Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def _get_grprdflt():
"""Get Grouper defaults."""
gosubdag = _get_gosubdag()
fin_slim = os.path.join(REPO, 'goslim_generic.obo')
return GrouperDflts(gosubdag, fin_slim)
def _get_sortobj():
"""Get object for grouping GO IDs."""
fin_godag = os.path.join(REPO, "go-basic.obo")
godag = get_godag(fin_godag, prt=None, loading_bar=False, optional_attrs=['relationship'])
gosubdag = GoSubDag(USER_GOS, godag, relationships=True, tcntobj=None)
grprdflt = GrouperDflts(gosubdag)
hdrobj = HdrgosSections(gosubdag, grprdflt.hdrgos_dflt, SECTIONS)
grprobj = Grouper("wrusrgos", USER_GOS, hdrobj, gosubdag)
return Sorter(grprobj)
def _get_grprdflt(gosubdag):
"""Get Grouper defaults."""
fin_slim = os.path.join(REPO, 'goslim_generic.obo')
return GrouperDflts(gosubdag, fin_slim)
def _get_grprdflt(gosubdag=None):
"""Get Grouper defaults."""
fin_slim = os.path.join(REPO, 'goslim_generic.obo')
return GrouperDflts(gosubdag, fin_slim)
def _get_grprdflt():
"""Get Grouper defaults."""
gosubdag = _get_gosubdag()
fin_slim = os.path.join(REPO, 'goslim_generic.obo')
return GrouperDflts(gosubdag, fin_slim)
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)
def __init__(self, objcli, godag_version):
# _goids = set(o.id for o in godag.values() if not o.children)
_goids = set(r.GO for r in objcli.results_all)
_tobj = TermCounts(objcli.godag, objcli.objgoeans.get_assoc())
# pylint: disable=line-too-long
self.gosubdag = GoSubDag(_goids, objcli.godag, relationships=True, tcntobj=_tobj, prt=sys.stdout)
self.grprdflt = GrouperDflts(self.gosubdag, objcli.args.goslim)
self.hdrobj = HdrgosSections(self.grprdflt.gosubdag, self.grprdflt.hdrgos_dflt, objcli.sections)
self.pval_fld = objcli.get_pval_field() # primary pvalue of interest
self.ver_list = [godag_version,
self.grprdflt.ver_goslims,
"Sections: {S}".format(S=objcli.args.sections)]
# self.objaartall = self._init_objaartall()