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 _add_gochildleaf(self, ret):
"""Add leaf-level GO children to GO list colored uniquely."""
leaf_gos = get_leaf_children(ret['GOs'], self.go2obj)
if leaf_gos:
ret['GOs'].update(leaf_gos)
leaf_go_color = Go2Color.key2col['go_leafchild']
go2color = ret['go2color']
for goid in leaf_gos:
if goid not in go2color:
go2color[goid] = leaf_go_color
def _init_go_sources(self, go_sources_arg, go2obj_arg):
"""Return GO sources which are present in GODag."""
gos_user = set(go_sources_arg)
if 'children' in self.kws and self.kws['children']:
gos_user |= get_leaf_children(gos_user, go2obj_arg)
gos_godag = set(go2obj_arg)
gos_source = gos_user.intersection(gos_godag)
gos_missing = gos_user.difference(gos_godag)
if not gos_missing:
return gos_source
sys.stdout.write("{N} GO IDs NOT FOUND IN GO DAG: {GOs}\n".format(
N=len(gos_missing), GOs=" ".join([str(e) for e in gos_missing])))
return gos_source
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']]
