def prt_hier_up(self, goids, prt=sys.stdout):
"""Write hierarchy for all GO IDs below GO ID in arg, goid."""
go2goterm_all = {go: self.gosubdag.go2obj[go] for go in goids}
objp = GoPaths()
items_list = []
for namespace, go2term_ns in self._get_namespace2go2term(
go2goterm_all).items():
goids_all = set() # GO IDs from user-specfied GO to root
for goid_usr, goterm in go2term_ns.items():
goids_all.add(goid_usr)
paths = objp.get_paths_from_to(goterm,
goid_end=None,
dn0_up1=True)
goids_all.update(set(o.id for p in paths for o in p))
# Only include GO IDs from user-specified GO to the root
if 'include_only' not in self.usrdct:
self.usrdct['include_only'] = set()
self.usrdct['include_only'].update(goids_all)
# Mark the user-specfied GO term
if 'item_marks' not in self.usrdct:
self.usrdct['item_marks'] = {}
for goid_usr in go2term_ns.keys():
if goid_usr not in self.usrdct['item_marks']:
self.usrdct['item_marks'][goid_usr] = '*'
# Write the hierarchy
wrhiercfg = self._get_wrhiercfg()
obj = WrHierPrt(self.gosubdag.go2obj, self.gosubdag.go2nt,
wrhiercfg, prt)
go_root = self._get_goroot(goids_all, namespace)
obj.prt_hier_rec(go_root)
items_list.extend(obj.items_list)
return items_list
def prt_hier_up(self, goids, prt=sys.stdout):
"""Write hierarchy for all GO IDs below GO ID in arg, goid."""
go2goterm_all = {go: self.gosubdag.go2obj[go] for go in goids}
objp = GoPaths()
gos_printed = set()
for namespace, go2term_ns in self._get_namespace2go2term(
go2goterm_all).items():
go_root = self.consts.NAMESPACE2GO[namespace]
goids_all = set() # GO IDs from user-specfied GO to root
for goid, goterm in go2term_ns.items():
goids_all.add(goid)
paths = objp.get_paths_from_to(goterm,
goid_end=None,
dn0_up1=True)
goids_all.update(set(o.id for p in paths for o in p))
# Only include GO IDs from user-specified GO to the root
if 'include_only' not in self.usrdct:
self.usrdct['include_only'] = set()
self.usrdct['include_only'].update(goids_all)
# Mark the user-specfied GO term
if 'go_marks' not in self.usrdct:
self.usrdct['go_marks'] = set()
self.usrdct['go_marks'].update(go2term_ns.keys())
obj = _WrHierPrt(self, prt) # , goids_all, set(go2term_ns.keys()))
gos_printed.update(obj.gos_printed)
obj.prt_hier_rec(go_root)
return gos_printed
def prt_hier_up(self, goids, prt=sys.stdout):
"""Write hierarchy for all GO IDs below GO ID in arg, goid."""
go2goterm_all = {go:self.gosubdag.go2obj[go] for go in goids}
objp = GoPaths()
items_list = []
for namespace, go2term_ns in self._get_namespace2go2term(go2goterm_all).items():
goids_all = set() # GO IDs from user-specfied GO to root
for goid_usr, goterm in go2term_ns.items():
goids_all.add(goid_usr)
paths = objp.get_paths_from_to(goterm, goid_end=None, dn0_up1=True)
goids_all.update(set(o.id for p in paths for o in p))
# Only include GO IDs from user-specified GO to the root
if 'include_only' not in self.usrdct:
self.usrdct['include_only'] = set()
self.usrdct['include_only'].update(goids_all)
# Mark the user-specfied GO term
if 'item_marks' not in self.usrdct:
self.usrdct['item_marks'] = {}
for goid_usr in go2term_ns.keys():
if goid_usr not in self.usrdct['item_marks']:
self.usrdct['item_marks'][goid_usr] = '*'
# Write the hierarchy
wrhiercfg = self._get_wrhiercfg()
obj = WrHierPrt(self.gosubdag.go2obj, self.gosubdag.go2nt, wrhiercfg, prt)
go_root = self._get_goroot(goids_all, namespace)
obj.prt_hier_rec(go_root)
items_list.extend(obj.items_list)
return items_list
def get_goids_all(go2term_ns):
"""GO IDs from user-specfied GO to root"""
goids_all = set() # GO IDs from user-specfied GO to root
objp = GoPaths()
for goid_usr, goterm in go2term_ns.items():
goids_all.add(goid_usr)
paths = objp.get_paths_from_to(goterm, goid_end=None, dn0_up1=True)
goids_all.update(set(o.id for p in paths for o in p))
return goids_all
def prt_hier_up(self, goids, prt=sys.stdout):
"""Write hierarchy for all GO IDs below GO ID in arg, goid."""
go2goterm_all = {go: self.gosubdag.go2obj[go] for go in goids}
objp = GoPaths()
for namespace, go2term_ns in self._get_namespace2go2term(
go2goterm_all).items():
go_root = self.consts.NAMESPACE2GO[namespace]
goids_all = set()
for goid, goterm in go2term_ns.items():
goids_all.add(goid)
paths = objp.get_paths_from_to(goterm,
goid_end=None,
dn0_up1=True)
goids_all.update(set(o.id for p in paths for o in p))
obj = _WrHierPrt(self, prt, goids_all, set(go2term_ns.keys()))
obj.prt_hier_rec(go_root)