):
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
self._prttex_summary_cnts(prt, cnts) | [
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242,308 | tanghaibao/goatools | goatools/rpt/rpt_lev_depth.py | RptLevDepth.write_summary_cnts_all | def write_summary_cnts_all(self):
"""Write summary of level and depth counts for all active GO Terms."""
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
self._write_summary_cnts(cnts) | python | def write_summary_cnts_all(self):
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
self._write_summary_cnts(cnts) | [
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242,309 | tanghaibao/goatools | goatools/rpt/rpt_lev_depth.py | RptLevDepth.write_summary_cnts | def write_summary_cnts(self, go_ids):
"""Write summary of level and depth counts for specific GO ids."""
obo = self.obo
cnts = self.get_cnts_levels_depths_recs([obo.get(GO) for GO in go_ids])
self._write_summary_cnts(cnts) | python | def write_summary_cnts(self, go_ids):
obo = self.obo
cnts = self.get_cnts_levels_depths_recs([obo.get(GO) for GO in go_ids])
self._write_summary_cnts(cnts) | [
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242,310 | tanghaibao/goatools | goatools/rpt/rpt_lev_depth.py | RptLevDepth.get_cnts_levels_depths_recs | def get_cnts_levels_depths_recs(recs):
"""Collect counts of levels and depths in a Group of GO Terms."""
cnts = cx.defaultdict(lambda: cx.defaultdict(cx.Counter))
for rec in recs:
if rec is not None and not rec.is_obsolete:
cnts['level'][rec.level][rec.namespace] += 1
cnts['depth'][rec.depth][rec.namespace] += 1
return cnts | python | def get_cnts_levels_depths_recs(recs):
cnts = cx.defaultdict(lambda: cx.defaultdict(cx.Counter))
for rec in recs:
if rec is not None and not rec.is_obsolete:
cnts['level'][rec.level][rec.namespace] += 1
cnts['depth'][rec.depth][rec.namespace] += 1
return cnts | [
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242,311 | tanghaibao/goatools | goatools/rpt/rpt_lev_depth.py | RptLevDepth.get_data | def get_data(self):
"""Collect counts of GO terms at all levels and depths."""
# Count level(shortest path to root) and depth(longest path to root)
# values for all unique GO Terms.
data = []
ntobj = cx.namedtuple("NtGoCnt", "Depth_Level BP_D MF_D CC_D BP_L MF_L CC_L")
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
max_val = max(max(dep for dep in cnts['depth']), max(lev for lev in cnts['level']))
for i in range(max_val+1):
vals = [i] + [cnts[desc][i][ns] for desc in cnts for ns in self.nss]
data.append(ntobj._make(vals))
return data | python | def get_data(self):
# Count level(shortest path to root) and depth(longest path to root)
# values for all unique GO Terms.
data = []
ntobj = cx.namedtuple("NtGoCnt", "Depth_Level BP_D MF_D CC_D BP_L MF_L CC_L")
cnts = self.get_cnts_levels_depths_recs(set(self.obo.values()))
max_val = max(max(dep for dep in cnts['depth']), max(lev for lev in cnts['level']))
for i in range(max_val+1):
vals = [i] + [cnts[desc][i][ns] for desc in cnts for ns in self.nss]
data.append(ntobj._make(vals))
return data | [
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242,312 | tanghaibao/goatools | scripts/find_enrichment.py | main | def main():
"""Run gene enrichment analysis."""
# Load study, population, associations, and GoDag. Run GOEA.
obj = GoeaCliFnc(GoeaCliArgs().args)
# Reduce results to significant results (pval<value)
results_specified = obj.get_results()
# Print results in a flat list
obj.prt_results(results_specified) | python | def main():
# Load study, population, associations, and GoDag. Run GOEA.
obj = GoeaCliFnc(GoeaCliArgs().args)
# Reduce results to significant results (pval<value)
results_specified = obj.get_results()
# Print results in a flat list
obj.prt_results(results_specified) | [
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242,313 | tanghaibao/goatools | goatools/anno/factory.py | get_objanno | def get_objanno(fin_anno, anno_type=None, **kws):
"""Read annotations in GAF, GPAD, Entrez gene2go, or text format."""
# kws get_objanno: taxids hdr_only prt allow_missing_symbol
anno_type = get_anno_desc(fin_anno, anno_type)
if anno_type is not None:
if anno_type == 'gene2go':
# kws: taxid taxids
return Gene2GoReader(fin_anno, **kws)
if anno_type == 'gaf':
return GafReader(fin_anno,
hdr_only=kws.get('hdr_only', False),
prt=kws.get('prt', sys.stdout),
allow_missing_symbol=kws.get('allow_missing_symbol', False))
if anno_type == 'gpad':
hdr_only = kws.get('hdr_only', False)
return GpadReader(fin_anno, hdr_only)
if anno_type == 'id2gos':
return IdToGosReader(fin_anno)
raise RuntimeError('UNEXPECTED ANNOTATION FILE FORMAT: {F} {D}'.format(
F=fin_anno, D=anno_type)) | python | def get_objanno(fin_anno, anno_type=None, **kws):
# kws get_objanno: taxids hdr_only prt allow_missing_symbol
anno_type = get_anno_desc(fin_anno, anno_type)
if anno_type is not None:
if anno_type == 'gene2go':
# kws: taxid taxids
return Gene2GoReader(fin_anno, **kws)
if anno_type == 'gaf':
return GafReader(fin_anno,
hdr_only=kws.get('hdr_only', False),
prt=kws.get('prt', sys.stdout),
allow_missing_symbol=kws.get('allow_missing_symbol', False))
if anno_type == 'gpad':
hdr_only = kws.get('hdr_only', False)
return GpadReader(fin_anno, hdr_only)
if anno_type == 'id2gos':
return IdToGosReader(fin_anno)
raise RuntimeError('UNEXPECTED ANNOTATION FILE FORMAT: {F} {D}'.format(
F=fin_anno, D=anno_type)) | [
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... | Read annotations in GAF, GPAD, Entrez gene2go, or text format. | [
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242,314 | tanghaibao/goatools | goatools/anno/gpad_reader.py | GpadReader.get_relation_cnt | def get_relation_cnt(self):
"""Return a Counter containing all relations contained in the Annotation Extensions."""
ctr = cx.Counter()
for ntgpad in self.associations:
if ntgpad.Extension is not None:
ctr += ntgpad.Extension.get_relations_cnt()
return ctr | python | def get_relation_cnt(self):
ctr = cx.Counter()
for ntgpad in self.associations:
if ntgpad.Extension is not None:
ctr += ntgpad.Extension.get_relations_cnt()
return ctr | [
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242,315 | tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc._get_id2gos | def _get_id2gos(self):
"""Return annotations as id2gos"""
kws = {}
if self.args.ev_inc is not None:
kws['ev_include'] = set(self.args.ev_inc.split(','))
if self.args.ev_exc is not None:
kws['ev_exclude'] = set(self.args.ev_exc.split(','))
return self.objanno.get_id2gos(**kws) | python | def _get_id2gos(self):
kws = {}
if self.args.ev_inc is not None:
kws['ev_include'] = set(self.args.ev_inc.split(','))
if self.args.ev_exc is not None:
kws['ev_exclude'] = set(self.args.ev_exc.split(','))
return self.objanno.get_id2gos(**kws) | [
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242,316 | 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 self.args.annofmt else 'id2gos'
kws = {'taxid': self.args.taxid} if anno_type == 'gene2go' else {}
return get_objanno(assoc_fn, anno_type, **kws) | python | def _get_objanno(self, assoc_fn):
# 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 self.args.annofmt else 'id2gos'
kws = {'taxid': self.args.taxid} if anno_type == 'gene2go' else {}
return get_objanno(assoc_fn, anno_type, **kws) | [
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242,317 | 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.compile(r'^\s*(\S+)[\s,;]+(\S+)')
with open(fin_id2sym) as ifstrm:
for line in ifstrm:
mtch = cmpl.search(line)
if mtch:
id2sym[mtch.group(1)] = mtch.group(2)
return id2sym | python | def _init_itemid2name(self):
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.compile(r'^\s*(\S+)[\s,;]+(\S+)')
with open(fin_id2sym) as ifstrm:
for line in ifstrm:
mtch = cmpl.search(line)
if mtch:
id2sym[mtch.group(1)] = mtch.group(2)
return id2sym | [
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242,318 | 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 to both tab-separated file and xlsx file in one run.
outfiles = self.args.outfile.split(",")
grpwr = self.prepgrp.get_objgrpwr(goea_results) if self.prepgrp else None
if grpwr is None:
self.prt_outfiles_flat(goea_results, outfiles)
else:
grpwr.prt_outfiles_grouped(outfiles) | python | def prt_results(self, goea_results):
# 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 to both tab-separated file and xlsx file in one run.
outfiles = self.args.outfile.split(",")
grpwr = self.prepgrp.get_objgrpwr(goea_results) if self.prepgrp else None
if grpwr is None:
self.prt_outfiles_flat(goea_results, outfiles)
else:
grpwr.prt_outfiles_grouped(outfiles) | [
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242,319 | 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(goea_results, min_ratio, self.args.pval)
if results_adj:
if not self.prepgrp:
self.objgoea.print_results_adj(results_adj, indent=self.args.indent)
else:
grpwr = self.prepgrp.get_objgrpwr(results_adj)
grpwr.prt_txt(sys.stdout) | python | def _prt_results(self, goea_results):
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(goea_results, min_ratio, self.args.pval)
if results_adj:
if not self.prepgrp:
self.objgoea.print_results_adj(results_adj, indent=self.args.indent)
else:
grpwr = self.prepgrp.get_objgrpwr(results_adj)
grpwr.prt_txt(sys.stdout) | [
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242,320 | 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 fraction of genomic ids that overlap between study and population
overlap = self.get_overlap(study, pop)
if overlap < 0.95:
sys.stderr.write("\nWARNING: only {} fraction of genes/proteins in study are found in "
"the population background.\n\n".format(overlap))
if overlap <= self.args.min_overlap:
exit("\nERROR: only {} of genes/proteins in the study are found in the "
"background population. Please check.\n".format(overlap))
# Population and associations
if assoc is not None and pop.isdisjoint(assoc.keys()):
if self.objanno.name == 'gene2go':
err = ('**FATAL: NO POPULATION ITEMS SEEN IN THE NCBI gene2go ANNOTATIONS '
'FOR taxid({T}). TRY: --taxid=<taxid number>')
exit(err.format(T=next(iter(self.objanno.taxid2asscs.keys()))))
else:
exit('**FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS') | python | def chk_genes(self, study, pop, assoc=None):
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 fraction of genomic ids that overlap between study and population
overlap = self.get_overlap(study, pop)
if overlap < 0.95:
sys.stderr.write("\nWARNING: only {} fraction of genes/proteins in study are found in "
"the population background.\n\n".format(overlap))
if overlap <= self.args.min_overlap:
exit("\nERROR: only {} of genes/proteins in the study are found in the "
"background population. Please check.\n".format(overlap))
# Population and associations
if assoc is not None and pop.isdisjoint(assoc.keys()):
if self.objanno.name == 'gene2go':
err = ('**FATAL: NO POPULATION ITEMS SEEN IN THE NCBI gene2go ANNOTATIONS '
'FOR taxid({T}). TRY: --taxid=<taxid number>')
exit(err.format(T=next(iter(self.objanno.taxid2asscs.keys()))))
else:
exit('**FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS') | [
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242,321 | 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),
M=len(self.results_all),
PVAL=self.args.pval))
pval_fld = self.get_pval_field()
results = [r for r in self.results_all if getattr(r, pval_fld) <= self.args.pval]
return results | python | def get_results_sig(self):
# 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),
M=len(self.results_all),
PVAL=self.args.pval))
pval_fld = self.get_pval_field()
results = [r for r in self.results_all if getattr(r, pval_fld) <= self.args.pval]
return results | [
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242,322 | 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_fld
# If only one method was used, use that instead of the uncorrected pvalue
elif len(self.methods) == 1:
pval_fld = 'p_' + self.methods[0]
# Use 'uncorrected pvalue' if there are many methods & none chosen using --pval_field
else:
pval_fld = 'p_uncorrected'
if self.results_all:
assert hasattr(next(iter(self.results_all)), pval_fld), \
'NO PVAL({P}). EXPECTED ONE OF: {E}'.format(
P=self.args.pval_field,
E=" ".join([k for k in dir(next(iter(self.results_all))) if k[:2] == 'p_']))
return pval_fld | python | def get_pval_field(self):
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_fld
# If only one method was used, use that instead of the uncorrected pvalue
elif len(self.methods) == 1:
pval_fld = 'p_' + self.methods[0]
# Use 'uncorrected pvalue' if there are many methods & none chosen using --pval_field
else:
pval_fld = 'p_uncorrected'
if self.results_all:
assert hasattr(next(iter(self.results_all)), pval_fld), \
'NO PVAL({P}). EXPECTED ONE OF: {E}'.format(
P=self.args.pval_field,
E=" ".join([k for k in dir(next(iter(self.results_all))) if k[:2] == 'p_']))
return pval_fld | [
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242,323 | 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):
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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242,324 | 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 = set(int(g) for g in pop)
study = frozenset(int(g) for g in study)
# some times the pop is a second group to compare, rather than the
# population in that case, we need to make sure the overlapping terms
# are removed first
if self.args.compare:
common = pop & study
pop |= study
pop -= common
study -= common
sys.stderr.write("removed %d overlapping items\n" % (len(common)))
sys.stderr.write("Set 1: {0}, Set 2: {1}\n".format(
len(study), len(pop)))
return study, pop | python | def _read_geneset(self, study_fn, pop_fn):
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 = set(int(g) for g in pop)
study = frozenset(int(g) for g in study)
# some times the pop is a second group to compare, rather than the
# population in that case, we need to make sure the overlapping terms
# are removed first
if self.args.compare:
common = pop & study
pop |= study
pop -= common
study -= common
sys.stderr.write("removed %d overlapping items\n" % (len(common)))
sys.stderr.write("Set 1: {0}, Set 2: {1}\n".format(
len(study), len(pop)))
return study, pop | [
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] | 407682e573a108864a79031f8ca19ee3bf377626 | https://github.com/tanghaibao/goatools/blob/407682e573a108864a79031f8ca19ee3bf377626/goatools/cli/find_enrichment.py#L333-L351 |
242,325 | 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):
sortobj = self.get_sortobj(goea_results)
return GrpWr(sortobj, self.pval_fld, ver_list=self.ver_list) | [
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242,326 | 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, self.hdrobj, self.grprdflt.gosubdag, go2nt=go2nt)
grprobj.prt_summary(sys.stdout)
# hdrgo_prt", "section_prt", "top_n", "use_sections"
sortobj = Sorter(grprobj, section_sortby=lambda nt: getattr(nt, self.pval_fld))
return sortobj | python | def get_sortobj(self, goea_results, **kws):
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, self.hdrobj, self.grprdflt.gosubdag, go2nt=go2nt)
grprobj.prt_summary(sys.stdout)
# hdrgo_prt", "section_prt", "top_n", "use_sections"
sortobj = Sorter(grprobj, section_sortby=lambda nt: getattr(nt, self.pval_fld))
return sortobj | [
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242,327 | 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} '
'{dcnt:5} {childcnt:3} R{reldepth:02} '
'{D1:5} {GO_name} ({study_count} study genes)\n'),
# Formatting for GO terms listed under each gene
'fmtgo2':('{hdr1usr01:2} {NS} {GO} {s_fdr_bh:8} '
'{dcnt:5} R{reldepth:02} '
'{GO_name} ({study_count} study genes)\n'),
# itemid2name=ensmusg2symbol}
}
return AArtGeneProductSetsAll(self.grprdflt, self.hdrobj, **kws) | python | def _init_objaartall(self):
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} '
'{dcnt:5} {childcnt:3} R{reldepth:02} '
'{D1:5} {GO_name} ({study_count} study genes)\n'),
# Formatting for GO terms listed under each gene
'fmtgo2':('{hdr1usr01:2} {NS} {GO} {s_fdr_bh:8} '
'{dcnt:5} R{reldepth:02} '
'{GO_name} ({study_count} study genes)\n'),
# itemid2name=ensmusg2symbol}
}
return AArtGeneProductSetsAll(self.grprdflt, self.hdrobj, **kws) | [
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242,328 | 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_in_study': {'align':'right'},
# 'ratio_in_pop':{'align':'right'}}
kws_xlsx = {
'title': self.ver_list,
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
#'ntfld_wbfmt': ntfld_wbfmt,
#### 'ntval2wbfmtdict': ntval2wbfmtdict,
#'hdrs': [],
'prt_flds': self.flds_cur}
objwr.wr_xlsx_nts(fout_xlsx, self.desc2nts, **kws_xlsx) | python | def wr_xlsx(self, fout_xlsx):
objwr = WrXlsxSortedGos("GOEA", self.sortobj)
#### fld2fmt['ratio_in_study'] = '{:>8}'
#### fld2fmt['ratio_in_pop'] = '{:>12}'
#### ntfld2wbfmtdict = {
# ntfld_wbfmt = {
# 'ratio_in_study': {'align':'right'},
# 'ratio_in_pop':{'align':'right'}}
kws_xlsx = {
'title': self.ver_list,
'fld2fmt': {f:'{:8.2e}' for f in self.flds_cur if f[:2] == 'p_'},
#'ntfld_wbfmt': ntfld_wbfmt,
#### 'ntval2wbfmtdict': ntval2wbfmtdict,
#'hdrs': [],
'prt_flds': self.flds_cur}
objwr.wr_xlsx_nts(fout_xlsx, self.desc2nts, **kws_xlsx) | [
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242,329 | 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, self.desc2nts['sections'], **kws_tsv)
print(" WROTE: {TSV}".format(TSV=fout_tsv)) | python | def wr_tsv(self, fout_tsv):
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, self.desc2nts['sections'], **kws_tsv)
print(" WROTE: {TSV}".format(TSV=fout_tsv)) | [
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242,330 | 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):
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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242,331 | 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):
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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242,332 | 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_items'
# 'study_n', 'study_count', 'study_items',
# 'is_ratio_different', 'level', 'is_obsolete',
# 'namespace', 'reldepth', 'alt_ids', 'format_txt', 'hdr_idx',
# 'is_hdrgo', 'is_usrgo', 'num_usrgos', 'hdr1usr01', 'alt', 'GO_name',
# 'dcnt', 'D1', 'tcnt', 'tfreq', 'tinfo', 'childcnt', 'REL',
# 'REL_short', 'rel', 'id')
flds0 = ['GO', 'NS', 'enrichment', self.pval_fld, 'dcnt', 'tinfo', 'depth',
'ratio_in_study', 'ratio_in_pop', 'name']
flds_p = [f for f in self.flds_all if f[:2] == 'p_' and f != self.pval_fld]
flds.extend(flds0)
if flds_p:
flds.extend(flds_p)
flds.append('study_count')
flds.append('study_items')
return flds | python | def _init_flds_cur(self):
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_items'
# 'study_n', 'study_count', 'study_items',
# 'is_ratio_different', 'level', 'is_obsolete',
# 'namespace', 'reldepth', 'alt_ids', 'format_txt', 'hdr_idx',
# 'is_hdrgo', 'is_usrgo', 'num_usrgos', 'hdr1usr01', 'alt', 'GO_name',
# 'dcnt', 'D1', 'tcnt', 'tfreq', 'tinfo', 'childcnt', 'REL',
# 'REL_short', 'rel', 'id')
flds0 = ['GO', 'NS', 'enrichment', self.pval_fld, 'dcnt', 'tinfo', 'depth',
'ratio_in_study', 'ratio_in_pop', 'name']
flds_p = [f for f in self.flds_all if f[:2] == 'p_' and f != self.pval_fld]
flds.extend(flds0)
if flds_p:
flds.extend(flds_p)
flds.append('study_count')
flds.append('study_items')
return flds | [
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242,333 | 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 hint is found.
elif self.hdr_ex in line:
self._init_hdr(line, hdrs_usr)
return True
return False | python | def do_hdr(self, line, hdrs_usr):
# 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 hint is found.
elif self.hdr_ex in line:
self._init_hdr(line, hdrs_usr)
return True
return False | [
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242,334 | 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')
hdr = hdr.replace('-', '_')
hdr = hdr.replace('"', '')
xform.append(hdr)
return xform | python | def hdr_xform(self, hdrs):
xform = []
hdrs = self.replace_nulls(hdrs)
for hdr in hdrs:
hdr = hdr.replace('.', '_')
hdr = hdr.replace(' ', '_')
hdr = hdr.replace('#', 'N')
hdr = hdr.replace('-', '_')
hdr = hdr.replace('"', '')
xform.append(hdr)
return xform | [
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242,335 | 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"_$", r"", line)
hdrs = re.split(self.sep, line)
if '' in hdrs:
hdrs = NCBIgeneFileReader.replace_nulls(hdrs)
# Init indexes which will be converted to int or float
self.idxs_int = [idx for idx, hdr in enumerate(hdrs) if hdr in self.int_hdrs]
self.idxs_float = [idx for idx, hdr in enumerate(hdrs) if hdr in self.float_hdrs]
assert hdrs[6] == 'Aliases'
return namedtuple('ntncbi', ' '.join(hdrs)) | python | def _init_nt_hdr(self, line):
line = line.replace('.', '_')
line = line.replace(' ', '_')
line = line.replace('#', 'N')
line = line.replace('-', '_')
line = line.replace('"', '')
#line = re.sub(r"_$", r"", line)
hdrs = re.split(self.sep, line)
if '' in hdrs:
hdrs = NCBIgeneFileReader.replace_nulls(hdrs)
# Init indexes which will be converted to int or float
self.idxs_int = [idx for idx, hdr in enumerate(hdrs) if hdr in self.int_hdrs]
self.idxs_float = [idx for idx, hdr in enumerate(hdrs) if hdr in self.float_hdrs]
assert hdrs[6] == 'Aliases'
return namedtuple('ntncbi', ' '.join(hdrs)) | [
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242,336 | 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):
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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242,337 | 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)
fnc(fld)
else:
for fld in enumerate(zip(self.hdr2idx.keys(), fld)):
print(fld)
for hdr in self.hdrs_usr:
print(hdr)
print('# ITEMS ON A LINE:', len(fld))
print('MAX USR IDX:', self.usr_max_idx)
raise Exception("ERROR ON LINE {} IN {}".format(lnum+1, self.fin)) | python | def _init_data_line(self, fnc, lnum, 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)
fnc(fld)
else:
for fld in enumerate(zip(self.hdr2idx.keys(), fld)):
print(fld)
for hdr in self.hdrs_usr:
print(hdr)
print('# ITEMS ON A LINE:', len(fld))
print('MAX USR IDX:', self.usr_max_idx)
raise Exception("ERROR ON LINE {} IN {}".format(lnum+1, self.fin)) | [
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242,338 | 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
flds[idx] = int(flds[idx]) if dig.isdigit() else dig
for idx in self.idxs_strpat:
hdr = self.hdr2idx.items()[idx][0]
pat = self.strpat_hdrs[hdr]
flds[idx] = pat.format(flds[idx]) | python | def convert_ints_floats(self, flds):
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
flds[idx] = int(flds[idx]) if dig.isdigit() else dig
for idx in self.idxs_strpat:
hdr = self.hdr2idx.items()[idx][0]
pat = self.strpat_hdrs[hdr]
flds[idx] = pat.format(flds[idx]) | [
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242,339 | 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...
if hdrs_usr is not None:
# Loop through the user headers
for usr_hdr in hdrs_usr:
# If the user header is contained in the file....
if usr_hdr in self.hdr2idx:
# Add the user header and the field index to a list
self.hdrs_usr.append([usr_hdr, self.hdr2idx[usr_hdr]])
else:
raise Exception("NO COLUMN({}) FOUND:\n HDR={}\n".format(
hdrs_usr, '\n HDR='.join(self.hdr2idx.keys())))
usr_hdrs = [E[0] for E in self.hdrs_usr] if self.hdrs_usr else self.hdr2idx
self._init_idxs_float(usr_hdrs)
self._init_idxs_int(usr_hdrs)
self._init_idxs_strpat(usr_hdrs)
self.usr_max_idx = max(E[1] for E in self.hdrs_usr) if self.hdrs_usr else len(self.hdr2idx)-1 | python | def _init_hdr(self, line, hdrs_usr):
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...
if hdrs_usr is not None:
# Loop through the user headers
for usr_hdr in hdrs_usr:
# If the user header is contained in the file....
if usr_hdr in self.hdr2idx:
# Add the user header and the field index to a list
self.hdrs_usr.append([usr_hdr, self.hdr2idx[usr_hdr]])
else:
raise Exception("NO COLUMN({}) FOUND:\n HDR={}\n".format(
hdrs_usr, '\n HDR='.join(self.hdr2idx.keys())))
usr_hdrs = [E[0] for E in self.hdrs_usr] if self.hdrs_usr else self.hdr2idx
self._init_idxs_float(usr_hdrs)
self._init_idxs_int(usr_hdrs)
self._init_idxs_strpat(usr_hdrs)
self.usr_max_idx = max(E[1] for E in self.hdrs_usr) if self.hdrs_usr else len(self.hdr2idx)-1 | [
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242,340 | 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):
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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242,341 | 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):
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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242,342 | 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):
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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242,343 | 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}".format(N=geneid, SYM=ntd.Symbol))
return geneid2nt | python | def _get_geneid2nt(nts):
geneid2nt = {}
for ntd in nts:
geneid = ntd.GeneID
if geneid not in geneid2nt:
geneid2nt[geneid] = ntd
else:
print("DUPLICATE GeneID FOUND {N:9} {SYM}".format(N=geneid, SYM=ntd.Symbol))
return geneid2nt | [
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242,344 | 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\n'.format(PYDOC=docstr))
ofstrm.write("from collections import namedtuple\n\n")
ofstrm.write('WRITTEN = "{DATE}"'.format(
DATE=re.sub('-', '_', str(datetime.date.today()))))
ofstrm.write(' # {N} items\n\n'.format(N=num_genes))
ntd = next(iter(geneid2nt.values())) # Access one dictionary value in Python 2
ofstrm.write("#pylint: disable=line-too-long,too-many-lines,invalid-name\n")
ofstrm.write("{NtName} = namedtuple('{NtName}', '{FLDS}')\n\n".format(
NtName=type(ntd).__name__, FLDS=' '.join(ntd._fields)))
ofstrm.write("GENEID2NT = {{ # {N:,} items\n".format(N=num_genes))
for geneid, ntd in sorted(geneid2nt.items(), key=lambda t: t[0]):
ofstrm.write(" {GeneID} : {NT},\n".format(GeneID=geneid, NT=ntd))
ofstrm.write("}\n")
log.write(" {N:9} geneids WROTE: {PY}\n".format(N=num_genes, PY=fout_py)) | python | def _wrpy_ncbi_gene_nts(fout_py, geneid2nt, log):
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\n'.format(PYDOC=docstr))
ofstrm.write("from collections import namedtuple\n\n")
ofstrm.write('WRITTEN = "{DATE}"'.format(
DATE=re.sub('-', '_', str(datetime.date.today()))))
ofstrm.write(' # {N} items\n\n'.format(N=num_genes))
ntd = next(iter(geneid2nt.values())) # Access one dictionary value in Python 2
ofstrm.write("#pylint: disable=line-too-long,too-many-lines,invalid-name\n")
ofstrm.write("{NtName} = namedtuple('{NtName}', '{FLDS}')\n\n".format(
NtName=type(ntd).__name__, FLDS=' '.join(ntd._fields)))
ofstrm.write("GENEID2NT = {{ # {N:,} items\n".format(N=num_genes))
for geneid, ntd in sorted(geneid2nt.items(), key=lambda t: t[0]):
ofstrm.write(" {GeneID} : {NT},\n".format(GeneID=geneid, NT=ntd))
ofstrm.write("}\n")
log.write(" {N:9} geneids WROTE: {PY}\n".format(N=num_genes, PY=fout_py)) | [
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242,345 | 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):
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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242,346 | 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):
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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242,347 | 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 goobj.id not in go2obj:
# Add main GO ID to go2obj
go2obj[goobj.id] = goobj | python | def fill_main_goids(go2obj, goids):
# 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 goobj.id not in go2obj:
# Add main GO ID to go2obj
go2obj[goobj.id] = goobj | [
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242,348 | 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):
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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242,349 | 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_relationshipgo2obj(goobj)
if goobj.relationship_rev:
obj.fill_relationshiprevgo2obj(goobj) | python | def fill_relationshipobjs(go2obj, relationships):
# Get all GO Term record objects that have relationships
obj = RelationshipFill(go2obj, relationships)
for goobj in go2obj.values():
if goobj.relationship:
obj.fill_relationshipgo2obj(goobj)
if goobj.relationship_rev:
obj.fill_relationshiprevgo2obj(goobj) | [
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242,350 | 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):
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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242,351 | 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 childgoid2obj.items() if not o.children) | python | def get_leaf_children(gos_user, go2obj_arg):
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 childgoid2obj.items() if not o.children) | [
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242,352 | 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 goid | python | def chk_goids(goids, msg=None, raise_except=True):
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 goid | [
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242,353 | 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_sorted_relationships(goterm_upper)
self.goterms_sorted.append(goterm) | python | def _get_sorted_relationships(self, goterm):
if goterm.id in self.goids_seen:
return
self.goids_seen.add(goterm.id)
for goterm_upper in goterm.get_goterms_upper():
self._get_sorted_relationships(goterm_upper)
self.goterms_sorted.append(goterm) | [
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242,354 | 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.exists(sections_file):
return ReadGoids().read_sections(sections_file, False, exclude_ungrouped)
# Is 'sections_file' a module string?
if '/' not in sections_file and r'\\' not in sections_file and \
pkgutil.find_loader(sections_file) is not None:
mod = importlib.import_module(sections_file)
var = getattr(mod, 'SECTIONS', None)
if var is not None:
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(var)
print(Grouper.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP="N/A", undesc="unused", ACTION="IMPORTED: ", FILE=sections_file))
return var
raise RuntimeError("NO 'SECTIONS' VARIABLE FOUND IN MODULE({M})".format(M=sections_file))
if prt:
prt.write("CANNOT READ: {SEC}\n".format(SEC=sections_file)) | python | def read_sections(sections_file, exclude_ungrouped=False, prt=sys.stdout):
if sections_file is None:
return None
assert isinstance(sections_file, str), "BAD SECTIONS FILENAME({S})".format(
S=sections_file)
if os.path.exists(sections_file):
return ReadGoids().read_sections(sections_file, False, exclude_ungrouped)
# Is 'sections_file' a module string?
if '/' not in sections_file and r'\\' not in sections_file and \
pkgutil.find_loader(sections_file) is not None:
mod = importlib.import_module(sections_file)
var = getattr(mod, 'SECTIONS', None)
if var is not None:
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(var)
print(Grouper.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP="N/A", undesc="unused", ACTION="IMPORTED: ", FILE=sections_file))
return var
raise RuntimeError("NO 'SECTIONS' VARIABLE FOUND IN MODULE({M})".format(M=sections_file))
if prt:
prt.write("CANNOT READ: {SEC}\n".format(SEC=sections_file)) | [
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242,355 | 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
if prt is not None:
self._prt_read_msg(prt, fin_txt, exclude_ungrouped)
return sections | python | def read_py(self, fin_txt, get_goids_only, exclude_ungrouped, prt=sys.stdout):
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
if prt is not None:
self._prt_read_msg(prt, fin_txt, exclude_ungrouped)
return sections | [
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242,356 | 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_only, exclude_ungrouped)
else:
file_contents = self.read_txt(sections_file, get_goids_only, exclude_ungrouped)
if file_contents:
return file_contents.get('sections', None) | python | def read_sections(self, sections_file, get_goids_only, exclude_ungrouped):
ext = os.path.splitext(sections_file)[1]
file_contents = None
if ext == '.py':
file_contents = self.read_py(sections_file, get_goids_only, exclude_ungrouped)
else:
file_contents = self.read_txt(sections_file, get_goids_only, exclude_ungrouped)
if file_contents:
return file_contents.get('sections', None) | [
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242,357 | 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):
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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242,358 | 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().summarize_sec2hdrgos(self.section2goids.items())
sys.stdout.write(Grouper.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP="N/A", undesc="unused", ACTION="READ: ", FILE=fin_txt))
elif self.goids_fin:
prt.write(" {G} GO IDs READ: {FIN}\n".format(G=len(self.goids_fin), FIN=fin_txt)) | python | def _prt_read_msg(self, prt, fin_txt, exclude_ungrouped):
if self.sections_seen or exclude_ungrouped:
# dat = Grouper.get_summary_data(self.section2goids.items(), HdrgosSections.secdflt)
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(self.section2goids.items())
sys.stdout.write(Grouper.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP="N/A", undesc="unused", ACTION="READ: ", FILE=fin_txt))
elif self.goids_fin:
prt.write(" {G} GO IDs READ: {FIN}\n".format(G=len(self.goids_fin), FIN=fin_txt)) | [
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242,359 | 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):
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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242,360 | 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] = edges_new
return edges_ret | python | def _rm_gos_edges_rel(self, rm_goids, edges_rel):
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] = edges_new
return edges_ret | [
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242,361 | 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.append((goid_child, goid_parent))
return edges_reduced | python | def _rm_gos_edges(rm_goids, edges_all):
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.append((goid_child, goid_parent))
return edges_reduced | [
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242,362 | 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)
return edge_nodes | python | def get_all_edge_nodes(self):
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)
return edge_nodes | [
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242,363 | 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):
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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242,364 | 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(
NM=name, N=len(missing_nodes), T=len(edge_nodes), GOs=missing_nodes) | python | def chk_edges_nodes(edges, nodes, name):
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(
NM=name, N=len(missing_nodes), T=len(edge_nodes), GOs=missing_nodes) | [
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242,365 | 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):
c2ps = defaultdict(set)
for goid_child, goid_parent in self.edges:
c2ps[goid_child].add(goid_parent)
return c2ps | [
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242,366 | 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 reltype in rel2src2dsts:
for parent, children in rel2src2dsts[reltype].items():
for child in children:
edge_from_to.append((child, parent))
if reltype in rel2dst2srcs:
for parent, children in rel2dst2srcs[reltype].items():
for child in children:
edge_from_to.append((child, parent))
edge_rel2fromto[reltype] = edge_from_to
return edge_rel2fromto | python | def _init_edges_relationships(rel2src2dsts, rel2dst2srcs):
edge_rel2fromto = {}
relationships = set(rel2src2dsts).union(rel2dst2srcs)
for reltype in relationships:
edge_from_to = []
if reltype in rel2src2dsts:
for parent, children in rel2src2dsts[reltype].items():
for child in children:
edge_from_to.append((child, parent))
if reltype in rel2dst2srcs:
for parent, children in rel2dst2srcs[reltype].items():
for child in children:
edge_from_to.append((child, parent))
edge_rel2fromto[reltype] = edge_from_to
return edge_rel2fromto | [
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242,367 | 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 goid_altid in goobj_child.alt_ids:
goids_seen.add(goid_altid)
##A self.go2obj[goid_altid] = goobj_child
# Loop through relationships of child object
for reltype, recs in goobj_child.relationship.items():
if reltype in self.relationships:
for relationship_obj in recs:
relationship_id = relationship_obj.id
rel2src2dsts[reltype][relationship_id].add(child_id)
# If relationship has not been seen, traverse
if relationship_id not in goids_seen:
self._traverse_relationship_objs(rel2src2dsts, relationship_obj, goids_seen) | python | def _traverse_relationship_objs(self, rel2src2dsts, goobj_child, goids_seen):
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 goid_altid in goobj_child.alt_ids:
goids_seen.add(goid_altid)
##A self.go2obj[goid_altid] = goobj_child
# Loop through relationships of child object
for reltype, recs in goobj_child.relationship.items():
if reltype in self.relationships:
for relationship_obj in recs:
relationship_id = relationship_obj.id
rel2src2dsts[reltype][relationship_id].add(child_id)
# If relationship has not been seen, traverse
if relationship_id not in goids_seen:
self._traverse_relationship_objs(rel2src2dsts, relationship_obj, goids_seen) | [
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242,368 | 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
for goid_src in go_sources:
goobj_src = go2obj[goid_src]
if goid_src not in goids_seen:
self._traverse_relationship_rev_objs(rel2dst2srcs, goobj_src, goids_seen)
return rel2dst2srcs | python | def _init_rel2dst2srcs(self, go_sources, traverse_child):
if not traverse_child or not self.relationships:
return {}
rel2dst2srcs = {r:defaultdict(set) for r in self.relationships}
goids_seen = set()
go2obj = self.go2obj
for goid_src in go_sources:
goobj_src = go2obj[goid_src]
if goid_src not in goids_seen:
self._traverse_relationship_rev_objs(rel2dst2srcs, goobj_src, goids_seen)
return rel2dst2srcs | [
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242,369 | 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 goid_src not in goids_seen:
##F self._traverse_child_objs(c2ps, goobj_src, go2obj, goids_seen)
self._traverse_child_objs(c2ps, goobj_src, goids_seen)
return c2ps | python | def _init_c2ps(self, go_sources, traverse_child):
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 goid_src not in goids_seen:
##F self._traverse_child_objs(c2ps, goobj_src, go2obj, goids_seen)
self._traverse_child_objs(c2ps, goobj_src, goids_seen)
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242,370 | 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") # optional 0 or greater
self._chk_fld(ntd, "DB_Name", 0, 1) # optional 0 or 1
self._chk_fld(ntd, "DB_Synonym") # optional 0 or greater
self._chk_fld(ntd, "Taxon", 1, 2)
flds = list(ntd)
self._chk_qty_eq_1(flds)
# self._chk_qualifier(ntd.Qualifier, flds, idx)
if not ntd.Taxon or len(ntd.Taxon) not in {1, 2}:
self.illegal_lines['BAD TAXON'].append((idx, '**{I}) TAXON: {NT}'.format(I=idx, NT=ntd)))
if self.illegal_lines:
self.prt_error_summary(fout_err)
return not self.illegal_lines | python | def chk(self, annotations, fout_err):
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") # optional 0 or greater
self._chk_fld(ntd, "DB_Name", 0, 1) # optional 0 or 1
self._chk_fld(ntd, "DB_Synonym") # optional 0 or greater
self._chk_fld(ntd, "Taxon", 1, 2)
flds = list(ntd)
self._chk_qty_eq_1(flds)
# self._chk_qualifier(ntd.Qualifier, flds, idx)
if not ntd.Taxon or len(ntd.Taxon) not in {1, 2}:
self.illegal_lines['BAD TAXON'].append((idx, '**{I}) TAXON: {NT}'.format(I=idx, NT=ntd)))
if self.illegal_lines:
self.prt_error_summary(fout_err)
return not self.illegal_lines | [
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242,371 | tanghaibao/goatools | goatools/anno/init/reader_gaf.py | GafData.get_gafvals | 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]) # 7 With_From
flds[8] = self.aspect2ns[flds[8]] # 8 GAF Aspect field converted to BP, MF, or CC
flds[9] = self._get_set(flds[9]) # 9 DB_Name
flds[10] = self._get_set(flds[10]) # 10 DB_Synonym
flds[12] = self._do_taxons(flds[12]) # 12 Taxon
flds[13] = GET_DATE_YYYYMMDD(flds[13]) # self.strptime(flds[13], '%Y%m%d').date(), # 13 Date 20190406
# Version 2.x has these additional fields not found in v1.0
if self.is_long:
flds[15] = get_extensions(flds[15]) # Extensions (or Annotation_Extension)
flds[16] = self._get_set(flds[16].rstrip())
else:
flds[14] = self._get_set(flds[14].rstrip())
return flds | python | def get_gafvals(self, line):
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]) # 7 With_From
flds[8] = self.aspect2ns[flds[8]] # 8 GAF Aspect field converted to BP, MF, or CC
flds[9] = self._get_set(flds[9]) # 9 DB_Name
flds[10] = self._get_set(flds[10]) # 10 DB_Synonym
flds[12] = self._do_taxons(flds[12]) # 12 Taxon
flds[13] = GET_DATE_YYYYMMDD(flds[13]) # self.strptime(flds[13], '%Y%m%d').date(), # 13 Date 20190406
# Version 2.x has these additional fields not found in v1.0
if self.is_long:
flds[15] = get_extensions(flds[15]) # Extensions (or Annotation_Extension)
flds[16] = self._get_set(flds[16].rstrip())
else:
flds[14] = self._get_set(flds[14].rstrip())
return flds | [
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242,372 | 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):
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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242,373 | 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(
(-1, "FIELD({F}): MIN QUANTITY({Q}) WASN'T MET: {V}".format(F=name, Q=qty_min, V=vals)))
if qty_max is not None:
if num_vals > qty_max:
self.illegal_lines['MAX QTY'].append(
(-1, "FIELD({F}): MAX QUANTITY({Q}) EXCEEDED: {V}\n{NT}".format(
F=name, Q=qty_max, V=vals, NT=ntd))) | python | def _chk_fld(self, ntd, name, qty_min=0, qty_max=None):
vals = getattr(ntd, name)
num_vals = len(vals)
if num_vals < qty_min:
self.illegal_lines['MIN QTY'].append(
(-1, "FIELD({F}): MIN QUANTITY({Q}) WASN'T MET: {V}".format(F=name, Q=qty_min, V=vals)))
if qty_max is not None:
if num_vals > qty_max:
self.illegal_lines['MAX QTY'].append(
(-1, "FIELD({F}): MAX QUANTITY({Q}) EXCEEDED: {V}\n{NT}".format(
F=name, Q=qty_max, V=vals, NT=ntd))) | [
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242,374 | 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):
values = line.split('\t')
self._prt_line_detail(prt, values) | [
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242,375 | 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) in enumerate(data)]
prt.write("{LNUM}\n{TXT}\n".format(LNUM=lnum, TXT="\n".join(txt))) | python | def _prt_line_detail(self, prt, values, lnum=""):
#### 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) in enumerate(data)]
prt.write("{LNUM}\n{TXT}\n".format(LNUM=lnum, TXT="\n".join(txt))) | [
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242,376 | 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_lines:
for err_name, errors in self.illegal_lines.items():
errcnts.append(" {N:9,} {ERROR}\n".format(N=len(errors), ERROR=err_name))
# Save error details into a log file
fout_log = self._wrlog_details_illegal_gaf(fout_err, errcnts)
sys.stdout.write(" WROTE GAF ERROR LOG: {LOG}:\n".format(LOG=fout_log))
for err_cnt in errcnts:
sys.stdout.write(err_cnt) | python | def prt_error_summary(self, fout_err):
# 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_lines:
for err_name, errors in self.illegal_lines.items():
errcnts.append(" {N:9,} {ERROR}\n".format(N=len(errors), ERROR=err_name))
# Save error details into a log file
fout_log = self._wrlog_details_illegal_gaf(fout_err, errcnts)
sys.stdout.write(" WROTE GAF ERROR LOG: {LOG}:\n".format(LOG=fout_log))
for err_cnt in errcnts:
sys.stdout.write(err_cnt) | [
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242,377 | 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")
for err_cnt in err_cnts:
prt.write(err_cnt)
prt.write("\n\nILLEGAL GAF ERROR DETAILS:\n\n")
for lnum, line in self.ignored:
prt.write("**WARNING: GAF LINE IGNORED: {FIN}[{LNUM}]:\n{L}\n".format(
FIN=gaf_base, L=line, LNUM=lnum))
self.prt_line_detail(prt, line)
prt.write("\n\n")
for error, lines in self.illegal_lines.items():
for lnum, line in lines:
prt.write("**WARNING: GAF LINE ILLEGAL({ERR}): {FIN}[{LNUM}]:\n{L}\n".format(
ERR=error, FIN=gaf_base, L=line, LNUM=lnum))
self.prt_line_detail(prt, line)
prt.write("\n\n")
return fout_err | python | def _wrlog_details_illegal_gaf(self, fout_err, err_cnts):
# 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")
for err_cnt in err_cnts:
prt.write(err_cnt)
prt.write("\n\nILLEGAL GAF ERROR DETAILS:\n\n")
for lnum, line in self.ignored:
prt.write("**WARNING: GAF LINE IGNORED: {FIN}[{LNUM}]:\n{L}\n".format(
FIN=gaf_base, L=line, LNUM=lnum))
self.prt_line_detail(prt, line)
prt.write("\n\n")
for error, lines in self.illegal_lines.items():
for lnum, line in lines:
prt.write("**WARNING: GAF LINE ILLEGAL({ERR}): {FIN}[{LNUM}]:\n{L}\n".format(
ERR=error, FIN=gaf_base, L=line, LNUM=lnum))
self.prt_line_detail(prt, line)
prt.write("\n\n")
return fout_err | [
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242,378 | 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 in relset)
# for relfwd_goid in relfwd_goids:
# assert relfwd_goid in self.go2obj, "{GO} {REL} NOT FOUND {GO_R}".format(
# GO=goid, REL=reltyp, GO_R=relfwd_goid)
print("CountRelativesInit RELLLLS", goid, goobj.id, reltyp, relfwd_goids) | python | def get_relationship_dicts(self):
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 in relset)
# for relfwd_goid in relfwd_goids:
# assert relfwd_goid in self.go2obj, "{GO} {REL} NOT FOUND {GO_R}".format(
# GO=goid, REL=reltyp, GO_R=relfwd_goid)
print("CountRelativesInit RELLLLS", goid, goobj.id, reltyp, relfwd_goids) | [
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242,379 | 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]
ns2dcntgoobj[goobj.namespace].append((dcnt, goobj))
# 2. Assign letters to level-01/depth-01 GO terms
go2nt = {}
ntobj = cx.namedtuple("NtGoLetters", "D1 dcnt goobj")
_go2abc = self.go2letter
letters = list(chain(range(ord('A'), ord('Z') + 1), range(ord('a'), ord('z') + 1)))
for list_dcnt_goobj in ns2dcntgoobj.values():
letter_idx = 0
for dcnt, goobj in sorted(list_dcnt_goobj, key=lambda t: t[0], reverse=True):
letter = chr(letters[letter_idx]) if _go2abc is None else _go2abc.get(goobj.id, '')
go2nt[goobj.id] = ntobj._make([letter, dcnt, goobj])
letter_idx += 1
return go2nt | python | def get_goone2ntletter(self, go2dcnt, depth2goobjs):
# 1. Group level-01/depth-01 GO terms by namespace
ns2dcntgoobj = cx.defaultdict(list)
for goobj in depth2goobjs[1]:
dcnt = go2dcnt[goobj.id]
ns2dcntgoobj[goobj.namespace].append((dcnt, goobj))
# 2. Assign letters to level-01/depth-01 GO terms
go2nt = {}
ntobj = cx.namedtuple("NtGoLetters", "D1 dcnt goobj")
_go2abc = self.go2letter
letters = list(chain(range(ord('A'), ord('Z') + 1), range(ord('a'), ord('z') + 1)))
for list_dcnt_goobj in ns2dcntgoobj.values():
letter_idx = 0
for dcnt, goobj in sorted(list_dcnt_goobj, key=lambda t: t[0], reverse=True):
letter = chr(letters[letter_idx]) if _go2abc is None else _go2abc.get(goobj.id, '')
go2nt[goobj.id] = ntobj._make([letter, dcnt, goobj])
letter_idx += 1
return go2nt | [
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242,380 | 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.keys()) | python | def _init_goslims(self, dagslim):
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.keys()) | [
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242,381 | 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)
return go_slims | python | def _get_goslimids_norel(self, dagslim):
go_slims = set()
go2obj = self.gosubdag.go2obj
for goid in dagslim:
goobj = go2obj[goid]
if not goobj.relationship:
go_slims.add(goobj.id)
return go_slims | [
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242,382 | 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:
go2obj = get_godag()
return GoSubDag(None, go2obj, rcntobj=True) | python | def get_gosubdag(gosubdag=None):
if gosubdag is not None:
if gosubdag.rcntobj is not None:
return gosubdag
else:
gosubdag.init_auxobjs()
return gosubdag
else:
go2obj = get_godag()
return GoSubDag(None, go2obj, rcntobj=True) | [
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242,383 | 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)],
)
return self.param2fnc[fnc_key] | python | def getfnc_qual_ev(self):
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)],
)
return self.param2fnc[fnc_key] | [
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242,384 | 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):
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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242,385 | 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(goid, "white"),
color=self.objcolor.get_bordercolor(goid)) | python | def get_node(self, goid, goobj):
# 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(goid, "white"),
color=self.objcolor.get_bordercolor(goid)) | [
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242,386 | 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):
# 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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242,387 | 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 fields
if self.gosubdag.relationships:
exclude.add('level')
return set(f for f in ntflds if f not in exclude) | python | def _get_prtflds(self):
# 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 fields
if self.gosubdag.relationships:
exclude.add('level')
return set(f for f in ntflds if f not in exclude) | [
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242,388 | 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):
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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242,389 | 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(goobj.parents) == len(set(goobj.parents))
hdr.append("p{N}".format(N=len(set(goobj.parents)))) | python | def _add_parent_cnt(self, hdr, goobj, c2ps):
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(goobj.parents) == len(set(goobj.parents))
hdr.append("p{N}".format(N=len(set(goobj.parents)))) | [
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242,390 | 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):
prt.write('**NOTE: No evidence codes in associations: {F}\n'.format(F=self.filename)) | [
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242,391 | 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):
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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242,392 | 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:
term2itemids[obo_dag[goid].id].add(gene)
if log is not None:
num_stu = len(genes)
num_pop = len(geneset)
perc = 100.0*num_stu/num_pop if num_pop != 0 else 0.0
log.write("{P:3.0f}% {N:>6,} of {M:>6,} {DESC} items found in association\n".format(
DESC=desc, N=num_stu, M=num_pop, P=perc))
return term2itemids | python | def get_terms(desc, geneset, assoc, obo_dag, log):
_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:
term2itemids[obo_dag[goid].id].add(gene)
if log is not None:
num_stu = len(genes)
num_pop = len(geneset)
perc = 100.0*num_stu/num_pop if num_pop != 0 else 0.0
log.write("{P:3.0f}% {N:>6,} of {M:>6,} {DESC} items found in association\n".format(
DESC=desc, N=num_stu, M=num_pop, P=perc))
return term2itemids | [
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242,393 | 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 gene2go, NOT go2gene: {EX}".format(
EX=assoc.items()[:2]))
return | python | def _chk_gene2go(assoc):
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:":
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242,394 | 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(goid)
if goids_missing:
print("MISSING GO IDs: {GOs}".format(GOs=goids_missing))
print("{N} of {M} GO IDs ARE MISSING".format(N=len(goids_missing), M=len(goids)))
return usrgos | python | def _init_usrgos(self, goids):
usrgos = set()
goids_missing = set()
_go2obj = self.gosubdag.go2obj
for goid in goids:
if goid in _go2obj:
usrgos.add(goid)
else:
goids_missing.add(goid)
if goids_missing:
print("MISSING GO IDs: {GOs}".format(GOs=goids_missing))
print("{N} of {M} GO IDs ARE MISSING".format(N=len(goids_missing), M=len(goids)))
return usrgos | [
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242,395 | 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
"""
gos_all = set()
# Get:
# * Header GO IDs that are not user GO IDs
# * User GO IDs that are under header GOs
for hdrgo, usrgos in self.hdrgo2usrgos.items():
gos_all.add(hdrgo)
gos_all |= usrgos
# User GO IDs that are header GOs in groups containing no other user GO IDs
gos_all |= self.hdrgo_is_usrgo
assert gos_all == self.usrgos.union(set(self.hdrgo2usrgos.keys()))
assert len(self.usrgos.difference(gos_all)) == 0, \
"GROUPER ERROR: {GOs}".format(GOs=self.usrgos.difference(gos_all))
return gos_all | python | def get_gos_all(self):
gos_all = set()
# Get:
# * Header GO IDs that are not user GO IDs
# * User GO IDs that are under header GOs
for hdrgo, usrgos in self.hdrgo2usrgos.items():
gos_all.add(hdrgo)
gos_all |= usrgos
# User GO IDs that are header GOs in groups containing no other user GO IDs
gos_all |= self.hdrgo_is_usrgo
assert gos_all == self.usrgos.union(set(self.hdrgo2usrgos.keys()))
assert len(self.usrgos.difference(gos_all)) == 0, \
"GROUPER ERROR: {GOs}".format(GOs=self.usrgos.difference(gos_all))
return gos_all | [
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] | 407682e573a108864a79031f8ca19ee3bf377626 | https://github.com/tanghaibao/goatools/blob/407682e573a108864a79031f8ca19ee3bf377626/goatools/grouper/grprobj_init.py#L64-L84 |
242,396 | 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:0048471', # child: D4 perinuclear region of cytoplasm
'GO:0016020':[ # grp_term: D1 membrane
'GO:0098589', # child: D2 membrane region
'GO:0005886', # child: D2 plasma membrane
]
"""
# Header GO IDs are main. User GO IDs are as specified by the user
hdrgo2usrgos = cx.defaultdict(set)
# Contains user GO IDs which are also header GO IDs, plus user main GO if needed
hdrgo_is_usrgo = set()
_go2nt = self.gosubdag.go2nt
objhi = GrouperInit.GetGoidHigh(self.gosubdag, self.hdrobj.hdrgos,
self.most_specific_fncs[fnc_most_specific])
for goid_usr in self.usrgos:
goid_main = _go2nt[goid_usr].id
# Add current GO ID to parents_all in case curr GO ID is a high GO.
goid_high = objhi.get_goid_high(goid_main)
# Don't add user GO ID if it is also the GO header
if goid_main != goid_high:
hdrgo2usrgos[goid_high].add(goid_usr)
elif goid_high not in hdrgo2usrgos:
hdrgo2usrgos[goid_high] = set()
if goid_main == goid_high:
hdrgo_is_usrgo.add(goid_main)
if goid_main != goid_usr:
hdrgo_is_usrgo.add(goid_usr)
# Initialize data members
self.hdrgo2usrgos = hdrgo2usrgos
self.hdrgo_is_usrgo = hdrgo_is_usrgo | python | def _init_h2us(self, fnc_most_specific):
# Header GO IDs are main. User GO IDs are as specified by the user
hdrgo2usrgos = cx.defaultdict(set)
# Contains user GO IDs which are also header GO IDs, plus user main GO if needed
hdrgo_is_usrgo = set()
_go2nt = self.gosubdag.go2nt
objhi = GrouperInit.GetGoidHigh(self.gosubdag, self.hdrobj.hdrgos,
self.most_specific_fncs[fnc_most_specific])
for goid_usr in self.usrgos:
goid_main = _go2nt[goid_usr].id
# Add current GO ID to parents_all in case curr GO ID is a high GO.
goid_high = objhi.get_goid_high(goid_main)
# Don't add user GO ID if it is also the GO header
if goid_main != goid_high:
hdrgo2usrgos[goid_high].add(goid_usr)
elif goid_high not in hdrgo2usrgos:
hdrgo2usrgos[goid_high] = set()
if goid_main == goid_high:
hdrgo_is_usrgo.add(goid_main)
if goid_main != goid_usr:
hdrgo_is_usrgo.add(goid_usr)
# Initialize data members
self.hdrgo2usrgos = hdrgo2usrgos
self.hdrgo_is_usrgo = hdrgo_is_usrgo | [
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Example of a grouped go list:
gos = ['GO:0044464':[ # grp_term: D1 cell part
'GO:0005737', # child: D3 cytoplasm
'GO:0048471', # child: D4 perinuclear region of cytoplasm
'GO:0016020':[ # grp_term: D1 membrane
'GO:0098589', # child: D2 membrane region
'GO:0005886', # child: D2 plasma membrane
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242,397 | 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']
if not usr_go2nt:
return self.__init_go2nt_dflt(gos_all, prt_flds_all)
usr_nt_flds = next(iter(usr_go2nt.values()))._fields
# If user namedtuple already contains all fields available, then return usr_go2nt
if len(set(prt_flds_all).difference(usr_nt_flds)) == 0:
return self._init_go2nt_aug(usr_go2nt)
# Otherwise, combine user fields and default Sorter fields
return self.__init_go2nt_w_usr(gos_all, usr_go2nt, prt_flds_all) | python | def get_go2nt(self, usr_go2nt):
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']
if not usr_go2nt:
return self.__init_go2nt_dflt(gos_all, prt_flds_all)
usr_nt_flds = next(iter(usr_go2nt.values()))._fields
# If user namedtuple already contains all fields available, then return usr_go2nt
if len(set(prt_flds_all).difference(usr_nt_flds)) == 0:
return self._init_go2nt_aug(usr_go2nt)
# Otherwise, combine user fields and default Sorter fields
return self.__init_go2nt_w_usr(gos_all, usr_go2nt, prt_flds_all) | [
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242,398 | 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:
alts = set(goobj.alt_ids)
alts.add(goobj.id)
for goid_alt in alts:
if goid_alt not in go2nt:
go2nt_aug[goid_alt] = nt_usr
# WAS
# Add alt GO IDs to go2nt
for goid, gont in go2nt_aug.items():
go2nt[goid] = gont
return go2nt | python | def _init_go2nt_aug(self, go2nt):
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:
alts = set(goobj.alt_ids)
alts.add(goobj.id)
for goid_alt in alts:
if goid_alt not in go2nt:
go2nt_aug[goid_alt] = nt_usr
# WAS
# Add alt GO IDs to go2nt
for goid, gont in go2nt_aug.items():
go2nt[goid] = gont
return go2nt | [
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242,399 | 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 cell
# shortcuts
obj = GrouperInit.NtMaker(self)
# Create go2nthdridx
for goid in gos_all:
go2nthdridx[goid] = obj.get_nt(goid)
return go2nthdridx | python | def _get_go2nthdridx(self, gos_all):
go2nthdridx = {}
# NtHdrIdx Namedtuple fields:
# * format_txt: Used to determine the format when writing Excel cells
# * hdr_idx: Value printed in an Excel cell
# shortcuts
obj = GrouperInit.NtMaker(self)
# Create go2nthdridx
for goid in gos_all:
go2nthdridx[goid] = obj.get_nt(goid)
return go2nthdridx | [
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