def get_go_color(self, **kws):
"""Return source GO IDs and GO color, if provided."""
ret = {'GOs': set(), 'go2color': {}}
if 'go_color_file' in kws:
_, go2color = ClassGetGOs.rdtxt_gos_color(kws['go_color_file'])
self._update_ret(ret, None, go2color)
if 'GO' in kws:
# goids, go2color = self._goargs(ret, kws['GO'])
goids, go2color = ClassGetGOs.get_goargs(kws['GO'], prt=sys.stdout)
self._update_ret(ret, goids, go2color)
if 'go_file' in kws:
goids, go2color = ClassGetGOs.rdtxt_gos_color(kws['go_file'])
self._update_ret(ret, goids, go2color)
if 'draw-children' in kws:
ret['GOs'].update(get_leaf_children(ret['GOs'], self.go2obj))
# If there have been no GO IDs explicitly specified by the user
if not ret['GOs']:
# If the GO-DAG is sufficiently small, print all GO IDs
if len(self.go2obj) < self.max_gos:
main_gos = set(o.id for go, o in self.go2obj.items()
if go != o.id)
go_leafs = set(go for go, o in self.go2obj.items()
if not o.children)
ret['GOs'] = go_leafs.difference(main_gos)
go2obj = {go: self.go2obj[go] for go in ret['GOs']}
ret['GOs'] = set(get_go2obj_unique(go2obj))
return [ret['GOs'], ret['go2color']]
def get_usrgos(self, fin_goids, prt):
"""Return source GO IDs ."""
ret = self.get_goids(None, fin_goids, prt)
# If there have been no GO IDs explicitly specified by the user
if not ret:
# If the GO-DAG is sufficiently small, print all GO IDs
if self.max_gos is not None and len(self.go2obj) < self.max_gos:
main_gos = set(o.id for go, o in self.go2obj.items() if go != o.id)
go_leafs = set(go for go, o in self.go2obj.items() if not o.children)
ret = go_leafs.difference(main_gos)
else:
raise RuntimeError("GO IDs NEEDED")
go2obj = self.get_go2obj(ret)
return get_go2obj_unique(go2obj)
def get_usrgos(self, fin_goids, prt):
"""Return source GO IDs ."""
ret = self.get_goids(None, fin_goids, prt)
# If there have been no GO IDs explicitly specified by the user
if not ret:
# If the GO-DAG is sufficiently small, print all GO IDs
if self.max_gos is not None and len(self.go2obj) < self.max_gos:
main_gos = set(o.id for go, o in self.go2obj.items()
if go != o.id)
go_leafs = set(go for go, o in self.go2obj.items()
if not o.children)
ret = go_leafs.difference(main_gos)
else:
raise RuntimeError("GO IDs NEEDED")
go2obj = self.get_go2obj(ret)
return get_go2obj_unique(go2obj)
def get_go_color(self, **kws):
"""Return source GO IDs ."""
ret = {'GOs':set(), 'go2color':{}}
if 'GO' in kws:
self._goargs(ret, kws['GO'])
if 'go_file' in kws:
self._rdtxt_gos(ret, kws['go_file'])
if 'draw-children' in kws:
ret['GOs'].update(get_leaf_children(ret['GOs'], self.go2obj))
# If there have been no GO IDs explicitly specified by the user
if not ret['GOs']:
# If the GO-DAG is sufficiently small, print all GO IDs
if len(self.go2obj) < self.max_gos:
main_gos = set(o.id for go, o in self.go2obj.items() if go != o.id)
go_leafs = set(go for go, o in self.go2obj.items() if not o.children)
ret['GOs'] = go_leafs.difference(main_gos)
else:
raise RuntimeError("GO IDs NEEDED")
go2obj = {go:self.go2obj[go] for go in ret['GOs']}
ret['GOs'] = set(get_go2obj_unique(go2obj))
return [ret['GOs'], ret['go2color']]
def get_go_color(self, **kws):
"""Return source GO IDs ."""
# kws: GO go_file draw-children
ret = {'GOs':set(), 'go2color':{}}
if 'GO' in kws:
self._goargs(ret, kws['GO'])
if 'go_file' in kws:
self._rdtxt_gos(ret, kws['go_file'])
if 'draw-children' in kws:
self._add_gochildleaf(ret)
# If there have been no GO IDs explicitly specified by the user
if not ret['GOs']:
# If the GO-DAG is sufficiently small, print all GO IDs
if len(self.go2obj) < self.max_gos:
self._add_all_leafs(ret)
else:
raise RuntimeError("GO IDs NEEDED")
go2obj = {go:self.go2obj[go] for go in ret['GOs']}
ret['GOs'] = set(get_go2obj_unique(go2obj))
return [ret['GOs'], ret['go2color']]