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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_gosrcs_upper | def _get_gosrcs_upper(self, goids, max_upper, go2parentids):
"""Get GO IDs for the upper portion of the GO DAG."""
gosrcs_upper = set()
get_nt = self.gosubdag.go2nt.get
go2nt = {g:get_nt(g) for g in goids}
# Sort by descending order of descendant counts to find potential new hdrgos
go_nt = sorted(go2nt.items(), key=lambda t: -1*t[1].dcnt)
goids_upper = set()
for goid, _ in go_nt: # Loop through GO ID, GO nt
goids_upper.add(goid)
if goid in go2parentids:
goids_upper |= go2parentids[goid]
#print "{} {:3} {}".format(goid, len(goids_upper), gont.GO_name)
if len(goids_upper) < max_upper:
gosrcs_upper.add(goid)
else:
break
return gosrcs_upper | python | def _get_gosrcs_upper(self, goids, max_upper, go2parentids):
"""Get GO IDs for the upper portion of the GO DAG."""
gosrcs_upper = set()
get_nt = self.gosubdag.go2nt.get
go2nt = {g:get_nt(g) for g in goids}
# Sort by descending order of descendant counts to find potential new hdrgos
go_nt = sorted(go2nt.items(), key=lambda t: -1*t[1].dcnt)
goids_upper = set()
for goid, _ in go_nt: # Loop through GO ID, GO nt
goids_upper.add(goid)
if goid in go2parentids:
goids_upper |= go2parentids[goid]
#print "{} {:3} {}".format(goid, len(goids_upper), gont.GO_name)
if len(goids_upper) < max_upper:
gosrcs_upper.add(goid)
else:
break
return gosrcs_upper | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_gosubdagplotnt | def _get_gosubdagplotnt(self, ntplt, title, go2color, pltargs):
"""Return GoSubDagPlotNt, which contains both a GoSubDagPlot object and ntobj."""
kws_plt = pltargs.get_kws_plt()
kws_plt['id'] = '"{ID}"'.format(ID=ntplt.hdrgo)
kws_plt['title'] = "{TITLE} of {M} user GOs".format(TITLE=title, M=ntplt.tot_usrgos)
kws_plt['go2color'] = go2color
kws_plt['go2bordercolor'] = pltargs.go2bordercolor
if ntplt.parentcnt:
kws_plt["parentcnt"] = True
gosubdagplot = GoSubDagPlot(ntplt.gosubdag, **kws_plt)
return GoSubDagPlotNt(self.grprobj, gosubdagplot, ntplt) | python | def _get_gosubdagplotnt(self, ntplt, title, go2color, pltargs):
"""Return GoSubDagPlotNt, which contains both a GoSubDagPlot object and ntobj."""
kws_plt = pltargs.get_kws_plt()
kws_plt['id'] = '"{ID}"'.format(ID=ntplt.hdrgo)
kws_plt['title'] = "{TITLE} of {M} user GOs".format(TITLE=title, M=ntplt.tot_usrgos)
kws_plt['go2color'] = go2color
kws_plt['go2bordercolor'] = pltargs.go2bordercolor
if ntplt.parentcnt:
kws_plt["parentcnt"] = True
gosubdagplot = GoSubDagPlot(ntplt.gosubdag, **kws_plt)
return GoSubDagPlotNt(self.grprobj, gosubdagplot, ntplt) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._no_ntplt | def _no_ntplt(self, ntplt):
"""Print a message about the GO DAG Plot we are NOT plotting."""
sys.stdout.write(" {GO_USR:>6,} usr {GO_ALL:>6,} GOs DID NOT WRITE: {B} {D}\n".format(
B=self.grprobj.get_fout_base(ntplt.hdrgo),
D=ntplt.desc,
GO_USR=len(ntplt.gosubdag.go_sources),
GO_ALL=len(ntplt.gosubdag.go2obj))) | python | def _no_ntplt(self, ntplt):
"""Print a message about the GO DAG Plot we are NOT plotting."""
sys.stdout.write(" {GO_USR:>6,} usr {GO_ALL:>6,} GOs DID NOT WRITE: {B} {D}\n".format(
B=self.grprobj.get_fout_base(ntplt.hdrgo),
D=ntplt.desc,
GO_USR=len(ntplt.gosubdag.go_sources),
GO_ALL=len(ntplt.gosubdag.go2obj))) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_pltdag_ancesters | def _get_pltdag_ancesters(self, hdrgo, usrgos, desc=""):
"""Get GoSubDag containing hdrgo and all usrgos and their ancesters."""
go_srcs = usrgos.union([hdrgo])
gosubdag = GoSubDag(go_srcs,
self.gosubdag.get_go2obj(go_srcs),
relationships=self.gosubdag.relationships,
rcntobj=self.gosubdag.rcntobj,
go2nt=self.gosubdag.go2nt)
tot_usrgos = len(set(gosubdag.go2obj.keys()).intersection(self.usrgos))
return self.ntpltgo(
hdrgo=hdrgo,
gosubdag=gosubdag,
tot_usrgos=tot_usrgos,
parentcnt=False,
desc=desc) | python | def _get_pltdag_ancesters(self, hdrgo, usrgos, desc=""):
"""Get GoSubDag containing hdrgo and all usrgos and their ancesters."""
go_srcs = usrgos.union([hdrgo])
gosubdag = GoSubDag(go_srcs,
self.gosubdag.get_go2obj(go_srcs),
relationships=self.gosubdag.relationships,
rcntobj=self.gosubdag.rcntobj,
go2nt=self.gosubdag.go2nt)
tot_usrgos = len(set(gosubdag.go2obj.keys()).intersection(self.usrgos))
return self.ntpltgo(
hdrgo=hdrgo,
gosubdag=gosubdag,
tot_usrgos=tot_usrgos,
parentcnt=False,
desc=desc) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_pltdag_path_hdr | def _get_pltdag_path_hdr(self, hdrgo, usrgos, desc="pruned"):
"""Get GoSubDag with paths from usrgos through hdrgo."""
go_sources = usrgos.union([hdrgo])
gosubdag = GoSubDag(go_sources,
self.gosubdag.get_go2obj(go_sources),
relationships=self.gosubdag.relationships,
rcntobj=self.gosubdag.rcntobj,
go2nt=self.gosubdag.go2nt,
dst_srcs_list=[(hdrgo, usrgos), (None, set([hdrgo]))])
tot_usrgos = len(set(gosubdag.go2obj.keys()).intersection(self.usrgos))
return self.ntpltgo(
hdrgo=hdrgo,
gosubdag=gosubdag,
tot_usrgos=tot_usrgos,
parentcnt=True,
desc=desc) | python | def _get_pltdag_path_hdr(self, hdrgo, usrgos, desc="pruned"):
"""Get GoSubDag with paths from usrgos through hdrgo."""
go_sources = usrgos.union([hdrgo])
gosubdag = GoSubDag(go_sources,
self.gosubdag.get_go2obj(go_sources),
relationships=self.gosubdag.relationships,
rcntobj=self.gosubdag.rcntobj,
go2nt=self.gosubdag.go2nt,
dst_srcs_list=[(hdrgo, usrgos), (None, set([hdrgo]))])
tot_usrgos = len(set(gosubdag.go2obj.keys()).intersection(self.usrgos))
return self.ntpltgo(
hdrgo=hdrgo,
gosubdag=gosubdag,
tot_usrgos=tot_usrgos,
parentcnt=True,
desc=desc) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | GoSubDagPlotNt.wrplt | def wrplt(self, fout_dir, plt_ext="png"):
"""Write png containing plot of GoSubDag."""
# Ex basename
basename = self.grprobj.get_fout_base(self.ntplt.hdrgo)
plt_pat = self.get_pltpat(plt_ext)
fout_basename = plt_pat.format(BASE=basename)
fout_plt = os.path.join(fout_dir, fout_basename)
self.gosubdagplot.plt_dag(fout_plt) # Create Plot
return fout_plt | python | def wrplt(self, fout_dir, plt_ext="png"):
"""Write png containing plot of GoSubDag."""
# Ex basename
basename = self.grprobj.get_fout_base(self.ntplt.hdrgo)
plt_pat = self.get_pltpat(plt_ext)
fout_basename = plt_pat.format(BASE=basename)
fout_plt = os.path.join(fout_dir, fout_basename)
self.gosubdagplot.plt_dag(fout_plt) # Create Plot
return fout_plt | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | GoSubDagPlotNt.get_dotstr | def get_dotstr(self):
"""Return a string containing DAG graph in Grpahviz's dot language."""
dotobj = self.gosubdagplot.get_pydot_graph() # pydot.Dot
dotstr = dotobj.create_dot()
return dotstr | python | def get_dotstr(self):
"""Return a string containing DAG graph in Grpahviz's dot language."""
dotobj = self.gosubdagplot.get_pydot_graph() # pydot.Dot
dotstr = dotobj.create_dot()
return dotstr | [
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tanghaibao/goatools | goatools/gosubdag/rpt/write_hierarchy.py | WrHierGO._get_wrhiercfg | def _get_wrhiercfg(self):
"""Initialize print format."""
prtfmt = self.gosubdag.prt_attr['fmt']
prtfmt = prtfmt.replace('{GO} # ', '')
prtfmt = prtfmt.replace('{D1:5} ', '')
return {'name2prtfmt':{'ITEM':prtfmt, 'ID':'{GO}{alt:1}'},
'max_indent': self.usrdct.get('max_indent'),
'include_only': self.usrdct.get('include_only'),
'item_marks': self.usrdct.get('item_marks', {}),
'concise_prt': 'concise' in self.usrset,
'indent': 'no_indent' not in self.usrset,
'dash_len': self.usrdct.get('dash_len', 6),
'sortby': self.usrdct.get('sortby')
} | python | def _get_wrhiercfg(self):
"""Initialize print format."""
prtfmt = self.gosubdag.prt_attr['fmt']
prtfmt = prtfmt.replace('{GO} # ', '')
prtfmt = prtfmt.replace('{D1:5} ', '')
return {'name2prtfmt':{'ITEM':prtfmt, 'ID':'{GO}{alt:1}'},
'max_indent': self.usrdct.get('max_indent'),
'include_only': self.usrdct.get('include_only'),
'item_marks': self.usrdct.get('item_marks', {}),
'concise_prt': 'concise' in self.usrset,
'indent': 'no_indent' not in self.usrset,
'dash_len': self.usrdct.get('dash_len', 6),
'sortby': self.usrdct.get('sortby')
} | [
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tanghaibao/goatools | goatools/gosubdag/rpt/write_hierarchy.py | WrHierGO._get_goroot | def _get_goroot(self, goids_all, namespace):
"""Get the top GO for the set of goids_all."""
root_goid = self.consts.NAMESPACE2GO[namespace]
if root_goid in goids_all:
return root_goid
root_goids = set()
for goid in goids_all:
goterm = self.gosubdag.go2obj[goid]
if goterm.depth == 0:
root_goids.add(goterm.id)
if len(root_goids) == 1:
return next(iter(root_goids))
raise RuntimeError("UNEXPECTED NUMBER OF ROOTS: {R}".format(R=root_goids)) | python | def _get_goroot(self, goids_all, namespace):
"""Get the top GO for the set of goids_all."""
root_goid = self.consts.NAMESPACE2GO[namespace]
if root_goid in goids_all:
return root_goid
root_goids = set()
for goid in goids_all:
goterm = self.gosubdag.go2obj[goid]
if goterm.depth == 0:
root_goids.add(goterm.id)
if len(root_goids) == 1:
return next(iter(root_goids))
raise RuntimeError("UNEXPECTED NUMBER OF ROOTS: {R}".format(R=root_goids)) | [
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tanghaibao/goatools | goatools/rpt/nts_xfrm.py | MgrNts.mknts | def mknts(self, add_dct):
"""Add information from add_dct to a new copy of namedtuples stored in nts."""
nts = []
assert len(add_dct) == len(self.nts)
flds = list(next(iter(self.nts))._fields) + list(next(iter(add_dct)).keys())
ntobj = cx.namedtuple("ntgoea", " ".join(flds))
for dct_new, ntgoea in zip(add_dct, self.nts):
dct_curr = ntgoea._asdict()
for key, val in dct_new.items():
dct_curr[key] = val
nts.append(ntobj(**dct_curr))
return nts | python | def mknts(self, add_dct):
"""Add information from add_dct to a new copy of namedtuples stored in nts."""
nts = []
assert len(add_dct) == len(self.nts)
flds = list(next(iter(self.nts))._fields) + list(next(iter(add_dct)).keys())
ntobj = cx.namedtuple("ntgoea", " ".join(flds))
for dct_new, ntgoea in zip(add_dct, self.nts):
dct_curr = ntgoea._asdict()
for key, val in dct_new.items():
dct_curr[key] = val
nts.append(ntobj(**dct_curr))
return nts | [
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tanghaibao/goatools | goatools/rpt/nts_xfrm.py | MgrNts.add_f2str | def add_f2str(self, dcts, srcfld, dstfld, dstfmt):
"""Add a namedtuple field of type string generated from an existing namedtuple field."""
# Example: f2str = objntmgr.add_f2str(dcts, "p_fdr_bh", "s_fdr_bh", "{:8.2e}")
# ntobj = self.get_ntobj()
# print(ntobj)
assert len(dcts) == len(self.nts)
for dct, ntgoea in zip(dcts, self.nts):
valorig = getattr(ntgoea, srcfld)
valstr = dstfmt.format(valorig)
dct[dstfld] = valstr | python | def add_f2str(self, dcts, srcfld, dstfld, dstfmt):
"""Add a namedtuple field of type string generated from an existing namedtuple field."""
# Example: f2str = objntmgr.add_f2str(dcts, "p_fdr_bh", "s_fdr_bh", "{:8.2e}")
# ntobj = self.get_ntobj()
# print(ntobj)
assert len(dcts) == len(self.nts)
for dct, ntgoea in zip(dcts, self.nts):
valorig = getattr(ntgoea, srcfld)
valstr = dstfmt.format(valorig)
dct[dstfld] = valstr | [
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tanghaibao/goatools | goatools/rpt/nts_xfrm.py | MgrNts.get_ntobj | def get_ntobj(self):
"""Create namedtuple object with GOEA fields."""
if self.nts:
return cx.namedtuple("ntgoea", " ".join(vars(next(iter(self.nts))).keys())) | python | def get_ntobj(self):
"""Create namedtuple object with GOEA fields."""
if self.nts:
return cx.namedtuple("ntgoea", " ".join(vars(next(iter(self.nts))).keys())) | [
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tanghaibao/goatools | goatools/semantic.py | get_info_content | def get_info_content(go_id, termcounts):
'''
Calculates the information content of a GO term.
'''
# Get the observed frequency of the GO term
freq = termcounts.get_term_freq(go_id)
# Calculate the information content (i.e., -log("freq of GO term")
return -1.0 * math.log(freq) if freq else 0 | python | def get_info_content(go_id, termcounts):
'''
Calculates the information content of a GO term.
'''
# Get the observed frequency of the GO term
freq = termcounts.get_term_freq(go_id)
# Calculate the information content (i.e., -log("freq of GO term")
return -1.0 * math.log(freq) if freq else 0 | [
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tanghaibao/goatools | goatools/semantic.py | resnik_sim | def resnik_sim(go_id1, go_id2, godag, termcounts):
'''
Computes Resnik's similarity measure.
'''
goterm1 = godag[go_id1]
goterm2 = godag[go_id2]
if goterm1.namespace == goterm2.namespace:
msca_goid = deepest_common_ancestor([go_id1, go_id2], godag)
return get_info_content(msca_goid, termcounts) | python | def resnik_sim(go_id1, go_id2, godag, termcounts):
'''
Computes Resnik's similarity measure.
'''
goterm1 = godag[go_id1]
goterm2 = godag[go_id2]
if goterm1.namespace == goterm2.namespace:
msca_goid = deepest_common_ancestor([go_id1, go_id2], godag)
return get_info_content(msca_goid, termcounts) | [
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tanghaibao/goatools | goatools/semantic.py | lin_sim | def lin_sim(goid1, goid2, godag, termcnts):
'''
Computes Lin's similarity measure.
'''
sim_r = resnik_sim(goid1, goid2, godag, termcnts)
return lin_sim_calc(goid1, goid2, sim_r, termcnts) | python | def lin_sim(goid1, goid2, godag, termcnts):
'''
Computes Lin's similarity measure.
'''
sim_r = resnik_sim(goid1, goid2, godag, termcnts)
return lin_sim_calc(goid1, goid2, sim_r, termcnts) | [
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tanghaibao/goatools | goatools/semantic.py | lin_sim_calc | def lin_sim_calc(goid1, goid2, sim_r, termcnts):
'''
Computes Lin's similarity measure using pre-calculated Resnik's similarities.
'''
if sim_r is not None:
info = get_info_content(goid1, termcnts) + get_info_content(goid2, termcnts)
if info != 0:
return (2*sim_r)/info | python | def lin_sim_calc(goid1, goid2, sim_r, termcnts):
'''
Computes Lin's similarity measure using pre-calculated Resnik's similarities.
'''
if sim_r is not None:
info = get_info_content(goid1, termcnts) + get_info_content(goid2, termcnts)
if info != 0:
return (2*sim_r)/info | [
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tanghaibao/goatools | goatools/semantic.py | common_parent_go_ids | def common_parent_go_ids(goids, godag):
'''
This function finds the common ancestors in the GO
tree of the list of goids in the input.
'''
# Find candidates from first
rec = godag[goids[0]]
candidates = rec.get_all_parents()
candidates.update({goids[0]})
# Find intersection with second to nth goid
for goid in goids[1:]:
rec = godag[goid]
parents = rec.get_all_parents()
parents.update({goid})
# Find the intersection with the candidates, and update.
candidates.intersection_update(parents)
return candidates | python | def common_parent_go_ids(goids, godag):
'''
This function finds the common ancestors in the GO
tree of the list of goids in the input.
'''
# Find candidates from first
rec = godag[goids[0]]
candidates = rec.get_all_parents()
candidates.update({goids[0]})
# Find intersection with second to nth goid
for goid in goids[1:]:
rec = godag[goid]
parents = rec.get_all_parents()
parents.update({goid})
# Find the intersection with the candidates, and update.
candidates.intersection_update(parents)
return candidates | [
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tanghaibao/goatools | goatools/semantic.py | deepest_common_ancestor | def deepest_common_ancestor(goterms, godag):
'''
This function gets the nearest common ancestor
using the above function.
Only returns single most specific - assumes unique exists.
'''
# Take the element at maximum depth.
return max(common_parent_go_ids(goterms, godag), key=lambda t: godag[t].depth) | python | def deepest_common_ancestor(goterms, godag):
'''
This function gets the nearest common ancestor
using the above function.
Only returns single most specific - assumes unique exists.
'''
# Take the element at maximum depth.
return max(common_parent_go_ids(goterms, godag), key=lambda t: godag[t].depth) | [
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tanghaibao/goatools | goatools/semantic.py | min_branch_length | def min_branch_length(go_id1, go_id2, godag, branch_dist):
'''
Finds the minimum branch length between two terms in the GO DAG.
'''
# First get the deepest common ancestor
goterm1 = godag[go_id1]
goterm2 = godag[go_id2]
if goterm1.namespace == goterm2.namespace:
dca = deepest_common_ancestor([go_id1, go_id2], godag)
# Then get the distance from the DCA to each term
dca_depth = godag[dca].depth
depth1 = goterm1.depth - dca_depth
depth2 = goterm2.depth - dca_depth
# Return the total distance - i.e., to the deepest common ancestor and back.
return depth1 + depth2
elif branch_dist is not None:
return goterm1.depth + goterm2.depth + branch_dist | python | def min_branch_length(go_id1, go_id2, godag, branch_dist):
'''
Finds the minimum branch length between two terms in the GO DAG.
'''
# First get the deepest common ancestor
goterm1 = godag[go_id1]
goterm2 = godag[go_id2]
if goterm1.namespace == goterm2.namespace:
dca = deepest_common_ancestor([go_id1, go_id2], godag)
# Then get the distance from the DCA to each term
dca_depth = godag[dca].depth
depth1 = goterm1.depth - dca_depth
depth2 = goterm2.depth - dca_depth
# Return the total distance - i.e., to the deepest common ancestor and back.
return depth1 + depth2
elif branch_dist is not None:
return goterm1.depth + goterm2.depth + branch_dist | [
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tanghaibao/goatools | goatools/semantic.py | TermCounts._init_count_terms | def _init_count_terms(self, annots):
'''
Fills in the counts and overall aspect counts.
'''
gonotindag = set()
gocnts = self.gocnts
go2obj = self.go2obj
# Fill gocnts with GO IDs in annotations and their corresponding counts
for terms in annots.values(): # key is 'gene'
# Make a union of all the terms for a gene, if term parents are
# propagated but they won't get double-counted for the gene
allterms = set()
for go_id in terms:
goobj = go2obj.get(go_id, None)
if goobj is not None:
allterms.add(go_id)
allterms |= goobj.get_all_parents()
else:
gonotindag.add(go_id)
for parent in allterms:
gocnts[parent] += 1
if gonotindag:
print("{N} Assc. GO IDs not found in the GODag\n".format(N=len(gonotindag))) | python | def _init_count_terms(self, annots):
'''
Fills in the counts and overall aspect counts.
'''
gonotindag = set()
gocnts = self.gocnts
go2obj = self.go2obj
# Fill gocnts with GO IDs in annotations and their corresponding counts
for terms in annots.values(): # key is 'gene'
# Make a union of all the terms for a gene, if term parents are
# propagated but they won't get double-counted for the gene
allterms = set()
for go_id in terms:
goobj = go2obj.get(go_id, None)
if goobj is not None:
allterms.add(go_id)
allterms |= goobj.get_all_parents()
else:
gonotindag.add(go_id)
for parent in allterms:
gocnts[parent] += 1
if gonotindag:
print("{N} Assc. GO IDs not found in the GODag\n".format(N=len(gonotindag))) | [
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tanghaibao/goatools | goatools/semantic.py | TermCounts._init_add_goid_alt | def _init_add_goid_alt(self):
'''
Add alternate GO IDs to term counts.
'''
# Fill aspect_counts. Find alternate GO IDs that may not be on gocnts
goid_alts = set()
go2cnt_add = {}
aspect_counts = self.aspect_counts
gocnts = self.gocnts
go2obj = self.go2obj
for go_id, cnt in gocnts.items():
goobj = go2obj[go_id]
assert cnt, "NO TERM COUNTS FOR {GO}".format(GO=goobj.item_id)
# Was the count set using an alternate GO?
if go_id != goobj.item_id:
go2cnt_add[goobj.item_id] = cnt
goid_alts |= goobj.alt_ids
# Group by namespace
aspect_counts[goobj.namespace] += cnt
# If alternate GO used to set count, add main GO ID
for goid, cnt in go2cnt_add.items():
gocnts[goid] = cnt
# Add missing alt GO IDs to gocnts
for alt_goid in goid_alts.difference(gocnts):
goobj = go2obj[alt_goid]
cnt = gocnts[goobj.item_id]
assert cnt, "NO TERM COUNTS FOR ALT_ID({GOa}) ID({GO}): {NAME}".format(
GOa=alt_goid, GO=goobj.item_id, NAME=goobj.name)
gocnts[alt_goid] = cnt | python | def _init_add_goid_alt(self):
'''
Add alternate GO IDs to term counts.
'''
# Fill aspect_counts. Find alternate GO IDs that may not be on gocnts
goid_alts = set()
go2cnt_add = {}
aspect_counts = self.aspect_counts
gocnts = self.gocnts
go2obj = self.go2obj
for go_id, cnt in gocnts.items():
goobj = go2obj[go_id]
assert cnt, "NO TERM COUNTS FOR {GO}".format(GO=goobj.item_id)
# Was the count set using an alternate GO?
if go_id != goobj.item_id:
go2cnt_add[goobj.item_id] = cnt
goid_alts |= goobj.alt_ids
# Group by namespace
aspect_counts[goobj.namespace] += cnt
# If alternate GO used to set count, add main GO ID
for goid, cnt in go2cnt_add.items():
gocnts[goid] = cnt
# Add missing alt GO IDs to gocnts
for alt_goid in goid_alts.difference(gocnts):
goobj = go2obj[alt_goid]
cnt = gocnts[goobj.item_id]
assert cnt, "NO TERM COUNTS FOR ALT_ID({GOa}) ID({GO}): {NAME}".format(
GOa=alt_goid, GO=goobj.item_id, NAME=goobj.name)
gocnts[alt_goid] = cnt | [
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tanghaibao/goatools | goatools/semantic.py | TermCounts.get_term_freq | def get_term_freq(self, go_id):
'''
Returns the frequency at which a particular GO term has
been observed in the annotations.
'''
num_ns = float(self.get_total_count(self.go2obj[go_id].namespace))
return float(self.get_count(go_id))/num_ns if num_ns != 0 else 0 | python | def get_term_freq(self, go_id):
'''
Returns the frequency at which a particular GO term has
been observed in the annotations.
'''
num_ns = float(self.get_total_count(self.go2obj[go_id].namespace))
return float(self.get_count(go_id))/num_ns if num_ns != 0 else 0 | [
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tanghaibao/goatools | goatools/grouper/hdrgos.py | HdrgosSections.get_sections | def get_sections(self, hdrgo, dflt_section=True):
"""Given a header GO, return the sections that contain it."""
dflt_list = []
# If the hdrgo is not in a section, return the default name for a section
if dflt_section:
dflt_list = [self.secdflt]
return self.hdrgo2sections.get(hdrgo, dflt_list) | python | def get_sections(self, hdrgo, dflt_section=True):
"""Given a header GO, return the sections that contain it."""
dflt_list = []
# If the hdrgo is not in a section, return the default name for a section
if dflt_section:
dflt_list = [self.secdflt]
return self.hdrgo2sections.get(hdrgo, dflt_list) | [
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tanghaibao/goatools | goatools/grouper/hdrgos.py | HdrgosSections.get_section_hdrgos | def get_section_hdrgos(self):
"""Get the GO group headers explicitly listed in sections."""
return set([h for _, hs in self.sections for h in hs]) if self.sections else set() | python | def get_section_hdrgos(self):
"""Get the GO group headers explicitly listed in sections."""
return set([h for _, hs in self.sections for h in hs]) if self.sections else set() | [
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tanghaibao/goatools | goatools/grouper/hdrgos.py | HdrgosSections._chk_sections | def _chk_sections(sections):
"""Check format of user-provided 'sections' variable"""
if sections:
assert len(sections[0]) == 2, \
"SECTIONS DATA MUST BE A 2-D LIST. FOUND: {S}".format(S=sections)
for _, hdrgos in sections:
chk_goids(hdrgos, "HdrgosSections::_chk_sections()") | python | def _chk_sections(sections):
"""Check format of user-provided 'sections' variable"""
if sections:
assert len(sections[0]) == 2, \
"SECTIONS DATA MUST BE A 2-D LIST. FOUND: {S}".format(S=sections)
for _, hdrgos in sections:
chk_goids(hdrgos, "HdrgosSections::_chk_sections()") | [
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tanghaibao/goatools | goatools/grouper/hdrgos.py | HdrgosSections._init_hdrgos | def _init_hdrgos(self, hdrgos_dflt, hdrgos_usr=None, add_dflt=True):
"""Initialize GO high"""
# Use default GO group header values
if (hdrgos_usr is None or hdrgos_usr is False) and not self.sections:
return set(hdrgos_dflt)
# Get GO group headers provided by user
hdrgos_init = set()
if hdrgos_usr:
chk_goids(hdrgos_usr, "User-provided GO group headers")
hdrgos_init |= set(hdrgos_usr)
if self.sections:
self._chk_sections(self.sections)
hdrgos_sec = set([hg for _, hdrgos in self.sections for hg in hdrgos])
chk_goids(hdrgos_sec, "User-provided GO group headers in sections")
hdrgos_init |= hdrgos_sec
# Add default depth-01 GOs to headers, if desired
if add_dflt:
return set(hdrgos_init).union(hdrgos_dflt)
# Return user-provided GO grouping headers
return hdrgos_init | python | def _init_hdrgos(self, hdrgos_dflt, hdrgos_usr=None, add_dflt=True):
"""Initialize GO high"""
# Use default GO group header values
if (hdrgos_usr is None or hdrgos_usr is False) and not self.sections:
return set(hdrgos_dflt)
# Get GO group headers provided by user
hdrgos_init = set()
if hdrgos_usr:
chk_goids(hdrgos_usr, "User-provided GO group headers")
hdrgos_init |= set(hdrgos_usr)
if self.sections:
self._chk_sections(self.sections)
hdrgos_sec = set([hg for _, hdrgos in self.sections for hg in hdrgos])
chk_goids(hdrgos_sec, "User-provided GO group headers in sections")
hdrgos_init |= hdrgos_sec
# Add default depth-01 GOs to headers, if desired
if add_dflt:
return set(hdrgos_init).union(hdrgos_dflt)
# Return user-provided GO grouping headers
return hdrgos_init | [
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tanghaibao/goatools | goatools/obo_tasks.py | get_all_parents | def get_all_parents(go_objs):
"""Return a set containing all GO Term parents of multiple GOTerm objects."""
go_parents = set()
for go_obj in go_objs:
go_parents |= go_obj.get_all_parents()
return go_parents | python | def get_all_parents(go_objs):
"""Return a set containing all GO Term parents of multiple GOTerm objects."""
go_parents = set()
for go_obj in go_objs:
go_parents |= go_obj.get_all_parents()
return go_parents | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe.prt_hdr | def prt_hdr(self, prt=sys.stdout, name="name "):
"""Print stats header in markdown style."""
hdr = "{NAME} | # {ITEMS:11} | range | 25th percentile | " \
" median | 75th percentile | mean | stddev\n".format(NAME=name, ITEMS=self.desc)
div = "{DASHES}|---------------|----------------------|" \
"-----------------|----------|-----------------|----------|-------\n".format(
DASHES='-'*(len(name)))
prt.write(hdr)
prt.write(div) | python | def prt_hdr(self, prt=sys.stdout, name="name "):
"""Print stats header in markdown style."""
hdr = "{NAME} | # {ITEMS:11} | range | 25th percentile | " \
" median | 75th percentile | mean | stddev\n".format(NAME=name, ITEMS=self.desc)
div = "{DASHES}|---------------|----------------------|" \
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DASHES='-'*(len(name)))
prt.write(hdr)
prt.write(div) | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe.prt_data | def prt_data(self, name, vals, prt=sys.stdout):
"""Print stats data in markdown style."""
fld2val = self.get_fld2val(name, vals)
prt.write(self.fmt.format(**fld2val))
return fld2val | python | def prt_data(self, name, vals, prt=sys.stdout):
"""Print stats data in markdown style."""
fld2val = self.get_fld2val(name, vals)
prt.write(self.fmt.format(**fld2val))
return fld2val | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe.getstr_data | def getstr_data(self, name, vals):
"""Return stats data string in markdown style."""
fld2val = self.get_fld2val(name, vals)
return self.fmt.format(**fld2val) | python | def getstr_data(self, name, vals):
"""Return stats data string in markdown style."""
fld2val = self.get_fld2val(name, vals)
return self.fmt.format(**fld2val) | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe.get_fld2val | def get_fld2val(self, name, vals):
"""Describe summary statistics for a list of numbers."""
if vals:
return self._init_fld2val_stats(name, vals)
return self._init_fld2val_null(name) | python | def get_fld2val(self, name, vals):
"""Describe summary statistics for a list of numbers."""
if vals:
return self._init_fld2val_stats(name, vals)
return self._init_fld2val_null(name) | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe._init_fld2val_stats | def _init_fld2val_stats(self, name, vals):
"""Return statistics on values."""
vals_stats = stats.describe(vals)
stddev = math.sqrt(vals_stats[3]) # stats variance
p25 = np.percentile(vals, 25)
p50 = np.percentile(vals, 50) # median
p75 = np.percentile(vals, 75)
fld2val = {
'name':name,
'qty'.format(ITEMS=self.desc):vals_stats[0], # stats nobs
'range':self._get_str_range(vals_stats),
'25th percentile':p25,
'median':p50,
'75th percentile':p75,
'mean':vals_stats[2], # stats mean
'stddev':stddev}
fmtflds = set(['25th percentile', 'median', '75th percentile', 'mean', 'stddev'])
mkint = "," in self.fmtstr
for key, val in fld2val.items():
if key in fmtflds:
if mkint:
val = int(round(val))
fld2val[key] = self.fmtstr.format(val)
return fld2val | python | def _init_fld2val_stats(self, name, vals):
"""Return statistics on values."""
vals_stats = stats.describe(vals)
stddev = math.sqrt(vals_stats[3]) # stats variance
p25 = np.percentile(vals, 25)
p50 = np.percentile(vals, 50) # median
p75 = np.percentile(vals, 75)
fld2val = {
'name':name,
'qty'.format(ITEMS=self.desc):vals_stats[0], # stats nobs
'range':self._get_str_range(vals_stats),
'25th percentile':p25,
'median':p50,
'75th percentile':p75,
'mean':vals_stats[2], # stats mean
'stddev':stddev}
fmtflds = set(['25th percentile', 'median', '75th percentile', 'mean', 'stddev'])
mkint = "," in self.fmtstr
for key, val in fld2val.items():
if key in fmtflds:
if mkint:
val = int(round(val))
fld2val[key] = self.fmtstr.format(val)
return fld2val | [
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tanghaibao/goatools | goatools/statsdescribe.py | StatsDescribe._get_str_range | def _get_str_range(self, vals_stats):
"""Return a string containing the range of values."""
minmax = vals_stats[1] # stats minmax
minval = self.fmtstr.format(minmax[0])
maxval = self.fmtstr.format(minmax[1])
return '{A} to {B:6>}'.format(A=minval, B=maxval) | python | def _get_str_range(self, vals_stats):
"""Return a string containing the range of values."""
minmax = vals_stats[1] # stats minmax
minval = self.fmtstr.format(minmax[0])
maxval = self.fmtstr.format(minmax[1])
return '{A} to {B:6>}'.format(A=minval, B=maxval) | [
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tanghaibao/goatools | goatools/grouper/tasks.py | SummarySec2dHdrGos.summarize_sec2hdrgos | def summarize_sec2hdrgos(self, sec2d_hdrgos):
"""Get counts of header GO IDs and sections."""
hdrgos_all = set([])
hdrgos_grouped = set()
hdrgos_ungrouped = set()
sections_grouped = set()
for sectionname, hdrgos in sec2d_hdrgos:
self._chk_hdrgoids(hdrgos)
hdrgos_all.update(hdrgos)
if sectionname != HdrgosSections.secdflt:
hdrgos_grouped.update(hdrgos)
sections_grouped.add(sectionname)
else:
hdrgos_ungrouped.update(hdrgos)
return {'G': hdrgos_grouped,
'S': sections_grouped,
'U': hdrgos_all.difference(hdrgos_grouped)} | python | def summarize_sec2hdrgos(self, sec2d_hdrgos):
"""Get counts of header GO IDs and sections."""
hdrgos_all = set([])
hdrgos_grouped = set()
hdrgos_ungrouped = set()
sections_grouped = set()
for sectionname, hdrgos in sec2d_hdrgos:
self._chk_hdrgoids(hdrgos)
hdrgos_all.update(hdrgos)
if sectionname != HdrgosSections.secdflt:
hdrgos_grouped.update(hdrgos)
sections_grouped.add(sectionname)
else:
hdrgos_ungrouped.update(hdrgos)
return {'G': hdrgos_grouped,
'S': sections_grouped,
'U': hdrgos_all.difference(hdrgos_grouped)} | [
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tanghaibao/goatools | goatools/grouper/tasks.py | SummarySec2dHdrGos.summarize_sec2hdrnts | def summarize_sec2hdrnts(self, sec2d_hdrnts):
"""Given namedtuples in each sectin, get counts of header GO IDs and sections."""
sec2d_hdrgos = [(s, set(nt.GO for nt in nts)) for s, nts in sec2d_hdrnts]
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"""Given namedtuples in each sectin, get counts of header GO IDs and sections."""
sec2d_hdrgos = [(s, set(nt.GO for nt in nts)) for s, nts in sec2d_hdrnts]
return self.summarize_sec2hdrgos(sec2d_hdrgos) | [
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tanghaibao/goatools | goatools/grouper/tasks.py | SummarySec2dHdrGos._chk_hdrgoids | def _chk_hdrgoids(hdrgos):
"""Check that hdrgo set is a set of GO IDs."""
goid = next(iter(hdrgos))
if isinstance(goid, str) and goid[:3] == "GO:":
return
assert False, "HDRGOS DO NOT CONTAIN GO IDs: {E}".format(E=goid) | python | def _chk_hdrgoids(hdrgos):
"""Check that hdrgo set is a set of GO IDs."""
goid = next(iter(hdrgos))
if isinstance(goid, str) and goid[:3] == "GO:":
return
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tanghaibao/goatools | goatools/go_search.py | GoSearch.get_matching_gos | def get_matching_gos(self, compiled_pattern, **kws):
"""Return all GOs which match the user regex pattern."""
# kws: prt gos
matching_gos = []
obo_dag = self.obo_dag
prt = kws['prt'] if 'prt' in kws else self.log
prt.write('\nPATTERN SEARCH: "{P}"\n'.format(P=compiled_pattern.pattern))
# Only look through GOs in annotation or user-specified GOs
srchgos = kws['gos'] if 'gos' in kws else self.go2items.keys()
for go_id in srchgos:
go_obj = obo_dag.get(go_id, None)
if go_obj is not None:
for hdr in self.goa_srch_hdrs:
if hdr in go_obj.__dict__:
fld_val = getattr(go_obj, hdr)
matches = self._search_vals(compiled_pattern, fld_val)
for mtch in matches:
prt.write("MATCH {go_id}({NAME}) {FLD}: {M}\n".format(
FLD=hdr, go_id=go_obj.id, NAME=go_obj.name, M=mtch))
if matches:
matching_gos.append(go_id)
else:
prt.write("**WARNING: {GO} found in annotation is not found in obo\n".format(
GO=go_id))
matching_gos = set(matching_gos)
# Print summary message
self._summary_matching_gos(prt, compiled_pattern.pattern, matching_gos, srchgos)
return matching_gos | python | def get_matching_gos(self, compiled_pattern, **kws):
"""Return all GOs which match the user regex pattern."""
# kws: prt gos
matching_gos = []
obo_dag = self.obo_dag
prt = kws['prt'] if 'prt' in kws else self.log
prt.write('\nPATTERN SEARCH: "{P}"\n'.format(P=compiled_pattern.pattern))
# Only look through GOs in annotation or user-specified GOs
srchgos = kws['gos'] if 'gos' in kws else self.go2items.keys()
for go_id in srchgos:
go_obj = obo_dag.get(go_id, None)
if go_obj is not None:
for hdr in self.goa_srch_hdrs:
if hdr in go_obj.__dict__:
fld_val = getattr(go_obj, hdr)
matches = self._search_vals(compiled_pattern, fld_val)
for mtch in matches:
prt.write("MATCH {go_id}({NAME}) {FLD}: {M}\n".format(
FLD=hdr, go_id=go_obj.id, NAME=go_obj.name, M=mtch))
if matches:
matching_gos.append(go_id)
else:
prt.write("**WARNING: {GO} found in annotation is not found in obo\n".format(
GO=go_id))
matching_gos = set(matching_gos)
# Print summary message
self._summary_matching_gos(prt, compiled_pattern.pattern, matching_gos, srchgos)
return matching_gos | [
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tanghaibao/goatools | goatools/go_search.py | GoSearch._summary_matching_gos | def _summary_matching_gos(prt, pattern, matching_gos, all_gos):
"""Print summary for get_matching_gos."""
msg = 'Found {N} GO(s) out of {M} matching pattern("{P}")\n'
num_gos = len(matching_gos)
num_all = len(all_gos)
prt.write(msg.format(N=num_gos, M=num_all, P=pattern)) | python | def _summary_matching_gos(prt, pattern, matching_gos, all_gos):
"""Print summary for get_matching_gos."""
msg = 'Found {N} GO(s) out of {M} matching pattern("{P}")\n'
num_gos = len(matching_gos)
num_all = len(all_gos)
prt.write(msg.format(N=num_gos, M=num_all, P=pattern)) | [
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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):
"""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 | [
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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):
"""Search for user-regex in scalar data values."""
mtch = compiled_pattern.search(fld_val)
if mtch:
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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):
"""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) | [
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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):
"""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) | [
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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(
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"""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(
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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):
"""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:
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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:
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go2color[goid] = color_dflt
return go2color | python | 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:
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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):
"""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()))
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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):
"""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) | [
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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):
"""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) | [
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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):
"""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
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return cnts | [
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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):
"""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 | [
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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():
"""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) | [
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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):
"""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)) | [
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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):
"""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 | [
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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):
"""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) | [
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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):
"""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) | [
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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):
"""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 | [
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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):
"""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) | [
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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):
"""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) | [
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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):
"""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') | [
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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):
"""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 | [
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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):
"""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 | [
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tanghaibao/goatools | goatools/cli/find_enrichment.py | GoeaCliFnc.rd_files | def rd_files(self, study_fn, pop_fn):
"""Read files and return study and population."""
study, pop = self._read_geneset(study_fn, pop_fn)
print("Study: {0} vs. Population {1}\n".format(len(study), len(pop)))
return study, pop | python | def rd_files(self, study_fn, pop_fn):
"""Read files and return study and population."""
study, pop = self._read_geneset(study_fn, pop_fn)
print("Study: {0} vs. Population {1}\n".format(len(study), len(pop)))
return study, pop | [
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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):
"""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 | [
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tanghaibao/goatools | goatools/cli/find_enrichment.py | GroupItems.get_objgrpwr | def get_objgrpwr(self, goea_results):
"""Get a GrpWr object to write grouped GOEA results."""
sortobj = self.get_sortobj(goea_results)
return GrpWr(sortobj, self.pval_fld, ver_list=self.ver_list) | python | def get_objgrpwr(self, goea_results):
"""Get a GrpWr object to write grouped GOEA results."""
sortobj = self.get_sortobj(goea_results)
return GrpWr(sortobj, self.pval_fld, ver_list=self.ver_list) | [
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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):
"""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 | [
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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):
"""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) | [
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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):
"""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) | [
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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):
"""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)) | [
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tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.wr_txt | def wr_txt(self, fout_txt):
"""Write to a file GOEA results in an ASCII text format."""
with open(fout_txt, 'w') as prt:
for line in self.ver_list:
prt.write("{LINE}\n".format(LINE=line))
self.prt_txt(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt)) | python | def wr_txt(self, fout_txt):
"""Write to a file GOEA results in an ASCII text format."""
with open(fout_txt, 'w') as prt:
for line in self.ver_list:
prt.write("{LINE}\n".format(LINE=line))
self.prt_txt(prt)
print(" WROTE: {TXT}".format(TXT=fout_txt)) | [
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tanghaibao/goatools | goatools/cli/find_enrichment.py | GrpWr.prt_tsv | def prt_tsv(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
WrSectionsTxt.prt_sections(prt, self.desc2nts['sections'], prtfmt, secspc=True) | python | def prt_tsv(self, prt=sys.stdout):
"""Print an ASCII text format."""
prtfmt = self.objprt.get_prtfmt_str(self.flds_cur)
prt.write("{FLDS}\n".format(FLDS=" ".join(self.flds_cur)))
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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):
"""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 | [
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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):
"""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 | [
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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):
"""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 | [
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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"_$", r"", line)
hdrs = re.split(self.sep, line)
if '' in hdrs:
hdrs = NCBIgeneFileReader.replace_nulls(hdrs)
# Init indexes which will be converted to int or float
self.idxs_int = [idx for idx, hdr in enumerate(hdrs) if hdr in self.int_hdrs]
self.idxs_float = [idx for idx, hdr in enumerate(hdrs) if hdr in self.float_hdrs]
assert hdrs[6] == 'Aliases'
return namedtuple('ntncbi', ' '.join(hdrs)) | python | def _init_nt_hdr(self, line):
"""Convert headers into valid namedtuple fields."""
line = line.replace('.', '_')
line = line.replace(' ', '_')
line = line.replace('#', 'N')
line = line.replace('-', '_')
line = line.replace('"', '')
#line = re.sub(r"_$", 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)) | [
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tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader.replace_nulls | def replace_nulls(hdrs):
"""Replace '' in hdrs."""
ret = []
idx = 0
for hdr in hdrs:
if hdr == '':
ret.append("no_hdr{}".format(idx))
else:
ret.append(hdr)
return ret | python | def replace_nulls(hdrs):
"""Replace '' in hdrs."""
ret = []
idx = 0
for hdr in hdrs:
if hdr == '':
ret.append("no_hdr{}".format(idx))
else:
ret.append(hdr)
return ret | [
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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):
"""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)) | [
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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):
"""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]) | [
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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):
"""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 | [
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tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_float | def _init_idxs_float(self, usr_hdrs):
"""List of indexes whose values will be floats."""
self.idxs_float = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.float_hdrs] | python | def _init_idxs_float(self, usr_hdrs):
"""List of indexes whose values will be floats."""
self.idxs_float = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.float_hdrs] | [
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tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_int | def _init_idxs_int(self, usr_hdrs):
"""List of indexes whose values will be ints."""
self.idxs_int = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.int_hdrs] | python | def _init_idxs_int(self, usr_hdrs):
"""List of indexes whose values will be ints."""
self.idxs_int = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in self.int_hdrs] | [
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tanghaibao/goatools | goatools/parsers/ncbi_gene_file_reader.py | NCBIgeneFileReader._init_idxs_strpat | def _init_idxs_strpat(self, usr_hdrs):
"""List of indexes whose values will be strings."""
strpat = self.strpat_hdrs.keys()
self.idxs_strpat = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in strpat] | python | def _init_idxs_strpat(self, usr_hdrs):
"""List of indexes whose values will be strings."""
strpat = self.strpat_hdrs.keys()
self.idxs_strpat = [
Idx for Hdr, Idx in self.hdr2idx.items() if Hdr in usr_hdrs and Hdr in strpat] | [
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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):
"""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 | [
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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):
"""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)) | [
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tanghaibao/goatools | goatools/gosubdag/go_tasks.py | get_goobjs_altgo2goobj | def get_goobjs_altgo2goobj(go2obj):
"""Separate alt GO IDs and key GO IDs."""
goobjs = set()
altgo2goobj = {}
for goid, goobj in go2obj.items():
goobjs.add(goobj)
if goid != goobj.id:
altgo2goobj[goid] = goobj
return goobjs, altgo2goobj | python | def get_goobjs_altgo2goobj(go2obj):
"""Separate alt GO IDs and key GO IDs."""
goobjs = set()
altgo2goobj = {}
for goid, goobj in go2obj.items():
goobjs.add(goobj)
if goid != goobj.id:
altgo2goobj[goid] = goobj
return goobjs, altgo2goobj | [
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tanghaibao/goatools | goatools/gosubdag/go_tasks.py | add_alt_goids | def add_alt_goids(go2values, altgo2goobj):
"""Add alternate source GO IDs."""
for goobj_key in altgo2goobj.values():
values_curr = go2values[goobj_key.id]
for goid_alt in goobj_key.alt_ids:
go2values[goid_alt] = values_curr
return go2values | python | def add_alt_goids(go2values, altgo2goobj):
"""Add alternate source GO IDs."""
for goobj_key in altgo2goobj.values():
values_curr = go2values[goobj_key.id]
for goid_alt in goobj_key.alt_ids:
go2values[goid_alt] = values_curr
return go2values | [
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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):
"""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 | [
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tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_altgoids | def fill_altgoids(go2obj):
"""Given a go2obj containing key GO IDs, fill with all alternate GO IDs."""
alt2obj = {altgo:goobj for goobj in go2obj.values() for altgo in goobj.alt_ids}
for goid, goobj in alt2obj.items():
go2obj[goid] = goobj | python | def fill_altgoids(go2obj):
"""Given a go2obj containing key GO IDs, fill with all alternate GO IDs."""
alt2obj = {altgo:goobj for goobj in go2obj.values() for altgo in goobj.alt_ids}
for goid, goobj in alt2obj.items():
go2obj[goid] = goobj | [
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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):
"""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) | [
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tanghaibao/goatools | goatools/gosubdag/go_tasks.py | fill_childgoid2obj | def fill_childgoid2obj(childgoid2obj, parent_obj):
"""Fill childgoid2obj with all child key GO IDs and their objects."""
for child_obj in parent_obj.children:
if child_obj.id not in childgoid2obj:
childgoid2obj[child_obj.id] = child_obj
fill_childgoid2obj(childgoid2obj, child_obj) | python | def fill_childgoid2obj(childgoid2obj, parent_obj):
"""Fill childgoid2obj with all child key GO IDs and their objects."""
for child_obj in parent_obj.children:
if child_obj.id not in childgoid2obj:
childgoid2obj[child_obj.id] = child_obj
fill_childgoid2obj(childgoid2obj, child_obj) | [
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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):
"""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) | [
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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):
"""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 | [
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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):
"""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) | [
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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):
"""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)) | [
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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):
"""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 | [
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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):
"""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) | [
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tanghaibao/goatools | goatools/grouper/read_goids.py | ReadGoids._rpt_unused_sections | def _rpt_unused_sections(self, prt):
"""Report unused sections."""
sections_unused = set(self.sections_seen).difference(self.section2goids.keys())
for sec in sections_unused:
prt.write(" UNUSED SECTION: {SEC}\n".format(SEC=sec)) | python | def _rpt_unused_sections(self, prt):
"""Report unused sections."""
sections_unused = set(self.sections_seen).difference(self.section2goids.keys())
for sec in sections_unused:
prt.write(" UNUSED SECTION: {SEC}\n".format(SEC=sec)) | [
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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):
"""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)) | [
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tanghaibao/goatools | goatools/gosubdag/go_edges.py | EdgesBase.rm_gos | def rm_gos(self, rm_goids):
"""Remove any edges that contain user-specified edges."""
self.edges = self._rm_gos_edges(rm_goids, self.edges)
self.edges_rel = self._rm_gos_edges_rel(rm_goids, self.edges_rel) | python | def rm_gos(self, rm_goids):
"""Remove any edges that contain user-specified edges."""
self.edges = self._rm_gos_edges(rm_goids, self.edges)
self.edges_rel = self._rm_gos_edges_rel(rm_goids, self.edges_rel) | [
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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):
"""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 | [
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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):
"""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 | [
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