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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | _Init.get_sec2gos | def get_sec2gos(sortobj):
"""Initialize section_name2goids."""
sec_gos = []
for section_name, nts in sortobj.get_desc2nts_fnc(hdrgo_prt=True)['sections']:
sec_gos.append((section_name, set(nt.GO for nt in nts)))
return cx.OrderedDict(sec_gos) | python | def get_sec2gos(sortobj):
"""Initialize section_name2goids."""
sec_gos = []
for section_name, nts in sortobj.get_desc2nts_fnc(hdrgo_prt=True)['sections']:
sec_gos.append((section_name, set(nt.GO for nt in nts)))
return cx.OrderedDict(sec_gos) | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | _Init.get_gene2gos | def get_gene2gos(go2nt):
"""Create a gene product to GO set dict."""
gene2gos = cx.defaultdict(set)
nt0 = next(iter(go2nt.values()))
b_str = isinstance(nt0.study_items, str)
# print("NNNNTTTT", nt0)
for goid, ntgo in go2nt.items():
study_items = ntgo.study_items.split(', ') if b_str else ntgo.study_items
for geneid in study_items:
gene2gos[geneid].add(goid)
if b_str:
b_set = set(isinstance(g.isdigit(), int) for g in nt0.study_items.split(', '))
if b_set == set([True]):
return {int(g):gos for g, gos in gene2gos.items()}
return {g:gos for g, gos in gene2gos.items()} | python | def get_gene2gos(go2nt):
"""Create a gene product to GO set dict."""
gene2gos = cx.defaultdict(set)
nt0 = next(iter(go2nt.values()))
b_str = isinstance(nt0.study_items, str)
# print("NNNNTTTT", nt0)
for goid, ntgo in go2nt.items():
study_items = ntgo.study_items.split(', ') if b_str else ntgo.study_items
for geneid in study_items:
gene2gos[geneid].add(goid)
if b_str:
b_set = set(isinstance(g.isdigit(), int) for g in nt0.study_items.split(', '))
if b_set == set([True]):
return {int(g):gos for g, gos in gene2gos.items()}
return {g:gos for g, gos in gene2gos.items()} | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | _Init.get_gene2aart | def get_gene2aart(gene2section2gos, sec2chr):
"""Return a string for each gene representing GO section membership."""
geneid2str = {}
for geneid, section2gos_gene in gene2section2gos.items():
letters = [abc if s in section2gos_gene else "." for s, abc in sec2chr.items()]
geneid2str[geneid] = "".join(letters)
return geneid2str | python | def get_gene2aart(gene2section2gos, sec2chr):
"""Return a string for each gene representing GO section membership."""
geneid2str = {}
for geneid, section2gos_gene in gene2section2gos.items():
letters = [abc if s in section2gos_gene else "." for s, abc in sec2chr.items()]
geneid2str[geneid] = "".join(letters)
return geneid2str | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | _Init.get_gene2section2gos | def get_gene2section2gos(gene2gos, sec2gos):
"""Get a list of section aliases for each gene product ID."""
gene2section2gos = {}
for geneid, gos_gene in gene2gos.items():
section2gos = {}
for section_name, gos_sec in sec2gos.items():
gos_secgene = gos_gene.intersection(gos_sec)
if gos_secgene:
section2gos[section_name] = gos_secgene
gene2section2gos[geneid] = section2gos
return gene2section2gos | python | def get_gene2section2gos(gene2gos, sec2gos):
"""Get a list of section aliases for each gene product ID."""
gene2section2gos = {}
for geneid, gos_gene in gene2gos.items():
section2gos = {}
for section_name, gos_sec in sec2gos.items():
gos_secgene = gos_gene.intersection(gos_sec)
if gos_secgene:
section2gos[section_name] = gos_secgene
gene2section2gos[geneid] = section2gos
return gene2section2gos | [
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tanghaibao/goatools | goatools/gosubdag/plot/gosubdag_plot.py | GoSubDagPlot._init_objcolor | def _init_objcolor(self, node_opts, **kwu):
"""Return user-created Go2Color object or create one."""
objgoea = node_opts.kws['dict'].get('objgoea', None)
# kwu: go2color go2bordercolor dflt_bordercolor key2col
return Go2Color(self.gosubdag, objgoea, **kwu) | python | def _init_objcolor(self, node_opts, **kwu):
"""Return user-created Go2Color object or create one."""
objgoea = node_opts.kws['dict'].get('objgoea', None)
# kwu: go2color go2bordercolor dflt_bordercolor key2col
return Go2Color(self.gosubdag, objgoea, **kwu) | [
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tanghaibao/goatools | goatools/gosubdag/plot/gosubdag_plot.py | GoSubDagPlot._init_gonodeopts | def _init_gonodeopts(self, **kws_usr):
"""Initialize a GO Node plot options object, GoNodeOpts."""
options = GoNodeOpts(self.gosubdag, **self.kws['node_go'])
# Add parent edge count if either is in kws: parentcnt, prt_pcnt
if not options.kws['set'].isdisjoint(['parentcnt', 'prt_pcnt']):
options.kws['dict']['c2ps'] = self.edgesobj.get_c2ps()
# GoeaResults(kws['goea_results'], **self.kws['goea']) if 'goea_results' in kws else None
if 'goea_results' in kws_usr:
objgoea = GoeaResults(kws_usr['goea_results'], **self.kws['goea'])
options.kws['dict']['objgoea'] = objgoea
return options | python | def _init_gonodeopts(self, **kws_usr):
"""Initialize a GO Node plot options object, GoNodeOpts."""
options = GoNodeOpts(self.gosubdag, **self.kws['node_go'])
# Add parent edge count if either is in kws: parentcnt, prt_pcnt
if not options.kws['set'].isdisjoint(['parentcnt', 'prt_pcnt']):
options.kws['dict']['c2ps'] = self.edgesobj.get_c2ps()
# GoeaResults(kws['goea_results'], **self.kws['goea']) if 'goea_results' in kws else None
if 'goea_results' in kws_usr:
objgoea = GoeaResults(kws_usr['goea_results'], **self.kws['goea'])
options.kws['dict']['objgoea'] = objgoea
return options | [
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tanghaibao/goatools | goatools/gosubdag/plot/gosubdag_plot.py | GoSubDagPlot.prt_goids | def prt_goids(self, prt):
"""Print all GO IDs in the plot, plus their color."""
fmt = self.gosubdag.prt_attr['fmta']
nts = sorted(self.gosubdag.go2nt.values(), key=lambda nt: [nt.NS, nt.depth, nt.alt])
_get_color = self.pydotnodego.go2color.get
for ntgo in nts:
gostr = fmt.format(**ntgo._asdict())
col = _get_color(ntgo.GO, "")
prt.write("{COLOR:7} {GO}\n".format(COLOR=col, GO=gostr)) | python | def prt_goids(self, prt):
"""Print all GO IDs in the plot, plus their color."""
fmt = self.gosubdag.prt_attr['fmta']
nts = sorted(self.gosubdag.go2nt.values(), key=lambda nt: [nt.NS, nt.depth, nt.alt])
_get_color = self.pydotnodego.go2color.get
for ntgo in nts:
gostr = fmt.format(**ntgo._asdict())
col = _get_color(ntgo.GO, "")
prt.write("{COLOR:7} {GO}\n".format(COLOR=col, GO=gostr)) | [
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tanghaibao/goatools | goatools/gosubdag/plot/gosubdag_plot.py | GoSubDagPlot._init_kws | def _init_kws(self, **kws_usr):
"""Return a dict containing user-specified plotting options."""
kws_self = {}
user_keys = set(kws_usr)
for objname, expset in self.exp_keys.items():
usrkeys_curr = user_keys.intersection(expset)
kws_self[objname] = get_kwargs(kws_usr, usrkeys_curr, usrkeys_curr)
dpi = str(kws_self['dag'].get('dpi', self.dflts['dpi']))
kws_self['dag']['dpi'] = dpi
return kws_self | python | def _init_kws(self, **kws_usr):
"""Return a dict containing user-specified plotting options."""
kws_self = {}
user_keys = set(kws_usr)
for objname, expset in self.exp_keys.items():
usrkeys_curr = user_keys.intersection(expset)
kws_self[objname] = get_kwargs(kws_usr, usrkeys_curr, usrkeys_curr)
dpi = str(kws_self['dag'].get('dpi', self.dflts['dpi']))
kws_self['dag']['dpi'] = dpi
return kws_self | [
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tanghaibao/goatools | goatools/gosubdag/plot/gosubdag_plot.py | GoSubDagPlot._prt_edge | def _prt_edge(dag_edge, attr):
"""Print edge attribute"""
# sequence parent_graph points attributes type parent_edge_list
print("Edge {ATTR}: {VAL}".format(ATTR=attr, VAL=dag_edge.obj_dict[attr])) | python | def _prt_edge(dag_edge, attr):
"""Print edge attribute"""
# sequence parent_graph points attributes type parent_edge_list
print("Edge {ATTR}: {VAL}".format(ATTR=attr, VAL=dag_edge.obj_dict[attr])) | [
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tanghaibao/goatools | goatools/gosubdag/gosubdag.py | GoSubDag.prt_goids | def prt_goids(self, goids=None, prtfmt=None, sortby=True, prt=sys.stdout):
"""Given GO IDs, print decriptive info about each GO Term."""
if goids is None:
goids = self.go_sources
nts = self.get_nts(goids, sortby)
if prtfmt is None:
prtfmt = self.prt_attr['fmta']
for ntgo in nts:
key2val = ntgo._asdict()
prt.write("{GO}\n".format(GO=prtfmt.format(**key2val)))
return nts | python | def prt_goids(self, goids=None, prtfmt=None, sortby=True, prt=sys.stdout):
"""Given GO IDs, print decriptive info about each GO Term."""
if goids is None:
goids = self.go_sources
nts = self.get_nts(goids, sortby)
if prtfmt is None:
prtfmt = self.prt_attr['fmta']
for ntgo in nts:
key2val = ntgo._asdict()
prt.write("{GO}\n".format(GO=prtfmt.format(**key2val)))
return nts | [
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tanghaibao/goatools | goatools/gosubdag/gosubdag.py | GoSubDag.get_nts | def get_nts(self, goids=None, sortby=None):
"""Given GO IDs, get a list of namedtuples."""
nts = []
# User GO IDs
if goids is None:
goids = self.go_sources
else:
chk_goids(goids, "GoSubDag::get_nts")
if goids:
ntobj = cx.namedtuple("NtGo", " ".join(self.prt_attr['flds']))
go2nt = self.get_go2nt(goids)
for goid, ntgo in self._get_sorted_go2nt(go2nt, sortby):
assert ntgo is not None, "{GO} NOT IN go2nt".format(GO=goid)
if goid == ntgo.GO:
nts.append(ntgo)
else:
fld2vals = ntgo._asdict()
fld2vals['GO'] = goid
nts.append(ntobj(**fld2vals))
return nts | python | def get_nts(self, goids=None, sortby=None):
"""Given GO IDs, get a list of namedtuples."""
nts = []
# User GO IDs
if goids is None:
goids = self.go_sources
else:
chk_goids(goids, "GoSubDag::get_nts")
if goids:
ntobj = cx.namedtuple("NtGo", " ".join(self.prt_attr['flds']))
go2nt = self.get_go2nt(goids)
for goid, ntgo in self._get_sorted_go2nt(go2nt, sortby):
assert ntgo is not None, "{GO} NOT IN go2nt".format(GO=goid)
if goid == ntgo.GO:
nts.append(ntgo)
else:
fld2vals = ntgo._asdict()
fld2vals['GO'] = goid
nts.append(ntobj(**fld2vals))
return nts | [
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tanghaibao/goatools | goatools/gosubdag/gosubdag.py | GoSubDag.get_go2nt | def get_go2nt(self, goids):
"""Return dict of GO ID as key and GO object information in namedtuple."""
get_nt = self.go2nt
goids_present = set(goids).intersection(self.go2obj)
if len(goids_present) != len(goids):
print("GO IDs NOT FOUND IN DAG: {GOs}".format(
GOs=" ".join(set(goids).difference(goids_present))))
return {g:get_nt[g] for g in goids_present} | python | def get_go2nt(self, goids):
"""Return dict of GO ID as key and GO object information in namedtuple."""
get_nt = self.go2nt
goids_present = set(goids).intersection(self.go2obj)
if len(goids_present) != len(goids):
print("GO IDs NOT FOUND IN DAG: {GOs}".format(
GOs=" ".join(set(goids).difference(goids_present))))
return {g:get_nt[g] for g in goids_present} | [
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tanghaibao/goatools | goatools/gosubdag/gosubdag.py | GoSubDag.get_key_goids | def get_key_goids(self, goids):
"""Given GO IDs, return key GO IDs."""
go2obj = self.go2obj
return set(go2obj[go].id for go in goids) | python | def get_key_goids(self, goids):
"""Given GO IDs, return key GO IDs."""
go2obj = self.go2obj
return set(go2obj[go].id for go in goids) | [
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tanghaibao/goatools | goatools/gosubdag/gosubdag.py | GoSubDag.prt_objdesc | def prt_objdesc(self, prt):
"""Return description of this GoSubDag object."""
txt = "INITIALIZING GoSubDag: {N:3} sources in {M:3} GOs rcnt({R}). {A} alt GO IDs\n"
alt2obj = {go:o for go, o in self.go2obj.items() if go != o.id}
prt.write(txt.format(
N=len(self.go_sources),
M=len(self.go2obj),
R=self.rcntobj is not None,
A=len(alt2obj)))
prt.write(" GoSubDag: namedtuple fields: {FLDS}\n".format(
FLDS=" ".join(self.prt_attr['flds'])))
prt.write(" GoSubDag: relationships: {RELS}\n".format(RELS=self.relationships)) | python | def prt_objdesc(self, prt):
"""Return description of this GoSubDag object."""
txt = "INITIALIZING GoSubDag: {N:3} sources in {M:3} GOs rcnt({R}). {A} alt GO IDs\n"
alt2obj = {go:o for go, o in self.go2obj.items() if go != o.id}
prt.write(txt.format(
N=len(self.go_sources),
M=len(self.go2obj),
R=self.rcntobj is not None,
A=len(alt2obj)))
prt.write(" GoSubDag: namedtuple fields: {FLDS}\n".format(
FLDS=" ".join(self.prt_attr['flds'])))
prt.write(" GoSubDag: relationships: {RELS}\n".format(RELS=self.relationships)) | [
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tanghaibao/goatools | goatools/anno/init/reader_genetogo.py | InitAssc._init_taxids | def _init_taxids(taxid, taxids):
"""Return taxid set"""
ret = set()
if taxids is not None:
if taxids is True:
return True
if isinstance(taxids, int):
ret.add(taxids)
else:
ret.update(taxids)
if taxid is not None:
ret.add(taxid)
if not ret:
ret.add(9606)
# pylint: disable=superfluous-parens
print('**NOTE: DEFAULT TAXID STORED FROM gene2go IS 9606 (human)\n')
return ret | python | def _init_taxids(taxid, taxids):
"""Return taxid set"""
ret = set()
if taxids is not None:
if taxids is True:
return True
if isinstance(taxids, int):
ret.add(taxids)
else:
ret.update(taxids)
if taxid is not None:
ret.add(taxid)
if not ret:
ret.add(9606)
# pylint: disable=superfluous-parens
print('**NOTE: DEFAULT TAXID STORED FROM gene2go IS 9606 (human)\n')
return ret | [
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tanghaibao/goatools | goatools/anno/init/reader_genetogo.py | InitAssc.init_associations | def init_associations(self, fin_anno, taxids=None):
"""Read annotation file. Store annotation data in a list of namedtuples."""
nts = []
if fin_anno is None:
return nts
tic = timeit.default_timer()
lnum = -1
line = "\t"*len(self.flds)
try:
with open(fin_anno) as ifstrm:
category2ns = {'Process':'BP', 'Function':'MF', 'Component':'CC'}
ntobj = cx.namedtuple('ntanno', self.flds)
# Get: 1) Specified taxids, default taxid(human), or all taxids
get_all = taxids is True
taxids = self.taxids
for lnum, line in enumerate(ifstrm, 1):
# Read data
if line[0] != '#':
vals = line.split('\t')
taxid = int(vals[0])
if get_all or taxid in taxids:
# assert len(vals) == 8
ntd = ntobj(
tax_id=taxid,
DB_ID=int(vals[1]),
GO_ID=vals[2],
Evidence_Code=vals[3],
Qualifier=self._get_qualifiers(vals[4]),
GO_term=vals[5],
DB_Reference=self._get_pmids(vals[6]),
NS=category2ns[vals[7].rstrip()])
#self._chk_qualifiers(qualifiers, lnum, ntd)
nts.append(ntd)
# Read header
elif line[0] == '#':
assert line[1:-1].split('\t') == self.hdrs
# pylint: disable=broad-except
except Exception as inst:
import traceback
traceback.print_exc()
sys.stderr.write("\n **FATAL: {MSG}\n\n".format(MSG=str(inst)))
sys.stderr.write("**FATAL: {FIN}[{LNUM}]:\n{L}".format(FIN=fin_anno, L=line, LNUM=lnum))
self._prt_line_detail(sys.stdout, line, lnum)
sys.exit(1)
print('HMS:{HMS} {N:7,} annotations READ: {ANNO}'.format(
N=len(nts), ANNO=fin_anno,
HMS=str(datetime.timedelta(seconds=(timeit.default_timer()-tic)))))
return nts | python | def init_associations(self, fin_anno, taxids=None):
"""Read annotation file. Store annotation data in a list of namedtuples."""
nts = []
if fin_anno is None:
return nts
tic = timeit.default_timer()
lnum = -1
line = "\t"*len(self.flds)
try:
with open(fin_anno) as ifstrm:
category2ns = {'Process':'BP', 'Function':'MF', 'Component':'CC'}
ntobj = cx.namedtuple('ntanno', self.flds)
# Get: 1) Specified taxids, default taxid(human), or all taxids
get_all = taxids is True
taxids = self.taxids
for lnum, line in enumerate(ifstrm, 1):
# Read data
if line[0] != '#':
vals = line.split('\t')
taxid = int(vals[0])
if get_all or taxid in taxids:
# assert len(vals) == 8
ntd = ntobj(
tax_id=taxid,
DB_ID=int(vals[1]),
GO_ID=vals[2],
Evidence_Code=vals[3],
Qualifier=self._get_qualifiers(vals[4]),
GO_term=vals[5],
DB_Reference=self._get_pmids(vals[6]),
NS=category2ns[vals[7].rstrip()])
#self._chk_qualifiers(qualifiers, lnum, ntd)
nts.append(ntd)
# Read header
elif line[0] == '#':
assert line[1:-1].split('\t') == self.hdrs
# pylint: disable=broad-except
except Exception as inst:
import traceback
traceback.print_exc()
sys.stderr.write("\n **FATAL: {MSG}\n\n".format(MSG=str(inst)))
sys.stderr.write("**FATAL: {FIN}[{LNUM}]:\n{L}".format(FIN=fin_anno, L=line, LNUM=lnum))
self._prt_line_detail(sys.stdout, line, lnum)
sys.exit(1)
print('HMS:{HMS} {N:7,} annotations READ: {ANNO}'.format(
N=len(nts), ANNO=fin_anno,
HMS=str(datetime.timedelta(seconds=(timeit.default_timer()-tic)))))
return nts | [
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tanghaibao/goatools | goatools/anno/init/reader_genetogo.py | InitAssc._prt_line_detail | def _prt_line_detail(self, prt, line, lnum=""):
"""Print each field and its value."""
data = zip(self.flds, line.split('\t'))
txt = ["{:2}) {:13} {}".format(i, hdr, val) for i, (hdr, val) in enumerate(data)]
prt.write("{LNUM}\n{TXT}\n".format(LNUM=lnum, TXT='\n'.join(txt))) | python | def _prt_line_detail(self, prt, line, lnum=""):
"""Print each field and its value."""
data = zip(self.flds, line.split('\t'))
txt = ["{:2}) {:13} {}".format(i, hdr, val) for i, (hdr, val) in enumerate(data)]
prt.write("{LNUM}\n{TXT}\n".format(LNUM=lnum, TXT='\n'.join(txt))) | [
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tanghaibao/goatools | goatools/anno/gaf_reader.py | GafReader.chk_associations | def chk_associations(self, fout_err="gaf.err"):
"""Check that fields are legal in GAF"""
obj = GafData("2.1")
return obj.chk(self.associations, fout_err) | python | def chk_associations(self, fout_err="gaf.err"):
"""Check that fields are legal in GAF"""
obj = GafData("2.1")
return obj.chk(self.associations, fout_err) | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | GetGOs._update_ret | def _update_ret(ret, goids, go2color):
"""Update 'GOs' and 'go2color' in dict with goids and go2color."""
if goids:
ret['GOs'].update(goids)
if go2color:
for goid, color in go2color.items():
ret['go2color'][goid] = color | python | def _update_ret(ret, goids, go2color):
"""Update 'GOs' and 'go2color' in dict with goids and go2color."""
if goids:
ret['GOs'].update(goids)
if go2color:
for goid, color in go2color.items():
ret['go2color'][goid] = color | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._plt_gogrouped | def _plt_gogrouped(self, goids, go2color_usr, **kws):
"""Plot grouped GO IDs."""
fout_img = self.get_outfile(kws['outfile'], goids)
sections = read_sections(kws['sections'], exclude_ungrouped=True)
# print ("KWWSSSSSSSS", kws)
# kws_plt = {k:v for k, v in kws.items if k in self.kws_plt}
grprobj_cur = self._get_grprobj(goids, sections)
# GO: purple=hdr-only, green=hdr&usr, yellow=usr-only
# BORDER: Black=hdr Blu=hdr&usr
grpcolor = GrouperColors(grprobj_cur) # get_bordercolor get_go2color_users
grp_go2color = grpcolor.get_go2color_users()
grp_go2bordercolor = grpcolor.get_bordercolor()
for goid, color in go2color_usr.items():
grp_go2color[goid] = color
objcolor = Go2Color(self.gosubdag, objgoea=None,
go2color=grp_go2color, go2bordercolor=grp_go2bordercolor)
go2txt = GrouperPlot.get_go2txt(grprobj_cur, grp_go2color, grp_go2bordercolor)
objplt = GoSubDagPlot(self.gosubdag, Go2Color=objcolor, go2txt=go2txt, **kws)
objplt.prt_goids(sys.stdout)
objplt.plt_dag(fout_img)
sys.stdout.write("{N:>6} sections read\n".format(
N="NO" if sections is None else len(sections)))
return fout_img | python | def _plt_gogrouped(self, goids, go2color_usr, **kws):
"""Plot grouped GO IDs."""
fout_img = self.get_outfile(kws['outfile'], goids)
sections = read_sections(kws['sections'], exclude_ungrouped=True)
# print ("KWWSSSSSSSS", kws)
# kws_plt = {k:v for k, v in kws.items if k in self.kws_plt}
grprobj_cur = self._get_grprobj(goids, sections)
# GO: purple=hdr-only, green=hdr&usr, yellow=usr-only
# BORDER: Black=hdr Blu=hdr&usr
grpcolor = GrouperColors(grprobj_cur) # get_bordercolor get_go2color_users
grp_go2color = grpcolor.get_go2color_users()
grp_go2bordercolor = grpcolor.get_bordercolor()
for goid, color in go2color_usr.items():
grp_go2color[goid] = color
objcolor = Go2Color(self.gosubdag, objgoea=None,
go2color=grp_go2color, go2bordercolor=grp_go2bordercolor)
go2txt = GrouperPlot.get_go2txt(grprobj_cur, grp_go2color, grp_go2bordercolor)
objplt = GoSubDagPlot(self.gosubdag, Go2Color=objcolor, go2txt=go2txt, **kws)
objplt.prt_goids(sys.stdout)
objplt.plt_dag(fout_img)
sys.stdout.write("{N:>6} sections read\n".format(
N="NO" if sections is None else len(sections)))
return fout_img | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._get_grprobj | def _get_grprobj(self, goids, sections):
"""Get Grouper, given GO IDs and sections."""
grprdflt = GrouperDflts(self.gosubdag, "goslim_generic.obo")
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
return Grouper("sections", goids, hdrobj, self.gosubdag) | python | def _get_grprobj(self, goids, sections):
"""Get Grouper, given GO IDs and sections."""
grprdflt = GrouperDflts(self.gosubdag, "goslim_generic.obo")
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
return Grouper("sections", goids, hdrobj, self.gosubdag) | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._get_kwsdag | def _get_kwsdag(self, goids, go2obj, **kws_all):
"""Get keyword args for a GoSubDag."""
kws_dag = {}
# Term Counts for GO Term information score
tcntobj = self._get_tcntobj(goids, go2obj, **kws_all) # TermCounts or None
if tcntobj is not None:
kws_dag['tcntobj'] = tcntobj
# GO letters specified by the user
if 'go_aliases' in kws_all:
fin_go_aliases = kws_all['go_aliases']
if os.path.exists(fin_go_aliases):
go2letter = read_d1_letter(fin_go_aliases)
if go2letter:
kws_dag['go2letter'] = go2letter
return kws_dag | python | def _get_kwsdag(self, goids, go2obj, **kws_all):
"""Get keyword args for a GoSubDag."""
kws_dag = {}
# Term Counts for GO Term information score
tcntobj = self._get_tcntobj(goids, go2obj, **kws_all) # TermCounts or None
if tcntobj is not None:
kws_dag['tcntobj'] = tcntobj
# GO letters specified by the user
if 'go_aliases' in kws_all:
fin_go_aliases = kws_all['go_aliases']
if os.path.exists(fin_go_aliases):
go2letter = read_d1_letter(fin_go_aliases)
if go2letter:
kws_dag['go2letter'] = go2letter
return kws_dag | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._chk_docopts | def _chk_docopts(self, kws):
"""Check for common user command-line errors."""
# outfile should contain .png, .png, etc.
outfile = kws['outfile']
if len(kws) == 2 and os.path.basename(kws['obo']) == "go-basic.obo" and \
kws['outfile'] == self.dflt_outfile:
self._err("NO GO IDS SPECFIED", err=False)
if 'obo' in outfile:
self._err("BAD outfile({O})".format(O=outfile))
if 'gaf' in kws and 'gene2go' in kws:
self._err("SPECIFY ANNOTAIONS FROM ONE FILE")
if 'gene2go' in kws:
if 'taxid' not in kws:
self._err("SPECIFIY taxid WHEN READ NCBI'S gene2go FILE") | python | def _chk_docopts(self, kws):
"""Check for common user command-line errors."""
# outfile should contain .png, .png, etc.
outfile = kws['outfile']
if len(kws) == 2 and os.path.basename(kws['obo']) == "go-basic.obo" and \
kws['outfile'] == self.dflt_outfile:
self._err("NO GO IDS SPECFIED", err=False)
if 'obo' in outfile:
self._err("BAD outfile({O})".format(O=outfile))
if 'gaf' in kws and 'gene2go' in kws:
self._err("SPECIFY ANNOTAIONS FROM ONE FILE")
if 'gene2go' in kws:
if 'taxid' not in kws:
self._err("SPECIFIY taxid WHEN READ NCBI'S gene2go FILE") | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._err | def _err(self, msg, err=True):
"""Print useage and error before exiting."""
severity = "FATAL" if err else "NOTE"
txt = "".join([self.objdoc.doc,
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if err:
raise RuntimeError(txt)
sys.stdout.write(txt)
sys.exit(0) | python | def _err(self, msg, err=True):
"""Print useage and error before exiting."""
severity = "FATAL" if err else "NOTE"
txt = "".join([self.objdoc.doc,
"User's command-line:\n\n",
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sys.stdout.write(txt)
sys.exit(0) | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli.get_outfile | def get_outfile(self, outfile, goids=None):
"""Return output file for GO Term plot."""
# 1. Use the user-specfied output filename for the GO Term plot
if outfile != self.dflt_outfile:
return outfile
# 2. If only plotting 1 GO term, use GO is in plot name
if goids is not None and len(goids) == 1:
goid = next(iter(goids))
goobj = self.gosubdag.go2obj[goid]
fout = "GO_{NN}_{NM}".format(NN=goid.replace("GO:", ""), NM=goobj.name)
return ".".join([re.sub(r"[\s#'()+,-./:<=>\[\]_}]", '_', fout), 'png'])
# 3. Return default name
return self.dflt_outfile | python | def get_outfile(self, outfile, goids=None):
"""Return output file for GO Term plot."""
# 1. Use the user-specfied output filename for the GO Term plot
if outfile != self.dflt_outfile:
return outfile
# 2. If only plotting 1 GO term, use GO is in plot name
if goids is not None and len(goids) == 1:
goid = next(iter(goids))
goobj = self.gosubdag.go2obj[goid]
fout = "GO_{NN}_{NM}".format(NN=goid.replace("GO:", ""), NM=goobj.name)
return ".".join([re.sub(r"[\s#'()+,-./:<=>\[\]_}]", '_', fout), 'png'])
# 3. Return default name
return self.dflt_outfile | [
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tanghaibao/goatools | goatools/cli/gosubdag_plot.py | PlotCli._get_optional_attrs | def _get_optional_attrs(kws):
"""Given keyword args, return optional_attributes to be loaded into the GODag."""
vals = OboOptionalAttrs.attributes.intersection(kws.keys())
if 'sections' in kws:
vals.add('relationship')
if 'norel' in kws:
vals.discard('relationship')
return vals | python | def _get_optional_attrs(kws):
"""Given keyword args, return optional_attributes to be loaded into the GODag."""
vals = OboOptionalAttrs.attributes.intersection(kws.keys())
if 'sections' in kws:
vals.add('relationship')
if 'norel' in kws:
vals.discard('relationship')
return vals | [
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tanghaibao/goatools | goatools/cli/wr_sections.py | WrSectionsCli._read_sections | def _read_sections(ifile):
"""Read sections_in.txt file, if it exists."""
if os.path.exists(ifile):
return read_sections(ifile, exclude_ungrouped=True, prt=None) | python | def _read_sections(ifile):
"""Read sections_in.txt file, if it exists."""
if os.path.exists(ifile):
return read_sections(ifile, exclude_ungrouped=True, prt=None) | [
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tanghaibao/goatools | goatools/gosubdag/go_paths.py | GoPaths.get_paths_from_to | def get_paths_from_to(self, goobj_start, goid_end=None, dn0_up1=True):
"""Get a list of paths from goobj_start to either top or goid_end."""
paths = []
# Queue of terms to be examined (and storage for their paths)
working_q = cx.deque([[goobj_start]])
# Loop thru GO terms until we have examined all needed GO terms
adjfnc = self.adjdir[dn0_up1]
while working_q:
#print "WORKING QUEUE LEN({})".format(len(working_q))
path_curr = working_q.popleft()
goobj_curr = path_curr[-1]
go_adjlst = adjfnc(goobj_curr)
#print 'END', goid_end, goobj_curr
# If this GO term is the endpoint, Stop. Store path.
if (goid_end is not None and goobj_curr.id == goid_end) or \
(goid_end is None and not go_adjlst):
paths.append(path_curr)
# Else if this GO term is the not the end, add neighbors to path
else:
for go_neighbor in go_adjlst:
if go_neighbor not in path_curr:
#print "{}'s NEIGHBOR IS {}".format(goobj_curr.id, go_neighbor.id)
new_path = path_curr + [go_neighbor]
#sys.stdout.write(" {}'s {} {}\n".format(goobj_curr, up_dn, go_neighbor))
working_q.append(new_path)
#self.prt_paths(paths)
return paths | python | def get_paths_from_to(self, goobj_start, goid_end=None, dn0_up1=True):
"""Get a list of paths from goobj_start to either top or goid_end."""
paths = []
# Queue of terms to be examined (and storage for their paths)
working_q = cx.deque([[goobj_start]])
# Loop thru GO terms until we have examined all needed GO terms
adjfnc = self.adjdir[dn0_up1]
while working_q:
#print "WORKING QUEUE LEN({})".format(len(working_q))
path_curr = working_q.popleft()
goobj_curr = path_curr[-1]
go_adjlst = adjfnc(goobj_curr)
#print 'END', goid_end, goobj_curr
# If this GO term is the endpoint, Stop. Store path.
if (goid_end is not None and goobj_curr.id == goid_end) or \
(goid_end is None and not go_adjlst):
paths.append(path_curr)
# Else if this GO term is the not the end, add neighbors to path
else:
for go_neighbor in go_adjlst:
if go_neighbor not in path_curr:
#print "{}'s NEIGHBOR IS {}".format(goobj_curr.id, go_neighbor.id)
new_path = path_curr + [go_neighbor]
#sys.stdout.write(" {}'s {} {}\n".format(goobj_curr, up_dn, go_neighbor))
working_q.append(new_path)
#self.prt_paths(paths)
return paths | [
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tanghaibao/goatools | goatools/gosubdag/go_paths.py | GoPaths.prt_paths | def prt_paths(paths, prt=sys.stdout):
"""Print list of paths."""
pat = "PATHES: {GO} L{L:02} D{D:02}\n"
for path in paths:
for go_obj in path:
prt.write(pat.format(GO=go_obj.id, L=go_obj.level, D=go_obj.depth))
prt.write("\n") | python | def prt_paths(paths, prt=sys.stdout):
"""Print list of paths."""
pat = "PATHES: {GO} L{L:02} D{D:02}\n"
for path in paths:
for go_obj in path:
prt.write(pat.format(GO=go_obj.id, L=go_obj.level, D=go_obj.depth))
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tanghaibao/goatools | goatools/godag/relationship_str.py | RelationshipStr.prt_keys | def prt_keys(self, prt, pre):
"""Print the alias for a relationship and its alias."""
prt.write('{PRE}Relationship to parent: {ABC}\n'.format(
PRE=pre, ABC=''.join(self.rel2chr.values())))
for rel, alias in self.rel2chr.items():
prt.write('{PRE} {A} {DESC}\n'.format(PRE=pre, A=alias, DESC=rel))
prt.write('\n{PRE}Relationship to child: {ABC}\n'.format(
PRE=pre, ABC=''.join(self.rev2chr.values())))
for rel, alias in self.rev2chr.items():
prt.write('{PRE} {A} {DESC}\n'.format(PRE=pre, A=alias, DESC=rel)) | python | def prt_keys(self, prt, pre):
"""Print the alias for a relationship and its alias."""
prt.write('{PRE}Relationship to parent: {ABC}\n'.format(
PRE=pre, ABC=''.join(self.rel2chr.values())))
for rel, alias in self.rel2chr.items():
prt.write('{PRE} {A} {DESC}\n'.format(PRE=pre, A=alias, DESC=rel))
prt.write('\n{PRE}Relationship to child: {ABC}\n'.format(
PRE=pre, ABC=''.join(self.rev2chr.values())))
for rel, alias in self.rev2chr.items():
prt.write('{PRE} {A} {DESC}\n'.format(PRE=pre, A=alias, DESC=rel)) | [
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tanghaibao/goatools | goatools/anno/annoreader_base.py | AnnoReaderBase._get_id2gos | def _get_id2gos(self, associations, **kws):
"""Return given associations in a dict, id2gos"""
options = AnnoOptions(self.evobj, **kws)
# Default reduction is to remove. For all options, see goatools/anno/opts.py:
# * Evidence_Code == ND -> No biological data No biological Data available
# * Qualifiers contain NOT
assc = self.reduce_annotations(associations, options)
return self._get_dbid2goids(assc) if options.b_geneid2gos else self._get_goid2dbids(assc) | python | def _get_id2gos(self, associations, **kws):
"""Return given associations in a dict, id2gos"""
options = AnnoOptions(self.evobj, **kws)
# Default reduction is to remove. For all options, see goatools/anno/opts.py:
# * Evidence_Code == ND -> No biological data No biological Data available
# * Qualifiers contain NOT
assc = self.reduce_annotations(associations, options)
return self._get_dbid2goids(assc) if options.b_geneid2gos else self._get_goid2dbids(assc) | [
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tanghaibao/goatools | goatools/anno/annoreader_base.py | AnnoReaderBase.get_date_yyyymmdd | def get_date_yyyymmdd(yyyymmdd):
"""Return datetime.date given string."""
return date(int(yyyymmdd[:4]), int(yyyymmdd[4:6], base=10), int(yyyymmdd[6:], base=10)) | python | def get_date_yyyymmdd(yyyymmdd):
"""Return datetime.date given string."""
return date(int(yyyymmdd[:4]), int(yyyymmdd[4:6], base=10), int(yyyymmdd[6:], base=10)) | [
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tanghaibao/goatools | goatools/anno/annoreader_base.py | AnnoReaderBase.hms | def hms(self, msg, tic=None, prt=sys.stdout):
"""Print elapsed time and message."""
if tic is None:
tic = self.tic
now = timeit.default_timer()
hms = str(datetime.timedelta(seconds=(now-tic)))
prt.write('{HMS}: {MSG}\n'.format(HMS=hms, MSG=msg))
return now | python | def hms(self, msg, tic=None, prt=sys.stdout):
"""Print elapsed time and message."""
if tic is None:
tic = self.tic
now = timeit.default_timer()
hms = str(datetime.timedelta(seconds=(now-tic)))
prt.write('{HMS}: {MSG}\n'.format(HMS=hms, MSG=msg))
return now | [
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tanghaibao/goatools | goatools/anno/annoreader_base.py | AnnoReaderBase.chk_qualifiers | def chk_qualifiers(self):
"""Check format of qualifier"""
if self.name == 'id2gos':
return
for ntd in self.associations:
# print(ntd)
qual = ntd.Qualifier
assert isinstance(qual, set), '{NAME}: QUALIFIER MUST BE A LIST: {NT}'.format(
NAME=self.name, NT=ntd)
assert qual != set(['']), ntd
assert qual != set(['-']), ntd
assert 'always' not in qual, 'SPEC SAID IT WOULD BE THERE' | python | def chk_qualifiers(self):
"""Check format of qualifier"""
if self.name == 'id2gos':
return
for ntd in self.associations:
# print(ntd)
qual = ntd.Qualifier
assert isinstance(qual, set), '{NAME}: QUALIFIER MUST BE A LIST: {NT}'.format(
NAME=self.name, NT=ntd)
assert qual != set(['']), ntd
assert qual != set(['-']), ntd
assert 'always' not in qual, 'SPEC SAID IT WOULD BE THERE' | [
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tanghaibao/goatools | goatools/anno/annoreader_base.py | AnnoReaderBase._has_not_qual | def _has_not_qual(ntd):
"""Return True if the qualifiers contain a 'NOT'"""
for qual in ntd.Qualifier:
if 'not' in qual:
return True
if 'NOT' in qual:
return True
return False | python | def _has_not_qual(ntd):
"""Return True if the qualifiers contain a 'NOT'"""
for qual in ntd.Qualifier:
if 'not' in qual:
return True
if 'NOT' in qual:
return True
return False | [
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tanghaibao/goatools | goatools/grouper/sorter_nts.py | SorterNts._get_sorted_section | def _get_sorted_section(self, nts_section):
"""Sort GO IDs in each section, if requested by user."""
#pylint: disable=unnecessary-lambda
if self.section_sortby is True:
return sorted(nts_section, key=lambda nt: self.sortgos.usrgo_sortby(nt))
if self.section_sortby is False or self.section_sortby is None:
return nts_section
# print('SORT GO IDS IN A SECTION')
return sorted(nts_section, key=lambda nt: self.section_sortby(nt)) | python | def _get_sorted_section(self, nts_section):
"""Sort GO IDs in each section, if requested by user."""
#pylint: disable=unnecessary-lambda
if self.section_sortby is True:
return sorted(nts_section, key=lambda nt: self.sortgos.usrgo_sortby(nt))
if self.section_sortby is False or self.section_sortby is None:
return nts_section
# print('SORT GO IDS IN A SECTION')
return sorted(nts_section, key=lambda nt: self.section_sortby(nt)) | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | get_relationship_targets | def get_relationship_targets(item_ids, relationships, id2rec):
"""Get item ID set of item IDs in a relationship target set."""
# Requirements to use this function:
# 1) item Terms must have been loaded with 'relationships'
# 2) item IDs in 'item_ids' arguement must be present in id2rec
# 3) Arg, 'relationships' must be True or an iterable
reltgt_objs_all = set()
for goid in item_ids:
obj = id2rec[goid]
for reltype, reltgt_objs_cur in obj.relationship.items():
if relationships is True or reltype in relationships:
reltgt_objs_all.update(reltgt_objs_cur)
return reltgt_objs_all | python | def get_relationship_targets(item_ids, relationships, id2rec):
"""Get item ID set of item IDs in a relationship target set."""
# Requirements to use this function:
# 1) item Terms must have been loaded with 'relationships'
# 2) item IDs in 'item_ids' arguement must be present in id2rec
# 3) Arg, 'relationships' must be True or an iterable
reltgt_objs_all = set()
for goid in item_ids:
obj = id2rec[goid]
for reltype, reltgt_objs_cur in obj.relationship.items():
if relationships is True or reltype in relationships:
reltgt_objs_all.update(reltgt_objs_cur)
return reltgt_objs_all | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | _get_id2parents | def _get_id2parents(id2parents, item_id, item_obj):
"""Add the parent item IDs for one item object and their parents."""
if item_id in id2parents:
return id2parents[item_id]
parent_ids = set()
for parent_obj in item_obj.parents:
parent_id = parent_obj.item_id
parent_ids.add(parent_id)
parent_ids |= _get_id2parents(id2parents, parent_id, parent_obj)
id2parents[item_id] = parent_ids
return parent_ids | python | def _get_id2parents(id2parents, item_id, item_obj):
"""Add the parent item IDs for one item object and their parents."""
if item_id in id2parents:
return id2parents[item_id]
parent_ids = set()
for parent_obj in item_obj.parents:
parent_id = parent_obj.item_id
parent_ids.add(parent_id)
parent_ids |= _get_id2parents(id2parents, parent_id, parent_obj)
id2parents[item_id] = parent_ids
return parent_ids | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | _get_id2children | def _get_id2children(id2children, item_id, item_obj):
"""Add the child item IDs for one item object and their children."""
if item_id in id2children:
return id2children[item_id]
child_ids = set()
for child_obj in item_obj.children:
child_id = child_obj.item_id
child_ids.add(child_id)
child_ids |= _get_id2children(id2children, child_id, child_obj)
id2children[item_id] = child_ids
return child_ids | python | def _get_id2children(id2children, item_id, item_obj):
"""Add the child item IDs for one item object and their children."""
if item_id in id2children:
return id2children[item_id]
child_ids = set()
for child_obj in item_obj.children:
child_id = child_obj.item_id
child_ids.add(child_id)
child_ids |= _get_id2children(id2children, child_id, child_obj)
id2children[item_id] = child_ids
return child_ids | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | _get_id2upper | def _get_id2upper(id2upper, item_id, item_obj):
"""Add the parent item IDs for one item object and their upper."""
if item_id in id2upper:
return id2upper[item_id]
upper_ids = set()
for upper_obj in item_obj.get_goterms_upper():
upper_id = upper_obj.item_id
upper_ids.add(upper_id)
upper_ids |= _get_id2upper(id2upper, upper_id, upper_obj)
id2upper[item_id] = upper_ids
return upper_ids | python | def _get_id2upper(id2upper, item_id, item_obj):
"""Add the parent item IDs for one item object and their upper."""
if item_id in id2upper:
return id2upper[item_id]
upper_ids = set()
for upper_obj in item_obj.get_goterms_upper():
upper_id = upper_obj.item_id
upper_ids.add(upper_id)
upper_ids |= _get_id2upper(id2upper, upper_id, upper_obj)
id2upper[item_id] = upper_ids
return upper_ids | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | _get_id2lower | def _get_id2lower(id2lower, item_id, item_obj):
"""Add the lower item IDs for one item object and the objects below them."""
if item_id in id2lower:
return id2lower[item_id]
lower_ids = set()
for lower_obj in item_obj.get_goterms_lower():
lower_id = lower_obj.item_id
lower_ids.add(lower_id)
lower_ids |= _get_id2lower(id2lower, lower_id, lower_obj)
id2lower[item_id] = lower_ids
return lower_ids | python | def _get_id2lower(id2lower, item_id, item_obj):
"""Add the lower item IDs for one item object and the objects below them."""
if item_id in id2lower:
return id2lower[item_id]
lower_ids = set()
for lower_obj in item_obj.get_goterms_lower():
lower_id = lower_obj.item_id
lower_ids.add(lower_id)
lower_ids |= _get_id2lower(id2lower, lower_id, lower_obj)
id2lower[item_id] = lower_ids
return lower_ids | [
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tanghaibao/goatools | goatools/godag/go_tasks.py | CurNHigher.fill_parentidid2obj_r0 | def fill_parentidid2obj_r0(self, id2obj, child_obj):
"""Fill id2obj with all parent key item IDs and their objects."""
for parent_obj in child_obj.parents:
if parent_obj.item_id not in id2obj:
id2obj[parent_obj.item_id] = parent_obj
self.fill_parentidid2obj_r0(id2obj, parent_obj) | python | def fill_parentidid2obj_r0(self, id2obj, child_obj):
"""Fill id2obj with all parent key item IDs and their objects."""
for parent_obj in child_obj.parents:
if parent_obj.item_id not in id2obj:
id2obj[parent_obj.item_id] = parent_obj
self.fill_parentidid2obj_r0(id2obj, parent_obj) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsBase.prt_ver | def prt_ver(self, prt):
"""Print version of GO-DAG for the GO and for GO slims."""
if self.ver_list is not None:
prt.write("# Versions:\n# {VER}\n\n".format(VER="\n# ".join(self.ver_list))) | python | def prt_ver(self, prt):
"""Print version of GO-DAG for the GO and for GO slims."""
if self.ver_list is not None:
prt.write("# Versions:\n# {VER}\n\n".format(VER="\n# ".join(self.ver_list))) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsBase.get_sections_2dnt | def get_sections_2dnt(self, sec2d_go):
"""Return a sections list containing sorted lists of namedtuples."""
return [(nm, self.get_ntgos_sorted(gos)) for nm, gos in sec2d_go] | python | def get_sections_2dnt(self, sec2d_go):
"""Return a sections list containing sorted lists of namedtuples."""
return [(nm, self.get_ntgos_sorted(gos)) for nm, gos in sec2d_go] | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsBase.get_ntgos_sorted | def get_ntgos_sorted(self, hdrgos):
"""Return sorted Grouper namedtuples if there are user GO IDs underneath."""
go2nt = self.grprobj.go2nt
return sorted([go2nt[go] for go in hdrgos if go in go2nt], key=self.fncsortnt) | python | def get_ntgos_sorted(self, hdrgos):
"""Return sorted Grouper namedtuples if there are user GO IDs underneath."""
go2nt = self.grprobj.go2nt
return sorted([go2nt[go] for go in hdrgos if go in go2nt], key=self.fncsortnt) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsBase.prt_ntgos | def prt_ntgos(self, prt, ntgos):
"""Print the Grouper namedtuples."""
for ntgo in ntgos:
key2val = ntgo._asdict()
prt.write("{GO_LINE}\n".format(GO_LINE=self.prtfmt.format(**key2val))) | python | def prt_ntgos(self, prt, ntgos):
"""Print the Grouper namedtuples."""
for ntgo in ntgos:
key2val = ntgo._asdict()
prt.write("{GO_LINE}\n".format(GO_LINE=self.prtfmt.format(**key2val))) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsPy.wr_py_sections_new | def wr_py_sections_new(self, fout_py, doc=None):
"""Write the first sections file."""
sections = self.grprobj.get_sections_2d()
return self.wr_py_sections(fout_py, sections, doc) | python | def wr_py_sections_new(self, fout_py, doc=None):
"""Write the first sections file."""
sections = self.grprobj.get_sections_2d()
return self.wr_py_sections(fout_py, sections, doc) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsPy.wr_py_sections | def wr_py_sections(self, fout_py, sections, doc=None):
"""Write sections 2-D list into a Python format list."""
if sections is None:
sections = self.grprobj.get_sections_2d()
sec2d_nt = self.get_sections_2dnt(sections) # lists of GO Grouper namedtuples
with open(fout_py, 'w') as prt:
self._prt_py_sections(sec2d_nt, prt, doc)
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(sections)
sys.stdout.write(self.grprobj.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP=len(dat['U']), undesc="unused",
ACTION="WROTE:", FILE=fout_py)) | python | def wr_py_sections(self, fout_py, sections, doc=None):
"""Write sections 2-D list into a Python format list."""
if sections is None:
sections = self.grprobj.get_sections_2d()
sec2d_nt = self.get_sections_2dnt(sections) # lists of GO Grouper namedtuples
with open(fout_py, 'w') as prt:
self._prt_py_sections(sec2d_nt, prt, doc)
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(sections)
sys.stdout.write(self.grprobj.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP=len(dat['U']), undesc="unused",
ACTION="WROTE:", FILE=fout_py)) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsPy._prt_py_sections | def _prt_py_sections(self, sec2d_nt, prt=sys.stdout, doc=None):
"""Print sections 2-D list into a Python format list."""
if doc is None:
doc = 'Sections variable'
prt.write('"""{DOC}"""\n\n'.format(DOC=doc))
self.prt_ver(prt)
prt.write("# pylint: disable=line-too-long\n")
strcnt = self.get_summary_str(sec2d_nt)
prt.write("SECTIONS = [ # {CNTS}\n".format(CNTS=strcnt))
prt.write(' # ("New Section", [\n')
prt.write(' # ]),\n')
for section_name, nthdrgos in sec2d_nt:
self._prt_py_section(prt, section_name, nthdrgos)
prt.write("]\n") | python | def _prt_py_sections(self, sec2d_nt, prt=sys.stdout, doc=None):
"""Print sections 2-D list into a Python format list."""
if doc is None:
doc = 'Sections variable'
prt.write('"""{DOC}"""\n\n'.format(DOC=doc))
self.prt_ver(prt)
prt.write("# pylint: disable=line-too-long\n")
strcnt = self.get_summary_str(sec2d_nt)
prt.write("SECTIONS = [ # {CNTS}\n".format(CNTS=strcnt))
prt.write(' # ("New Section", [\n')
prt.write(' # ]),\n')
for section_name, nthdrgos in sec2d_nt:
self._prt_py_section(prt, section_name, nthdrgos)
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsPy._prt_py_section | def _prt_py_section(self, prt, section_name, ntgos):
"""Print one section and its GO headers."""
prt.write(' ("{SEC}", [ # {N} GO-headers\n'.format(SEC=section_name, N=len(ntgos)))
self.prt_ntgos(prt, ntgos)
prt.write(" ]),\n") | python | def _prt_py_section(self, prt, section_name, ntgos):
"""Print one section and its GO headers."""
prt.write(' ("{SEC}", [ # {N} GO-headers\n'.format(SEC=section_name, N=len(ntgos)))
self.prt_ntgos(prt, ntgos)
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsTxt.prt_goid_cnt | def prt_goid_cnt(self, prt=sys.stdout):
"""Get number of hdrgos and usrgos in each section."""
for section_name, hdrgos_sec in self.grprobj.get_sections_2d():
prt.write("{NAME} {Us:5,} {Hs:5,} {SEC}\n".format(
NAME=self.grprobj.grpname,
Us=len(self.grprobj.get_usrgos_g_hdrgos(hdrgos_sec)),
Hs=len(hdrgos_sec),
SEC=section_name)) | python | def prt_goid_cnt(self, prt=sys.stdout):
"""Get number of hdrgos and usrgos in each section."""
for section_name, hdrgos_sec in self.grprobj.get_sections_2d():
prt.write("{NAME} {Us:5,} {Hs:5,} {SEC}\n".format(
NAME=self.grprobj.grpname,
Us=len(self.grprobj.get_usrgos_g_hdrgos(hdrgos_sec)),
Hs=len(hdrgos_sec),
SEC=section_name)) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsTxt.wr_txt_grouping_gos | def wr_txt_grouping_gos(self):
"""Write one file per GO group."""
prt_goids = self.grprobj.gosubdag.prt_goids
for hdrgo, usrgos in self.grprobj.hdrgo2usrgos.items():
keygos = usrgos.union([hdrgo])
fout_txt = "{BASE}.txt".format(BASE=self.grprobj.get_fout_base(hdrgo))
with open(fout_txt, 'w') as prt:
prt_goids(keygos, prt=prt)
sys.stdout.write(" {N:5,} GO IDs WROTE: {TXT}\n".format(
N=len(keygos), TXT=fout_txt)) | python | def wr_txt_grouping_gos(self):
"""Write one file per GO group."""
prt_goids = self.grprobj.gosubdag.prt_goids
for hdrgo, usrgos in self.grprobj.hdrgo2usrgos.items():
keygos = usrgos.union([hdrgo])
fout_txt = "{BASE}.txt".format(BASE=self.grprobj.get_fout_base(hdrgo))
with open(fout_txt, 'w') as prt:
prt_goids(keygos, prt=prt)
sys.stdout.write(" {N:5,} GO IDs WROTE: {TXT}\n".format(
N=len(keygos), TXT=fout_txt)) | [
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tanghaibao/goatools | goatools/grouper/wr_sections.py | WrSectionsTxt.wr_txt_section_hdrgos | def wr_txt_section_hdrgos(self, fout_txt, sortby=None, prt_section=True):
"""Write high GO IDs that are actually used to group current set of GO IDs."""
sec2d_go = self.grprobj.get_sections_2d() # lists of GO IDs
sec2d_nt = self.get_sections_2dnt(sec2d_go) # lists of GO Grouper namedtuples
if sortby is None:
sortby = self.fncsortnt
with open(fout_txt, 'w') as prt:
self.prt_ver(prt)
prt.write("# GROUP NAME: {NAME}\n".format(NAME=self.grprobj.grpname))
for section_name, nthdrgos_actual in sec2d_nt:
if prt_section:
prt.write("# SECTION: {SECTION}\n".format(SECTION=section_name))
self.prt_ntgos(prt, nthdrgos_actual)
if prt_section:
prt.write("\n")
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(sec2d_go)
sys.stdout.write(self.grprobj.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP=len(dat['U']), undesc="unused",
ACTION="WROTE:", FILE=fout_txt))
return sec2d_nt | python | def wr_txt_section_hdrgos(self, fout_txt, sortby=None, prt_section=True):
"""Write high GO IDs that are actually used to group current set of GO IDs."""
sec2d_go = self.grprobj.get_sections_2d() # lists of GO IDs
sec2d_nt = self.get_sections_2dnt(sec2d_go) # lists of GO Grouper namedtuples
if sortby is None:
sortby = self.fncsortnt
with open(fout_txt, 'w') as prt:
self.prt_ver(prt)
prt.write("# GROUP NAME: {NAME}\n".format(NAME=self.grprobj.grpname))
for section_name, nthdrgos_actual in sec2d_nt:
if prt_section:
prt.write("# SECTION: {SECTION}\n".format(SECTION=section_name))
self.prt_ntgos(prt, nthdrgos_actual)
if prt_section:
prt.write("\n")
dat = SummarySec2dHdrGos().summarize_sec2hdrgos(sec2d_go)
sys.stdout.write(self.grprobj.fmtsum.format(
GO_DESC='hdr', SECs=len(dat['S']), GOs=len(dat['G']),
UNGRP=len(dat['U']), undesc="unused",
ACTION="WROTE:", FILE=fout_txt))
return sec2d_nt | [
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tanghaibao/goatools | goatools/parsers/david_chart.py | DavidChartReader.prt_num_sig | def prt_num_sig(self, prt=sys.stdout, alpha=0.05):
"""Print the number of significant GO terms."""
ctr = self.get_num_sig(alpha)
prt.write("{N:6,} TOTAL: {TXT}\n".format(N=len(self.nts), TXT=" ".join([
"FDR({FDR:4})".format(FDR=ctr['FDR']),
"Bonferroni({B:4})".format(B=ctr['Bonferroni']),
"Benjamini({B:4})".format(B=ctr['Benjamini']),
"PValue({P:4})".format(P=ctr['PValue']),
os.path.basename(self.fin_davidchart)]))) | python | def prt_num_sig(self, prt=sys.stdout, alpha=0.05):
"""Print the number of significant GO terms."""
ctr = self.get_num_sig(alpha)
prt.write("{N:6,} TOTAL: {TXT}\n".format(N=len(self.nts), TXT=" ".join([
"FDR({FDR:4})".format(FDR=ctr['FDR']),
"Bonferroni({B:4})".format(B=ctr['Bonferroni']),
"Benjamini({B:4})".format(B=ctr['Benjamini']),
"PValue({P:4})".format(P=ctr['PValue']),
os.path.basename(self.fin_davidchart)]))) | [
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tanghaibao/goatools | goatools/parsers/david_chart.py | DavidChartReader.get_num_sig | def get_num_sig(self, alpha=0.05):
"""Print the number of significant results using various metrics."""
# Get the number of significant GO terms
ctr = cx.Counter()
flds = set(['FDR', 'Bonferroni', 'Benjamini', 'PValue'])
for ntd in self.nts:
for fld in flds:
if getattr(ntd, fld) < alpha:
ctr[fld] += 1
return ctr | python | def get_num_sig(self, alpha=0.05):
"""Print the number of significant results using various metrics."""
# Get the number of significant GO terms
ctr = cx.Counter()
flds = set(['FDR', 'Bonferroni', 'Benjamini', 'PValue'])
for ntd in self.nts:
for fld in flds:
if getattr(ntd, fld) < alpha:
ctr[fld] += 1
return ctr | [
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tanghaibao/goatools | goatools/parsers/david_chart.py | _Init.get_nts | def get_nts(self, fin_davidchart):
"""Read DAVID Chart file. Store each line in a namedtuple."""
nts = []
with open(fin_davidchart) as ifstrm:
hdr_seen = False
for line in ifstrm:
line = line.rstrip()
flds = line.split('\t')
if hdr_seen:
ntd = self._init_nt(flds)
nts.append(ntd)
else:
if line[:8] == 'Category':
assert len(flds) == 13, len(flds)
hdr_seen = True
sys.stdout.write(" READ {N:5} GO IDs from DAVID Chart: {TSV}\n".format(
N=len(nts), TSV=fin_davidchart))
return nts | python | def get_nts(self, fin_davidchart):
"""Read DAVID Chart file. Store each line in a namedtuple."""
nts = []
with open(fin_davidchart) as ifstrm:
hdr_seen = False
for line in ifstrm:
line = line.rstrip()
flds = line.split('\t')
if hdr_seen:
ntd = self._init_nt(flds)
nts.append(ntd)
else:
if line[:8] == 'Category':
assert len(flds) == 13, len(flds)
hdr_seen = True
sys.stdout.write(" READ {N:5} GO IDs from DAVID Chart: {TSV}\n".format(
N=len(nts), TSV=fin_davidchart))
return nts | [
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tanghaibao/goatools | goatools/parsers/david_chart.py | _Init._init_nt | def _init_nt(self, flds):
"""Given string fields from a DAVID chart file, return namedtuple."""
term = flds[1]
genes_str = flds[5]
# pylint: disable=bad-whitespace
return self.ntobj(
Category = flds[0],
GO = term[:10], # 1 GO:0045202~synapse
name = term[10:], # 1 GO:0045202~synapse
Count = int(flds[2]), # 2 94
Perc = float(flds[3]), # 3 9.456740442655935
PValue = float(flds[4]), # 4 6.102654380458156E-20
Genes = genes_str, # 5 ['ENSMUSG00000052613', ...]
Genes_set = self.get_genes(genes_str), # 5 ['ENSMUSG00000052613', ...]
List_Total = int(flds[6]), # 6 920
Pop_Hits = int(flds[7]), # 7 444
Pop_Total = int(flds[8]), # 8 12002
Fold_Enrichment = float(flds[9]), # 9 2.7619173521347435
Bonferroni = float(flds[10]), # 10 3.3930758355347344E-17
Benjamini = float(flds[11]), # 11 3.3930758355347344E-17
FDR = float(flds[12])) | python | def _init_nt(self, flds):
"""Given string fields from a DAVID chart file, return namedtuple."""
term = flds[1]
genes_str = flds[5]
# pylint: disable=bad-whitespace
return self.ntobj(
Category = flds[0],
GO = term[:10], # 1 GO:0045202~synapse
name = term[10:], # 1 GO:0045202~synapse
Count = int(flds[2]), # 2 94
Perc = float(flds[3]), # 3 9.456740442655935
PValue = float(flds[4]), # 4 6.102654380458156E-20
Genes = genes_str, # 5 ['ENSMUSG00000052613', ...]
Genes_set = self.get_genes(genes_str), # 5 ['ENSMUSG00000052613', ...]
List_Total = int(flds[6]), # 6 920
Pop_Hits = int(flds[7]), # 7 444
Pop_Total = int(flds[8]), # 8 12002
Fold_Enrichment = float(flds[9]), # 9 2.7619173521347435
Bonferroni = float(flds[10]), # 10 3.3930758355347344E-17
Benjamini = float(flds[11]), # 11 3.3930758355347344E-17
FDR = float(flds[12])) | [
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tanghaibao/goatools | goatools/parsers/david_chart.py | _Init.get_genes | def get_genes(genes_str):
"""Given a string containng genes, return a list."""
gene_set = genes_str.split(', ')
if gene_set and gene_set[0].isdigit():
gene_set = set(int(g) for g in gene_set)
return gene_set | python | def get_genes(genes_str):
"""Given a string containng genes, return a list."""
gene_set = genes_str.split(', ')
if gene_set and gene_set[0].isdigit():
gene_set = set(int(g) for g in gene_set)
return gene_set | [
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tanghaibao/goatools | goatools/anno/extensions/factory.py | get_extensions | def get_extensions(extstr):
"""Return zero or greater Annotation Extensions, given a line of text."""
# Extension examples:
# has_direct_input(UniProtKB:P37840),occurs_in(GO:0005576)
# part_of(UBERON:0006618),part_of(UBERON:0002302)
# occurs_in(CL:0000988)|occurs_in(CL:0001021)
if not extstr:
return None
exts = []
for ext_lst in extstr.split('|'):
grp = []
for ext in ext_lst.split(','):
idx = ext.find('(')
if idx != -1 and ext[-1] == ')':
grp.append(AnnotationExtension(ext[:idx], ext[idx+1:-1]))
else:
# Ignore improperly formatted Extensions
sys.stdout.write('BAD Extension({E})\n'.format(E=ext))
exts.append(grp)
return AnnotationExtensions(exts) | python | def get_extensions(extstr):
"""Return zero or greater Annotation Extensions, given a line of text."""
# Extension examples:
# has_direct_input(UniProtKB:P37840),occurs_in(GO:0005576)
# part_of(UBERON:0006618),part_of(UBERON:0002302)
# occurs_in(CL:0000988)|occurs_in(CL:0001021)
if not extstr:
return None
exts = []
for ext_lst in extstr.split('|'):
grp = []
for ext in ext_lst.split(','):
idx = ext.find('(')
if idx != -1 and ext[-1] == ')':
grp.append(AnnotationExtension(ext[:idx], ext[idx+1:-1]))
else:
# Ignore improperly formatted Extensions
sys.stdout.write('BAD Extension({E})\n'.format(E=ext))
exts.append(grp)
return AnnotationExtensions(exts) | [
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tanghaibao/goatools | goatools/cli/docopt_parse.py | DocOptParse._set_intvals | def _set_intvals(kws, keys):
"""Convert keyword values to int."""
for key in keys:
if key in kws:
kws[key] = int(kws[key]) | python | def _set_intvals(kws, keys):
"""Convert keyword values to int."""
for key in keys:
if key in kws:
kws[key] = int(kws[key]) | [
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tanghaibao/goatools | goatools/cli/docopt_parse.py | DocOptParse._chk_docopt_exit | def _chk_docopt_exit(self, args, exp_letters):
"""Check if docopt exit was for an unknown argument."""
if args is None:
args = sys.argv[1:]
keys_all = self.exp_keys.union(self.exp_elems)
if exp_letters:
keys_all |= exp_letters
unknown_args = self._chk_docunknown(args, keys_all)
if unknown_args:
raise RuntimeError("{USAGE}\n **FATAL: UNKNOWN ARGS: {UNK}".format(
USAGE=self.doc, UNK=" ".join(unknown_args))) | python | def _chk_docopt_exit(self, args, exp_letters):
"""Check if docopt exit was for an unknown argument."""
if args is None:
args = sys.argv[1:]
keys_all = self.exp_keys.union(self.exp_elems)
if exp_letters:
keys_all |= exp_letters
unknown_args = self._chk_docunknown(args, keys_all)
if unknown_args:
raise RuntimeError("{USAGE}\n **FATAL: UNKNOWN ARGS: {UNK}".format(
USAGE=self.doc, UNK=" ".join(unknown_args))) | [
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tanghaibao/goatools | goatools/cli/docopt_parse.py | DocOptParse._chk_docopt_kws | def _chk_docopt_kws(self, docdict, exp):
"""Check for common user errors when running from the command-line."""
for key, val in docdict.items():
if isinstance(val, str):
assert '=' not in val, self._err("'=' FOUND IN VALUE", key, val, exp)
elif key != 'help' and key not in self.exp_keys and key not in self.exp_elems:
raise RuntimeError(self._err("UNKNOWN KEY", key, val, exp)) | python | def _chk_docopt_kws(self, docdict, exp):
"""Check for common user errors when running from the command-line."""
for key, val in docdict.items():
if isinstance(val, str):
assert '=' not in val, self._err("'=' FOUND IN VALUE", key, val, exp)
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tanghaibao/goatools | goatools/cli/docopt_parse.py | DocOptParse._chk_docunknown | def _chk_docunknown(args, exp):
"""Return any unknown args."""
unknown = []
for arg in args:
if arg[:2] == '--':
val = arg[2:]
if val not in exp:
unknown.append(arg)
elif arg[:1] == '-':
val = arg[1:]
if val not in exp:
unknown.append(arg)
if '-h' in unknown or '--help' in unknown:
return []
return unknown | python | def _chk_docunknown(args, exp):
"""Return any unknown args."""
unknown = []
for arg in args:
if arg[:2] == '--':
val = arg[2:]
if val not in exp:
unknown.append(arg)
elif arg[:1] == '-':
val = arg[1:]
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unknown.append(arg)
if '-h' in unknown or '--help' in unknown:
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return unknown | [
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tanghaibao/goatools | goatools/anno/dnld_ebi_goa.py | DnldGoa.dnld_goa | def dnld_goa(self, species, ext='gaf', item=None, fileout=None):
"""Download GOA source file name on EMBL-EBI ftp server."""
basename = self.get_basename(species, ext, item)
src = os.path.join(self.ftp_src_goa, species.upper(), "{F}.gz".format(F=basename))
dst = os.path.join(os.getcwd(), basename) if fileout is None else fileout
dnld_file(src, dst, prt=sys.stdout, loading_bar=None)
return dst | python | def dnld_goa(self, species, ext='gaf', item=None, fileout=None):
"""Download GOA source file name on EMBL-EBI ftp server."""
basename = self.get_basename(species, ext, item)
src = os.path.join(self.ftp_src_goa, species.upper(), "{F}.gz".format(F=basename))
dst = os.path.join(os.getcwd(), basename) if fileout is None else fileout
dnld_file(src, dst, prt=sys.stdout, loading_bar=None)
return dst | [
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tanghaibao/goatools | goatools/associations.py | read_associations | def read_associations(assoc_fn, anno_type='id2gos', **kws):
"""Return associatinos in id2gos format"""
# kws get_objanno: taxids hdr_only prt allow_missing_symbol
obj = get_objanno(assoc_fn, anno_type, **kws)
# kws get_id2gos: ev_include ev_exclude keep_ND keep_NOT b_geneid2gos go2geneids
return obj.get_id2gos(**kws) | python | def read_associations(assoc_fn, anno_type='id2gos', **kws):
"""Return associatinos in id2gos format"""
# kws get_objanno: taxids hdr_only prt allow_missing_symbol
obj = get_objanno(assoc_fn, anno_type, **kws)
# kws get_id2gos: ev_include ev_exclude keep_ND keep_NOT b_geneid2gos go2geneids
return obj.get_id2gos(**kws) | [
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tanghaibao/goatools | goatools/associations.py | dnld_ncbi_gene_file | def dnld_ncbi_gene_file(fin, force_dnld=False, log=sys.stdout, loading_bar=True):
"""Download a file from NCBI Gene's ftp server."""
if not os.path.exists(fin) or force_dnld:
import gzip
fin_dir, fin_base = os.path.split(fin)
fin_gz = "{F}.gz".format(F=fin_base)
fin_gz = os.path.join(fin_dir, fin_gz)
if os.path.exists(fin_gz):
os.remove(fin_gz)
fin_ftp = "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/{F}.gz".format(F=fin_base)
## if log is not None:
## log.write(" DOWNLOADING GZIP: {GZ}\n".format(GZ=fin_ftp))
## if loading_bar:
## loading_bar = wget.bar_adaptive
## wget.download(fin_ftp, bar=loading_bar)
## rsp = wget(fin_ftp)
ftp_get(fin_ftp, fin_gz)
with gzip.open(fin_gz, 'rb') as zstrm:
if log is not None:
log.write("\n READ GZIP: {F}\n".format(F=fin_gz))
with open(fin, 'wb') as ostrm:
ostrm.write(zstrm.read())
if log is not None:
log.write(" WROTE UNZIPPED: {F}\n".format(F=fin)) | python | def dnld_ncbi_gene_file(fin, force_dnld=False, log=sys.stdout, loading_bar=True):
"""Download a file from NCBI Gene's ftp server."""
if not os.path.exists(fin) or force_dnld:
import gzip
fin_dir, fin_base = os.path.split(fin)
fin_gz = "{F}.gz".format(F=fin_base)
fin_gz = os.path.join(fin_dir, fin_gz)
if os.path.exists(fin_gz):
os.remove(fin_gz)
fin_ftp = "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/{F}.gz".format(F=fin_base)
## if log is not None:
## log.write(" DOWNLOADING GZIP: {GZ}\n".format(GZ=fin_ftp))
## if loading_bar:
## loading_bar = wget.bar_adaptive
## wget.download(fin_ftp, bar=loading_bar)
## rsp = wget(fin_ftp)
ftp_get(fin_ftp, fin_gz)
with gzip.open(fin_gz, 'rb') as zstrm:
if log is not None:
log.write("\n READ GZIP: {F}\n".format(F=fin_gz))
with open(fin, 'wb') as ostrm:
ostrm.write(zstrm.read())
if log is not None:
log.write(" WROTE UNZIPPED: {F}\n".format(F=fin)) | [
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tanghaibao/goatools | goatools/associations.py | dnld_annofile | def dnld_annofile(fin_anno, anno_type):
"""Download annotation file, if needed"""
if os.path.exists(fin_anno):
return
anno_type = get_anno_desc(fin_anno, anno_type)
if anno_type == 'gene2go':
dnld_ncbi_gene_file(fin_anno)
if anno_type in {'gaf', 'gpad'}:
dnld_annotation(fin_anno) | python | def dnld_annofile(fin_anno, anno_type):
"""Download annotation file, if needed"""
if os.path.exists(fin_anno):
return
anno_type = get_anno_desc(fin_anno, anno_type)
if anno_type == 'gene2go':
dnld_ncbi_gene_file(fin_anno)
if anno_type in {'gaf', 'gpad'}:
dnld_annotation(fin_anno) | [
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tanghaibao/goatools | goatools/associations.py | read_ncbi_gene2go | def read_ncbi_gene2go(fin_gene2go, taxids=None, **kws):
"""Read NCBI's gene2go. Return gene2go data for user-specified taxids."""
obj = Gene2GoReader(fin_gene2go, taxids=taxids)
# By default, return id2gos. User can cause go2geneids to be returned by:
# >>> read_ncbi_gene2go(..., go2geneids=True
if 'taxid2asscs' not in kws:
if len(obj.taxid2asscs) == 1:
taxid = next(iter(obj.taxid2asscs))
kws_ncbi = {k:v for k, v in kws.items() if k in AnnoOptions.keys_exp}
kws_ncbi['taxid'] = taxid
return obj.get_id2gos(**kws_ncbi)
# Optional detailed associations split by taxid and having both ID2GOs & GO2IDs
# e.g., taxid2asscs = defaultdict(lambda: defaultdict(lambda: defaultdict(set))
t2asscs_ret = obj.get_taxid2asscs(taxids, **kws)
t2asscs_usr = kws.get('taxid2asscs', defaultdict(lambda: defaultdict(lambda: defaultdict(set))))
if 'taxid2asscs' in kws:
obj.fill_taxid2asscs(t2asscs_usr, t2asscs_ret)
return obj.get_id2gos_all(t2asscs_ret) | python | def read_ncbi_gene2go(fin_gene2go, taxids=None, **kws):
"""Read NCBI's gene2go. Return gene2go data for user-specified taxids."""
obj = Gene2GoReader(fin_gene2go, taxids=taxids)
# By default, return id2gos. User can cause go2geneids to be returned by:
# >>> read_ncbi_gene2go(..., go2geneids=True
if 'taxid2asscs' not in kws:
if len(obj.taxid2asscs) == 1:
taxid = next(iter(obj.taxid2asscs))
kws_ncbi = {k:v for k, v in kws.items() if k in AnnoOptions.keys_exp}
kws_ncbi['taxid'] = taxid
return obj.get_id2gos(**kws_ncbi)
# Optional detailed associations split by taxid and having both ID2GOs & GO2IDs
# e.g., taxid2asscs = defaultdict(lambda: defaultdict(lambda: defaultdict(set))
t2asscs_ret = obj.get_taxid2asscs(taxids, **kws)
t2asscs_usr = kws.get('taxid2asscs', defaultdict(lambda: defaultdict(lambda: defaultdict(set))))
if 'taxid2asscs' in kws:
obj.fill_taxid2asscs(t2asscs_usr, t2asscs_ret)
return obj.get_id2gos_all(t2asscs_ret) | [
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tanghaibao/goatools | goatools/associations.py | get_b2aset | def get_b2aset(a2bset):
"""Given gene2gos, return go2genes. Given go2genes, return gene2gos."""
b2aset = {}
for a_item, bset in a2bset.items():
for b_item in bset:
if b_item in b2aset:
b2aset[b_item].add(a_item)
else:
b2aset[b_item] = set([a_item])
return b2aset | python | def get_b2aset(a2bset):
"""Given gene2gos, return go2genes. Given go2genes, return gene2gos."""
b2aset = {}
for a_item, bset in a2bset.items():
for b_item in bset:
if b_item in b2aset:
b2aset[b_item].add(a_item)
else:
b2aset[b_item] = set([a_item])
return b2aset | [
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tanghaibao/goatools | goatools/associations.py | get_assc_pruned | def get_assc_pruned(assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys.stdout):
"""Remove GO IDs associated with large numbers of genes. Used in stochastic simulations."""
# DEFN WAS: get_assc_pruned(assc_geneid2gos, max_genecnt=None, prt=sys.stdout):
# ADDED min_genecnt argument and functionality
if max_genecnt is None and min_genecnt is None:
return assc_geneid2gos, set()
go2genes_orig = get_b2aset(assc_geneid2gos)
# go2genes_prun = {go:gs for go, gs in go2genes_orig.items() if len(gs) <= max_genecnt}
go2genes_prun = {}
for goid, genes in go2genes_orig.items():
num_genes = len(genes)
if (min_genecnt is None or num_genes >= min_genecnt) and \
(max_genecnt is None or num_genes <= max_genecnt):
go2genes_prun[goid] = genes
num_was = len(go2genes_orig)
num_now = len(go2genes_prun)
gos_rm = set(go2genes_orig.keys()).difference(set(go2genes_prun.keys()))
assert num_was-num_now == len(gos_rm)
if prt is not None:
if min_genecnt is None:
min_genecnt = 1
if max_genecnt is None:
max_genecnt = "Max"
prt.write("{N:4} GO IDs pruned. Kept {NOW} GOs assc w/({m} to {M} genes)\n".format(
m=min_genecnt, M=max_genecnt, N=num_was-num_now, NOW=num_now))
return get_b2aset(go2genes_prun), gos_rm | python | def get_assc_pruned(assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys.stdout):
"""Remove GO IDs associated with large numbers of genes. Used in stochastic simulations."""
# DEFN WAS: get_assc_pruned(assc_geneid2gos, max_genecnt=None, prt=sys.stdout):
# ADDED min_genecnt argument and functionality
if max_genecnt is None and min_genecnt is None:
return assc_geneid2gos, set()
go2genes_orig = get_b2aset(assc_geneid2gos)
# go2genes_prun = {go:gs for go, gs in go2genes_orig.items() if len(gs) <= max_genecnt}
go2genes_prun = {}
for goid, genes in go2genes_orig.items():
num_genes = len(genes)
if (min_genecnt is None or num_genes >= min_genecnt) and \
(max_genecnt is None or num_genes <= max_genecnt):
go2genes_prun[goid] = genes
num_was = len(go2genes_orig)
num_now = len(go2genes_prun)
gos_rm = set(go2genes_orig.keys()).difference(set(go2genes_prun.keys()))
assert num_was-num_now == len(gos_rm)
if prt is not None:
if min_genecnt is None:
min_genecnt = 1
if max_genecnt is None:
max_genecnt = "Max"
prt.write("{N:4} GO IDs pruned. Kept {NOW} GOs assc w/({m} to {M} genes)\n".format(
m=min_genecnt, M=max_genecnt, N=num_was-num_now, NOW=num_now))
return get_b2aset(go2genes_prun), gos_rm | [
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tanghaibao/goatools | goatools/associations.py | read_annotations | def read_annotations(**kws):
"""Read annotations from either a GAF file or NCBI's gene2go file."""
if 'gaf' not in kws and 'gene2go' not in kws:
return
gene2gos = None
if 'gaf' in kws:
gene2gos = read_gaf(kws['gaf'], prt=sys.stdout)
if not gene2gos:
raise RuntimeError("NO ASSOCIATIONS LOADED FROM {F}".format(F=kws['gaf']))
elif 'gene2go' in kws:
assert 'taxid' in kws, 'taxid IS REQUIRED WHEN READING gene2go'
gene2gos = read_ncbi_gene2go(kws['gene2go'], taxids=[kws['taxid']])
if not gene2gos:
raise RuntimeError("NO ASSOCIATIONS LOADED FROM {F} FOR TAXID({T})".format(
F=kws['gene2go'], T=kws['taxid']))
return gene2gos | python | def read_annotations(**kws):
"""Read annotations from either a GAF file or NCBI's gene2go file."""
if 'gaf' not in kws and 'gene2go' not in kws:
return
gene2gos = None
if 'gaf' in kws:
gene2gos = read_gaf(kws['gaf'], prt=sys.stdout)
if not gene2gos:
raise RuntimeError("NO ASSOCIATIONS LOADED FROM {F}".format(F=kws['gaf']))
elif 'gene2go' in kws:
assert 'taxid' in kws, 'taxid IS REQUIRED WHEN READING gene2go'
gene2gos = read_ncbi_gene2go(kws['gene2go'], taxids=[kws['taxid']])
if not gene2gos:
raise RuntimeError("NO ASSOCIATIONS LOADED FROM {F} FOR TAXID({T})".format(
F=kws['gene2go'], T=kws['taxid']))
return gene2gos | [
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tanghaibao/goatools | goatools/associations.py | get_tcntobj | def get_tcntobj(go2obj, **kws):
"""Return a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf gene2go
annots = read_annotations(**kws)
if annots:
return TermCounts(go2obj, annots) | python | def get_tcntobj(go2obj, **kws):
"""Return a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf gene2go
annots = read_annotations(**kws)
if annots:
return TermCounts(go2obj, annots) | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | get_hdrs | def get_hdrs(flds_all, **kws):
"""Return headers, given user-specified key-word args."""
# Return Headers if the user explicitly lists them.
hdrs = kws.get('hdrs', None)
if hdrs is not None:
return hdrs
# User may specify a subset of fields or a column order using prt_flds
if 'prt_flds' in kws:
return kws['prt_flds']
# All fields in the namedtuple will be in the headers
return flds_all | python | def get_hdrs(flds_all, **kws):
"""Return headers, given user-specified key-word args."""
# Return Headers if the user explicitly lists them.
hdrs = kws.get('hdrs', None)
if hdrs is not None:
return hdrs
# User may specify a subset of fields or a column order using prt_flds
if 'prt_flds' in kws:
return kws['prt_flds']
# All fields in the namedtuple will be in the headers
return flds_all | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx.wr_row_mergeall | def wr_row_mergeall(self, worksheet, txtstr, fmt, row_idx):
"""Merge all columns and place text string in widened cell."""
hdridxval = len(self.hdrs) - 1
worksheet.merge_range(row_idx, 0, row_idx, hdridxval, txtstr, fmt)
return row_idx + 1 | python | def wr_row_mergeall(self, worksheet, txtstr, fmt, row_idx):
"""Merge all columns and place text string in widened cell."""
hdridxval = len(self.hdrs) - 1
worksheet.merge_range(row_idx, 0, row_idx, hdridxval, txtstr, fmt)
return row_idx + 1 | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx.wr_hdrs | def wr_hdrs(self, worksheet, row_idx):
"""Print row of column headers"""
for col_idx, hdr in enumerate(self.hdrs):
# print("ROW({R}) COL({C}) HDR({H}) FMT({F})\n".format(
# R=row_idx, C=col_idx, H=hdr, F=self.fmt_hdr))
worksheet.write(row_idx, col_idx, hdr, self.fmt_hdr)
row_idx += 1
return row_idx | python | def wr_hdrs(self, worksheet, row_idx):
"""Print row of column headers"""
for col_idx, hdr in enumerate(self.hdrs):
# print("ROW({R}) COL({C}) HDR({H}) FMT({F})\n".format(
# R=row_idx, C=col_idx, H=hdr, F=self.fmt_hdr))
worksheet.write(row_idx, col_idx, hdr, self.fmt_hdr)
row_idx += 1
return row_idx | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx.wr_data | def wr_data(self, xlsx_data, row_i, worksheet):
"""Write data into xlsx worksheet."""
fld2fmt = self.vars.fld2fmt
# User may specify to skip rows based on values in row
prt_if = self.vars.prt_if
# User may specify a subset of columns to print or
# a column ordering different from the _fields seen in the namedtuple
prt_flds = self.wbfmtobj.get_prt_flds()
get_wbfmt = self.wbfmtobj.get_wbfmt
if self.vars.sort_by is not None:
xlsx_data = sorted(xlsx_data, key=self.vars.sort_by)
try:
for data_nt in xlsx_data:
if prt_if is None or prt_if(data_nt):
wbfmt = get_wbfmt(data_nt) # xlsxwriter.format.Format created w/add_format
# Print an xlsx row by printing each column in order.
for col_i, fld in enumerate(prt_flds):
try:
# If fld "format_txt" present, use val for formatting, but don't print.
val = getattr(data_nt, fld, "")
# Optional user-formatting of specific fields, eg, pval: "{:8.2e}"
# If field value is empty (""), don't use fld2fmt
if fld2fmt is not None and fld in fld2fmt and val != "" and val != "*":
val = fld2fmt[fld].format(val)
worksheet.write(row_i, col_i, val, wbfmt)
except:
raise RuntimeError(self._get_err_msg(row_i, col_i, fld, val, prt_flds))
row_i += 1
except RuntimeError as inst:
import traceback
traceback.print_exc()
sys.stderr.write("\n **FATAL in wr_data: {MSG}\n\n".format(MSG=str(inst)))
sys.exit(1)
return row_i | python | def wr_data(self, xlsx_data, row_i, worksheet):
"""Write data into xlsx worksheet."""
fld2fmt = self.vars.fld2fmt
# User may specify to skip rows based on values in row
prt_if = self.vars.prt_if
# User may specify a subset of columns to print or
# a column ordering different from the _fields seen in the namedtuple
prt_flds = self.wbfmtobj.get_prt_flds()
get_wbfmt = self.wbfmtobj.get_wbfmt
if self.vars.sort_by is not None:
xlsx_data = sorted(xlsx_data, key=self.vars.sort_by)
try:
for data_nt in xlsx_data:
if prt_if is None or prt_if(data_nt):
wbfmt = get_wbfmt(data_nt) # xlsxwriter.format.Format created w/add_format
# Print an xlsx row by printing each column in order.
for col_i, fld in enumerate(prt_flds):
try:
# If fld "format_txt" present, use val for formatting, but don't print.
val = getattr(data_nt, fld, "")
# Optional user-formatting of specific fields, eg, pval: "{:8.2e}"
# If field value is empty (""), don't use fld2fmt
if fld2fmt is not None and fld in fld2fmt and val != "" and val != "*":
val = fld2fmt[fld].format(val)
worksheet.write(row_i, col_i, val, wbfmt)
except:
raise RuntimeError(self._get_err_msg(row_i, col_i, fld, val, prt_flds))
row_i += 1
except RuntimeError as inst:
import traceback
traceback.print_exc()
sys.stderr.write("\n **FATAL in wr_data: {MSG}\n\n".format(MSG=str(inst)))
sys.exit(1)
return row_i | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx._get_err_msg | def _get_err_msg(row, col, fld, val, prt_flds):
"""Return an informative message with details of xlsx write attempt."""
import traceback
traceback.print_exc()
err_msg = (
"ROW({R}) COL({C}) FIELD({F}) VAL({V})\n".format(R=row, C=col, F=fld, V=val),
"PRINT FIELDS({N}): {F}".format(N=len(prt_flds), F=" ".join(prt_flds)))
return "\n".join(err_msg) | python | def _get_err_msg(row, col, fld, val, prt_flds):
"""Return an informative message with details of xlsx write attempt."""
import traceback
traceback.print_exc()
err_msg = (
"ROW({R}) COL({C}) FIELD({F}) VAL({V})\n".format(R=row, C=col, F=fld, V=val),
"PRINT FIELDS({N}): {F}".format(N=len(prt_flds), F=" ".join(prt_flds)))
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx.add_worksheet | def add_worksheet(self):
"""Add a worksheet to the workbook."""
wsh = self.workbook.add_worksheet()
if self.vars.fld2col_widths is not None:
self.set_xlsx_colwidths(wsh, self.vars.fld2col_widths, self.wbfmtobj.get_prt_flds())
return wsh | python | def add_worksheet(self):
"""Add a worksheet to the workbook."""
wsh = self.workbook.add_worksheet()
if self.vars.fld2col_widths is not None:
self.set_xlsx_colwidths(wsh, self.vars.fld2col_widths, self.wbfmtobj.get_prt_flds())
return wsh | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WrXlsx.set_xlsx_colwidths | def set_xlsx_colwidths(worksheet, fld2col_widths, fldnames):
"""Set xlsx column widths using fld2col_widths."""
for col_idx, fld in enumerate(fldnames):
col_width = fld2col_widths.get(fld, None)
if col_width is not None:
worksheet.set_column(col_idx, col_idx, col_width) | python | def set_xlsx_colwidths(worksheet, fld2col_widths, fldnames):
"""Set xlsx column widths using fld2col_widths."""
for col_idx, fld in enumerate(fldnames):
col_width = fld2col_widths.get(fld, None)
if col_width is not None:
worksheet.set_column(col_idx, col_idx, col_width) | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt.get_hdrs | def get_hdrs(self, **kws):
"""Initialize column headers."""
hdrs = get_hdrs(self.prt_flds, **kws)
# Values in a "format_txt" "column" are used for formatting, not printing
return [h for h in hdrs if h != "format_txt"] | python | def get_hdrs(self, **kws):
"""Initialize column headers."""
hdrs = get_hdrs(self.prt_flds, **kws)
# Values in a "format_txt" "column" are used for formatting, not printing
return [h for h in hdrs if h != "format_txt"] | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt._init_fmtname2wbfmtobj | def _init_fmtname2wbfmtobj(self, workbook, **kws):
"""Initialize fmtname2wbfmtobj."""
wbfmtdict = [
kws.get('format_txt0', self.dflt_wbfmtdict[0]),
kws.get('format_txt1', self.dflt_wbfmtdict[1]),
kws.get('format_txt2', self.dflt_wbfmtdict[2]),
kws.get('format_txt3', self.dflt_wbfmtdict[3])]
fmtname2wbfmtobj = {
'plain': workbook.add_format(wbfmtdict[0]),
'plain bold': workbook.add_format(wbfmtdict[3]),
'very light grey' : workbook.add_format(wbfmtdict[1]),
'light grey' :workbook.add_format(wbfmtdict[2])}
# Use a xlsx namedtuple field value to set row color
ntval2wbfmtdict = kws.get('ntval2wbfmtdict', None)
if ntval2wbfmtdict is not None:
for ntval, wbfmtdict in ntval2wbfmtdict.items():
fmtname2wbfmtobj[ntval] = workbook.add_format(wbfmtdict)
if 'ntfld_wbfmt' not in kws:
sys.stdout.write("**WARNING: 'ntfld_wbfmt' NOT PRESENT\n")
return fmtname2wbfmtobj | python | def _init_fmtname2wbfmtobj(self, workbook, **kws):
"""Initialize fmtname2wbfmtobj."""
wbfmtdict = [
kws.get('format_txt0', self.dflt_wbfmtdict[0]),
kws.get('format_txt1', self.dflt_wbfmtdict[1]),
kws.get('format_txt2', self.dflt_wbfmtdict[2]),
kws.get('format_txt3', self.dflt_wbfmtdict[3])]
fmtname2wbfmtobj = {
'plain': workbook.add_format(wbfmtdict[0]),
'plain bold': workbook.add_format(wbfmtdict[3]),
'very light grey' : workbook.add_format(wbfmtdict[1]),
'light grey' :workbook.add_format(wbfmtdict[2])}
# Use a xlsx namedtuple field value to set row color
ntval2wbfmtdict = kws.get('ntval2wbfmtdict', None)
if ntval2wbfmtdict is not None:
for ntval, wbfmtdict in ntval2wbfmtdict.items():
fmtname2wbfmtobj[ntval] = workbook.add_format(wbfmtdict)
if 'ntfld_wbfmt' not in kws:
sys.stdout.write("**WARNING: 'ntfld_wbfmt' NOT PRESENT\n")
return fmtname2wbfmtobj | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt.get_wbfmt | def get_wbfmt(self, data_nt=None):
"""Return format for text cell."""
if data_nt is None or self.b_plain:
return self.fmtname2wbfmtobj.get('plain')
# User namedtuple field/value for color
if self.ntfld_wbfmt is not None:
return self.__get_wbfmt_usrfld(data_nt)
# namedtuple format_txt for color/bold/border
if self.b_format_txt:
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return wbfmt
# 'ntfld_wbfmt': namedtuple field which contains a value used as a key for a xlsx format
# 'ntval2wbfmtdict': namedtuple value and corresponding xlsx format dict.
return self.fmtname2wbfmtobj.get('plain') | python | def get_wbfmt(self, data_nt=None):
"""Return format for text cell."""
if data_nt is None or self.b_plain:
return self.fmtname2wbfmtobj.get('plain')
# User namedtuple field/value for color
if self.ntfld_wbfmt is not None:
return self.__get_wbfmt_usrfld(data_nt)
# namedtuple format_txt for color/bold/border
if self.b_format_txt:
wbfmt = self.__get_wbfmt_format_txt(data_nt)
if wbfmt is not None:
return wbfmt
# 'ntfld_wbfmt': namedtuple field which contains a value used as a key for a xlsx format
# 'ntval2wbfmtdict': namedtuple value and corresponding xlsx format dict.
return self.fmtname2wbfmtobj.get('plain') | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt.__get_wbfmt_usrfld | def __get_wbfmt_usrfld(self, data_nt):
"""Return format for text cell from namedtuple field specified by 'ntfld_wbfmt'"""
if self.ntfld_wbfmt is not None:
if isinstance(self.ntfld_wbfmt, str):
ntval = getattr(data_nt, self.ntfld_wbfmt, None) # Ex: 'section'
if ntval is not None:
return self.fmtname2wbfmtobj.get(ntval, None) | python | def __get_wbfmt_usrfld(self, data_nt):
"""Return format for text cell from namedtuple field specified by 'ntfld_wbfmt'"""
if self.ntfld_wbfmt is not None:
if isinstance(self.ntfld_wbfmt, str):
ntval = getattr(data_nt, self.ntfld_wbfmt, None) # Ex: 'section'
if ntval is not None:
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt.__get_wbfmt_format_txt | def __get_wbfmt_format_txt(self, data_nt):
"""Return format for text cell from namedtuple field, 'format_txt'."""
format_txt_val = getattr(data_nt, "format_txt")
if format_txt_val == 1:
return self.fmtname2wbfmtobj.get("very light grey")
if format_txt_val == 2:
return self.fmtname2wbfmtobj.get("light grey")
return self.fmtname2wbfmtobj.get(format_txt_val) | python | def __get_wbfmt_format_txt(self, data_nt):
"""Return format for text cell from namedtuple field, 'format_txt'."""
format_txt_val = getattr(data_nt, "format_txt")
if format_txt_val == 1:
return self.fmtname2wbfmtobj.get("very light grey")
if format_txt_val == 2:
return self.fmtname2wbfmtobj.get("light grey")
return self.fmtname2wbfmtobj.get(format_txt_val) | [
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tanghaibao/goatools | goatools/wr_tbl_class.py | WbFmt.get_fmt_section | def get_fmt_section(self):
"""Grey if printing header GOs and plain if not printing header GOs."""
if self.b_format_txt:
return self.fmtname2wbfmtobj.get("light grey")
return self.fmtname2wbfmtobj.get("plain bold") | python | def get_fmt_section(self):
"""Grey if printing header GOs and plain if not printing header GOs."""
if self.b_format_txt:
return self.fmtname2wbfmtobj.get("light grey")
return self.fmtname2wbfmtobj.get("plain bold") | [
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader.get_id2gos | def get_id2gos(self, **kws):
#### def get_annotations_dct(self, taxid, options):
"""Return geneid2gos, or optionally go2geneids."""
if len(self.taxid2asscs) == 1:
taxid = next(iter(self.taxid2asscs.keys()))
return self._get_id2gos(self.taxid2asscs[taxid], **kws)
assert 'taxid' in kws, "**FATAL: 'taxid' NOT FOUND IN Gene2GoReader::get_id2gos({KW})".format(KW=kws)
taxid = kws['taxid']
assert taxid in self.taxid2asscs, '**FATAL: TAXID({T}) DATA MISSING'.format(T=taxid)
return self._get_id2gos(self.taxid2asscs[taxid], **kws) | python | def get_id2gos(self, **kws):
#### def get_annotations_dct(self, taxid, options):
"""Return geneid2gos, or optionally go2geneids."""
if len(self.taxid2asscs) == 1:
taxid = next(iter(self.taxid2asscs.keys()))
return self._get_id2gos(self.taxid2asscs[taxid], **kws)
assert 'taxid' in kws, "**FATAL: 'taxid' NOT FOUND IN Gene2GoReader::get_id2gos({KW})".format(KW=kws)
taxid = kws['taxid']
assert taxid in self.taxid2asscs, '**FATAL: TAXID({T}) DATA MISSING'.format(T=taxid)
return self._get_id2gos(self.taxid2asscs[taxid], **kws) | [
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader.get_name | def get_name(self):
"""Get name using taxid"""
if len(self.taxid2asscs) == 1:
return '{BASE}_{TAXID}'.format(
BASE=self.name, TAXID=next(iter(self.taxid2asscs.keys())))
return '{BASE}_various'.format(BASE=self.name) | python | def get_name(self):
"""Get name using taxid"""
if len(self.taxid2asscs) == 1:
return '{BASE}_{TAXID}'.format(
BASE=self.name, TAXID=next(iter(self.taxid2asscs.keys())))
return '{BASE}_various'.format(BASE=self.name) | [
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader.get_taxid | def get_taxid(self):
"""Return taxid, if one was provided. Other wise return True representing all taxids"""
return next(iter(self.taxid2asscs.keys())) if len(self.taxid2asscs) == 1 else True | python | def get_taxid(self):
"""Return taxid, if one was provided. Other wise return True representing all taxids"""
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader.fill_taxid2asscs | def fill_taxid2asscs(taxid2asscs_usr, taxid2asscs_ret):
"""Fill user taxid2asscs for backward compatibility."""
for taxid, ab_ret in taxid2asscs_ret.items():
taxid2asscs_usr[taxid]['ID2GOs'] = ab_ret['ID2GOs']
taxid2asscs_usr[taxid]['GO2IDs'] = ab_ret['GO2IDs'] | python | def fill_taxid2asscs(taxid2asscs_usr, taxid2asscs_ret):
"""Fill user taxid2asscs for backward compatibility."""
for taxid, ab_ret in taxid2asscs_ret.items():
taxid2asscs_usr[taxid]['ID2GOs'] = ab_ret['ID2GOs']
taxid2asscs_usr[taxid]['GO2IDs'] = ab_ret['GO2IDs'] | [
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader._get_taxids | def _get_taxids(self, taxids=None):
"""Return user-specified taxids or taxids in self.taxid2asscs"""
taxid_keys = set(self.taxid2asscs.keys())
return taxid_keys if taxids is None else set(taxids).intersection(taxid_keys) | python | def _get_taxids(self, taxids=None):
"""Return user-specified taxids or taxids in self.taxid2asscs"""
taxid_keys = set(self.taxid2asscs.keys())
return taxid_keys if taxids is None else set(taxids).intersection(taxid_keys) | [
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tanghaibao/goatools | goatools/anno/genetogo_reader.py | Gene2GoReader._init_taxid2asscs | def _init_taxid2asscs(self):
"""Create dict with taxid keys and annotation namedtuple list."""
taxid2asscs = cx.defaultdict(list)
for ntanno in self.associations:
taxid2asscs[ntanno.tax_id].append(ntanno)
assert len(taxid2asscs) != 0, "**FATAL: NO TAXIDS: {F}".format(F=self.filename)
# """Print the number of taxids stored."""
prt = sys.stdout
num_taxids = len(taxid2asscs)
prt.write('{N} taxids stored'.format(N=num_taxids))
if num_taxids < 5:
prt.write(': {Ts}'.format(Ts=' '.join(sorted(str(t) for t in taxid2asscs))))
prt.write('\n')
return dict(taxid2asscs) | python | def _init_taxid2asscs(self):
"""Create dict with taxid keys and annotation namedtuple list."""
taxid2asscs = cx.defaultdict(list)
for ntanno in self.associations:
taxid2asscs[ntanno.tax_id].append(ntanno)
assert len(taxid2asscs) != 0, "**FATAL: NO TAXIDS: {F}".format(F=self.filename)
# """Print the number of taxids stored."""
prt = sys.stdout
num_taxids = len(taxid2asscs)
prt.write('{N} taxids stored'.format(N=num_taxids))
if num_taxids < 5:
prt.write(': {Ts}'.format(Ts=' '.join(sorted(str(t) for t in taxid2asscs))))
prt.write('\n')
return dict(taxid2asscs) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGosArgs.get_go2color_inst | def get_go2color_inst(self, hdrgo):
"""Get a copy of go2color with GO group header colored."""
go2color = self.go2color.copy()
go2color[hdrgo] = self.hdrgo_dflt_color
return go2color | python | def get_go2color_inst(self, hdrgo):
"""Get a copy of go2color with GO group header colored."""
go2color = self.go2color.copy()
go2color[hdrgo] = self.hdrgo_dflt_color
return go2color | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGosArgs.get_kws_plt | def get_kws_plt(self):
"""Get keyword args for GoSubDagPlot from self unless they are None."""
kws_plt = {}
for key_plt in self.keys_plt:
key_val = getattr(self, key_plt, None)
if key_val is not None:
kws_plt[key_plt] = key_val
elif key_plt in self.kws:
kws_plt[key_plt] = self.kws[key_plt]
return kws_plt | python | def get_kws_plt(self):
"""Get keyword args for GoSubDagPlot from self unless they are None."""
kws_plt = {}
for key_plt in self.keys_plt:
key_val = getattr(self, key_plt, None)
if key_val is not None:
kws_plt[key_plt] = key_val
elif key_plt in self.kws:
kws_plt[key_plt] = self.kws[key_plt]
return kws_plt | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGosArgs._init_go2bordercolor | def _init_go2bordercolor(objcolors, **kws):
"""Initialize go2bordercolor with default to make hdrgos bright blue."""
go2bordercolor_ret = objcolors.get_bordercolor()
if 'go2bordercolor' not in kws:
return go2bordercolor_ret
go2bordercolor_usr = kws['go2bordercolor']
goids = set(go2bordercolor_ret).intersection(go2bordercolor_usr)
for goid in goids:
go2bordercolor_usr[goid] = go2bordercolor_ret[goid]
return go2bordercolor_usr | python | def _init_go2bordercolor(objcolors, **kws):
"""Initialize go2bordercolor with default to make hdrgos bright blue."""
go2bordercolor_ret = objcolors.get_bordercolor()
if 'go2bordercolor' not in kws:
return go2bordercolor_ret
go2bordercolor_usr = kws['go2bordercolor']
goids = set(go2bordercolor_ret).intersection(go2bordercolor_usr)
for goid in goids:
go2bordercolor_usr[goid] = go2bordercolor_ret[goid]
return go2bordercolor_usr | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos.plot_groups_unplaced | def plot_groups_unplaced(self, fout_dir=".", **kws_pltargs):
"""Plot GO DAGs for groups of user GOs which are not in a section."""
hdrgos = self.grprobj.get_hdrgos_unplaced()
pltargs = PltGroupedGosArgs(self.grprobj, fout_dir=fout_dir, **kws_pltargs)
return self._plot_groups_hdrgos(hdrgos, pltargs) | python | def plot_groups_unplaced(self, fout_dir=".", **kws_pltargs):
"""Plot GO DAGs for groups of user GOs which are not in a section."""
hdrgos = self.grprobj.get_hdrgos_unplaced()
pltargs = PltGroupedGosArgs(self.grprobj, fout_dir=fout_dir, **kws_pltargs)
return self._plot_groups_hdrgos(hdrgos, pltargs) | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_plt_data | def _get_plt_data(self, hdrgos_usr):
"""Given User GO IDs, return their GO headers and other GO info."""
hdrgo2usrgos = self.grprobj.get_hdrgo2usrgos(hdrgos_usr)
usrgos_actual = set([u for us in hdrgo2usrgos.values() for u in us])
go2obj = self.gosubdag.get_go2obj(usrgos_actual.union(hdrgo2usrgos.keys()))
return hdrgo2usrgos, go2obj | python | def _get_plt_data(self, hdrgos_usr):
"""Given User GO IDs, return their GO headers and other GO info."""
hdrgo2usrgos = self.grprobj.get_hdrgo2usrgos(hdrgos_usr)
usrgos_actual = set([u for us in hdrgo2usrgos.values() for u in us])
go2obj = self.gosubdag.get_go2obj(usrgos_actual.union(hdrgo2usrgos.keys()))
return hdrgo2usrgos, go2obj | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._plot_go_group | def _plot_go_group(self, hdrgo, usrgos, pltargs, go2parentids):
"""Plot an exploratory GO DAG for a single Group of user GOs."""
gosubdagplotnts = self._get_gosubdagplotnts(hdrgo, usrgos, pltargs, go2parentids)
# Create pngs and return png names
pngs = [obj.wrplt(pltargs.fout_dir, pltargs.plt_ext) for obj in gosubdagplotnts]
return pngs | python | def _plot_go_group(self, hdrgo, usrgos, pltargs, go2parentids):
"""Plot an exploratory GO DAG for a single Group of user GOs."""
gosubdagplotnts = self._get_gosubdagplotnts(hdrgo, usrgos, pltargs, go2parentids)
# Create pngs and return png names
pngs = [obj.wrplt(pltargs.fout_dir, pltargs.plt_ext) for obj in gosubdagplotnts]
return pngs | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_dotgraphs | def _get_dotgraphs(self, hdrgo, usrgos, pltargs, go2parentids):
"""Get a GO DAG in a dot-language string for a single Group of user GOs."""
gosubdagplotnts = self._get_gosubdagplotnts(hdrgo, usrgos, pltargs, go2parentids)
# Create DAG graphs as dot language strings. Loop through GoSubDagPlotNt list
dotstrs = [obj.get_dotstr() for obj in gosubdagplotnts]
return dotstrs | python | def _get_dotgraphs(self, hdrgo, usrgos, pltargs, go2parentids):
"""Get a GO DAG in a dot-language string for a single Group of user GOs."""
gosubdagplotnts = self._get_gosubdagplotnts(hdrgo, usrgos, pltargs, go2parentids)
# Create DAG graphs as dot language strings. Loop through GoSubDagPlotNt list
dotstrs = [obj.get_dotstr() for obj in gosubdagplotnts]
return dotstrs | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_gosubdagplotnts | def _get_gosubdagplotnts(self, hdrgo, usrgos, pltargs, go2parentids):
"""Get list of GoSubDagPlotNt for plotting an exploratory GODAG for 1 Group of user GOs."""
dotgraphs = []
go2color = pltargs.get_go2color_inst(hdrgo)
# namedtuple fields: hdrgo gosubdag tot_usrgos parentcnt desc
ntpltgo0 = self._get_pltdag_ancesters(hdrgo, usrgos, desc="")
ntpltgo1 = self._get_pltdag_path_hdr(hdrgo, usrgos, desc="pruned")
num_go0 = len(ntpltgo0.gosubdag.go2obj)
num_go1 = len(ntpltgo1.gosubdag.go2obj)
title = "{GO} {NAME}; {N} GO sources".format(
GO=hdrgo,
NAME=self.gosubdag.go2obj[hdrgo].name,
N=len(ntpltgo0.gosubdag.go_sources))
# print("PltGroupedGos::_get_gosubdagplotnts TITLE", title)
if num_go0 < pltargs.max_gos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo0 ALWAYS IF NOT TOO BIG")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo0, title, go2color, pltargs))
# PLOT A: Plot the entire GO ID group under GO header, hdrgo, if not too big
if num_go0 < pltargs.max_gos and \
ntpltgo0.tot_usrgos == ntpltgo1.tot_usrgos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo0 AAAAAAAAAAAAAAAAA")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo0, title, go2color, pltargs))
# PLOT B: Plot only the GO ID group passing thru the GO header, hdrgo, if not too big
elif num_go1 < pltargs.max_gos and ntpltgo0.tot_usrgos != ntpltgo1.tot_usrgos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo1(pruned) BBBBBBBBBBBBBBBBB")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo1, title, go2color, pltargs))
# PLOT C: If DAG is large, just print upper portion
# PLOT D: If DAG is large, just print upper portion passing through the GO header
elif num_go1 >= pltargs.upper_trigger:
# print("PltGroupedGos::_get_gosubdagplotnts upper_pruned CCCCCCCCCCCCCCCCC")
gos_upper = self._get_gos_upper(ntpltgo1, pltargs.max_upper, go2parentids)
#ntpltgo2 = self._get_pltdag_ancesters(hdrgo, gos_upper, "{BASE}_upper.png")
ntpltgo3 = self._get_pltdag_path_hdr(hdrgo, gos_upper, "upper_pruned")
# Middle GO terms chosen to be start points will be green unless reset back
for goid in gos_upper:
if goid not in go2color:
go2color[goid] = 'white'
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo3, title, go2color, pltargs))
else:
# print("PltGroupedGos::_get_gosubdagplotnts EEEEEEEEEEEEEEEEE")
self._no_ntplt(ntpltgo0)
return dotgraphs | python | def _get_gosubdagplotnts(self, hdrgo, usrgos, pltargs, go2parentids):
"""Get list of GoSubDagPlotNt for plotting an exploratory GODAG for 1 Group of user GOs."""
dotgraphs = []
go2color = pltargs.get_go2color_inst(hdrgo)
# namedtuple fields: hdrgo gosubdag tot_usrgos parentcnt desc
ntpltgo0 = self._get_pltdag_ancesters(hdrgo, usrgos, desc="")
ntpltgo1 = self._get_pltdag_path_hdr(hdrgo, usrgos, desc="pruned")
num_go0 = len(ntpltgo0.gosubdag.go2obj)
num_go1 = len(ntpltgo1.gosubdag.go2obj)
title = "{GO} {NAME}; {N} GO sources".format(
GO=hdrgo,
NAME=self.gosubdag.go2obj[hdrgo].name,
N=len(ntpltgo0.gosubdag.go_sources))
# print("PltGroupedGos::_get_gosubdagplotnts TITLE", title)
if num_go0 < pltargs.max_gos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo0 ALWAYS IF NOT TOO BIG")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo0, title, go2color, pltargs))
# PLOT A: Plot the entire GO ID group under GO header, hdrgo, if not too big
if num_go0 < pltargs.max_gos and \
ntpltgo0.tot_usrgos == ntpltgo1.tot_usrgos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo0 AAAAAAAAAAAAAAAAA")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo0, title, go2color, pltargs))
# PLOT B: Plot only the GO ID group passing thru the GO header, hdrgo, if not too big
elif num_go1 < pltargs.max_gos and ntpltgo0.tot_usrgos != ntpltgo1.tot_usrgos:
# print("PltGroupedGos::_get_gosubdagplotnts ntpltgo1(pruned) BBBBBBBBBBBBBBBBB")
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo1, title, go2color, pltargs))
# PLOT C: If DAG is large, just print upper portion
# PLOT D: If DAG is large, just print upper portion passing through the GO header
elif num_go1 >= pltargs.upper_trigger:
# print("PltGroupedGos::_get_gosubdagplotnts upper_pruned CCCCCCCCCCCCCCCCC")
gos_upper = self._get_gos_upper(ntpltgo1, pltargs.max_upper, go2parentids)
#ntpltgo2 = self._get_pltdag_ancesters(hdrgo, gos_upper, "{BASE}_upper.png")
ntpltgo3 = self._get_pltdag_path_hdr(hdrgo, gos_upper, "upper_pruned")
# Middle GO terms chosen to be start points will be green unless reset back
for goid in gos_upper:
if goid not in go2color:
go2color[goid] = 'white'
dotgraphs.append(self._get_gosubdagplotnt(ntpltgo3, title, go2color, pltargs))
else:
# print("PltGroupedGos::_get_gosubdagplotnts EEEEEEEEEEEEEEEEE")
self._no_ntplt(ntpltgo0)
return dotgraphs | [
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tanghaibao/goatools | goatools/grouper/plotobj.py | PltGroupedGos._get_gos_upper | def _get_gos_upper(self, ntpltgo1, max_upper, go2parentids):
"""Plot a GO DAG for the upper portion of a single Group of user GOs."""
# Get GO IDs which are in the hdrgo path
goids_possible = ntpltgo1.gosubdag.go2obj.keys()
# Get upper GO IDs which have the most descendants
return self._get_gosrcs_upper(goids_possible, max_upper, go2parentids) | python | def _get_gos_upper(self, ntpltgo1, max_upper, go2parentids):
"""Plot a GO DAG for the upper portion of a single Group of user GOs."""
# Get GO IDs which are in the hdrgo path
goids_possible = ntpltgo1.gosubdag.go2obj.keys()
# Get upper GO IDs which have the most descendants
return self._get_gosrcs_upper(goids_possible, max_upper, go2parentids) | [
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