def _get_tcntobj(goids, go2obj, **kws):
"""Get a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf (gene2go taxid)
if 'gaf' in kws or 'gene2go' in kws:
# Get a reduced go2obj set for TermCounts
_gosubdag = GoSubDag(goids, go2obj, rcntobj=False, prt=None)
return get_tcntobj(_gosubdag.go2obj, **kws) # TermCounts
def get_tcntobj(self, go_all, **kws):
"""Get a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf (gene2go taxid)
if 'gaf' in kws or 'gene2go' in kws:
# Get a reduced go2obj set for TermCounts
_gosubdag = GoSubDag(go_all, self.godag, rcntobj=False, prt=None)
return get_tcntobj(_gosubdag.go2obj, **kws) # TermCounts
def _get_tcntobj(goids, go2obj, **kws):
"""Get a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf (gene2go taxid)
if not AnnoReaderBase.valid_formats.isdisjoint(kws):
# Get a reduced go2obj set for TermCounts
_gosubdag = GoSubDag(goids, go2obj, rcntobj=False)
kws = dict(kws)
kws['godag'] = go2obj
return get_tcntobj(go2obj, **kws) # TermCounts
def __init__(self, args=None, prt=sys.stdout):
self.kws = DocOptParse(__doc__, self.kws_dct_all,
self.kws_set_all).get_docargs(
args,
intvals=set(['max_indent', 'dash_len']))
opt_attrs = OboOptionalAttrs.attributes.intersection(self.kws.keys())
godag = get_godag(self.kws['dag'], prt, optional_attrs=opt_attrs)
self.gosubdag = GoSubDag(godag.keys(),
godag,
relationships='relationship' in opt_attrs,
tcntobj=get_tcntobj(godag, **self.kws),
children=True,
prt=prt)
self.goids = GetGOs().get_goids(self.kws.get('GO'), self.kws.get('i'),
sys.stdout)
def _get_tcntobj(goids, go2obj, **kws):
"""Get a TermCounts object if the user provides an annotation file, otherwise None."""
# kws: gaf (gene2go taxid)
if 'gaf' in kws or 'gene2go' in kws:
return get_tcntobj(go2obj, **kws) # TermCounts
