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
def _read_sections(sec):
"""Get sections variable from file."""
if '/' in sec:
sec = os.path.join(REPO, sec)
var = read_sections(sec)
assert var, "EMPTY SECTIONS FILE({})".format(sec)
return var
def _read_sections(sec):
"""Get sections variable from file."""
if '/' in sec:
sec = os.path.join(REPO, sec)
var = read_sections(sec)
assert var, "EMPTY SECTIONS FILE({})".format(sec)
return var
def _get_objpltg(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)
return GoSubDagPlot(self.gosubdag,
Go2Color=objcolor,
go2txt=go2txt,
**kws)
def __init__(self, gosubdag, godag_version, **kws):
_kws = {k: v for k, v in kws.items() if k in self.kws_dict}
self.grprdflt = GrouperDflts(gosubdag, _kws['slims'])
self.ver_list = [godag_version, self.grprdflt.ver_goslims]
self.sections = read_sections(self._get_secstr(**_kws),
exclude_ungrouped=False)
self.hdrobj = HdrgosSections(gosubdag, self.grprdflt.hdrgos_dflt,
self.sections)
_go2nt = _kws.get('go2nt')
self.grprobj = Grouper("all",
gosubdag.go_sources,
self.hdrobj,
gosubdag,
go2nt=_go2nt)
def __init__(self, args):
self.args = args
self.sections = read_sections(self.args.sections) if self.args.sections else None
_optional_attrs = ['relationship'] if self.sections else None
self.godag = GODag(obo_file=self.args.obo, optional_attrs=_optional_attrs)
# Get GOEnrichmentStudy
_study, _pop, _assoc = self.rd_files()
if not self.args.compare: # sanity check
self.chk_genes(_study, _pop)
self.methods = self.args.method.split(",")
self.itemid2name = self._init_itemid2name()
self.objgoea = self._init_objgoea(_pop, _assoc)
# Run GOEA
self.results_all = self.objgoea.run_study(_study)
# Prepare for grouping, if user-specified. Create GroupItems
self.prepgrp = GroupItems(_assoc, self, self.godag.version) if self.sections else None
def _wr_sections_txt(fout_txt, usrgos, sections_file, grprdflt):
"""Given a list of usrgos and sections, write text file."""
try:
sections = read_sections(sections_file)
hdrobj = HdrgosSections(grprdflt.gosubdag,
grprdflt.hdrgos_dflt,
sections=sections)
grprobj = Grouper(fout_txt,
usrgos,
hdrobj,
grprdflt.gosubdag,
go2nt=None)
full_txt = os.path.join(REPO, fout_txt)
WrSections(grprobj).wr_txt_section_hdrgos(full_txt,
sortby=None,
prt_section=True)
assert os.path.exists(full_txt)
except RuntimeError as inst:
sys.stdout.write("\n **FATAL: {MSG}\n\n".format(MSG=str(inst)))
def __init__(self, args):
self.args = args
self.sections = read_sections(self.args.sections) if self.args.sections else None
_optional_attrs = ['relationship'] if self.sections else None
self.godag = GODag(obo_file=self.args.obo, optional_attrs=_optional_attrs)
# Get GOEnrichmentStudy
print('ARGS GoeaCliFnc', self.args)
self.objanno = self._get_objanno(self.args.filenames[2])
_ns2assoc = self.objanno.get_ns2assc(**self._get_anno_kws())
_study, _pop = self.rd_files(*self.args.filenames[:2])
if not self.args.compare: # sanity check
self.chk_genes(_study, _pop, self.objanno.associations)
self.methods = self.args.method.split(",")
self.itemid2name = self._init_itemid2name()
self.objgoeans = self._init_objgoeans(_pop, _ns2assoc)
# Run GOEA
self.results_all = self.objgoeans.run_study(_study)
# Prepare for grouping, if user-specified. Create GroupItems
self.prepgrp = GroupItems(self, self.godag.version) if self.sections else None
def __init__(self, args):
self.args = args
self.sections = read_sections(
self.args.sections) if self.args.sections else None
_optional_attrs = ['relationship'] if self.sections else None
self.godag = GODag(obo_file=self.args.obo,
optional_attrs=_optional_attrs)
# Get GOEnrichmentStudy
# print('ARGS GoeaCliFnc ', self.args)
self.objanno = self._get_objanno(self.args.filenames[2])
_ns2assoc = self.objanno.get_ns2assc(**self._get_anno_kws())
_study, _pop = self.rd_files(*self.args.filenames[:2])
if not self.args.compare: # sanity check
self.chk_genes(_study, _pop, self.objanno.associations)
self.methods = self.args.method.split(",")
self.itemid2name = self._init_itemid2name()
self.objgoeans = self._init_objgoeans(_pop, _ns2assoc)
# Run GOEA
self.results_all = self.objgoeans.run_study(_study)
# Prepare for grouping, if user-specified. Create GroupItems
self.prepgrp = GroupItems(
self, self.godag.version) if self.sections else None
def cli(self, prt=sys.stdout):
"""Command-line interface for go_draw script."""
kws = self.objdoc.get_docargs(prt=None)
godag = get_godag(kws['obo'],
prt=None,
loading_bar=False,
optional_attrs=['relationship'])
usrgos = GetGOs(godag, max_gos=200).get_usrgos(kws.get('GO_FILE'), prt)
tcntobj = self._get_tcntobj(usrgos, godag,
**kws) # Gets TermCounts or None
self.gosubdag = GoSubDag(usrgos,
godag,
relationships=True,
tcntobj=tcntobj,
prt=None)
grprdflt = GrouperDflts(self.gosubdag, kws['slims'])
ver_list = [godag.version, grprdflt.ver_goslims]
prt.write("{VER}\n".format(VER="\n".join(ver_list)))
sections = read_sections(kws['ifile'],
exclude_ungrouped=True,
prt=None)
# print("SECSECSEC", sections)
hdrobj = HdrgosSections(self.gosubdag, grprdflt.hdrgos_dflt, sections)
grprobj = Grouper("init", usrgos, hdrobj, self.gosubdag)
# Write sections
objsecwr = WrSections(grprobj, ver_list)
if not os.path.exists(kws['ifile']):
objsecwr.wr_txt_section_hdrgos(kws['ifile'])
objsecwr.wr_txt_section_hdrgos(kws['ofile'])
objsecpy = WrPySections(grprobj, ver_list)
if 'py' in kws:
objsecpy.wr_py_sections(kws['py'], sections, doc=godag.version)
# Write user GO IDs in sections
sortobj = Sorter(grprobj)
objgowr = WrXlsxSortedGos("init", sortobj, ver_list)
objgowr.wr_txt_gos(kws['txt'], sortby=objsecpy.fncsortnt)
#objwr.wr_txt_section_hdrgos(kws['ofile'], sortby=objwr.fncsortnt)
self._prt_cnt_usrgos(usrgos, sys.stdout)
def __init__(self, args):
self.args = args
self.sections = read_sections(
self.args.sections) if self.args.sections else None
godag_optional_attrs = self._get_optional_attrs()
self.godag = GODag(obo_file=self.args.obo,
optional_attrs=godag_optional_attrs)
## print('ARGS GoeaCliFnc ', self.args)
# GET: Gene2GoReader, GafReader, GpadReader, or IdToGosReader
self.objanno = self._get_objanno(self.args.filenames[2])
_study, _pop = self.rd_files(*self.args.filenames[:2])
if not self.args.compare:
# Compare population and study gene product sets
self.chk_genes(_study, _pop, self.objanno.associations)
self.methods = self.args.method.split(",")
self.itemid2name = self._init_itemid2name()
# Get GOEnrichmentStudyNS
self.objgoeans = self._init_objgoeans(_pop)
# Run GOEA
self.results_all = self.objgoeans.run_study(_study)
# Prepare for grouping, if user-specified. Create GroupItems
self.prepgrp = GroupItems(
self, self.godag.version) if self.sections else None
def _read_sections(fin):
"""Get sections variable from file."""
sec = os.path.join(REPO, fin)
assert read_sections(sec), "EMPTY SECTIONS FILE({})".format(sec)
return sec
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)
