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Create Resnik distances and save them as ftsv.

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This commit is contained in:
Einar Ryeng
2007-01-12 00:00:56 +00:00
parent 08b7d8dd85
commit ae3aa7e4aa
2 changed files with 21 additions and 12 deletions
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12
workflows/geneontology.py
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@@ -32,6 +32,7 @@ class GeneOntology(networkx.XDiGraph):
def __init__(self):
networkx.XDiGraph.__init__(self)
self.by_id = {}
self.undirected = None
def add_term(self, term):
self.add_node(term)
@@ -62,12 +63,12 @@ class GeneOntology(networkx.XDiGraph):
def subsumer(self, t1, t2):
if t1 == t2:
# print "t1 == t2"
return t1
go_undir = self.to_undirected()
# print go_undir.nodes()
path = networkx.shortest_path(go_undir, t1, t2)
if self.undirected == None:
self.undirected = self.to_undirected()
path = networkx.shortest_path(self.undirected, t1, t2)
if not path:
print "Woah, path not found."
return None
@@ -76,12 +77,9 @@ class GeneOntology(networkx.XDiGraph):
print "This shouldn't happen"
return t1
# print t1['id'], t2['id'], path
# print "path:", path
for t in path:
if networkx.shortest_path(self, t, t1) and \
networkx.shortest_path(self, t, t2):
# print " ", t1, t2, t
return t
print "GeneOntology.subsumer: should not reach this point"