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Small updates.

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This commit is contained in:
Einar Ryeng
2007-01-12 10:50:55 +00:00
parent ae3aa7e4aa
commit 58886726d8
2 changed files with 35 additions and 4 deletions
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15
workflows/go_workflow.py
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@@ -277,8 +277,11 @@ class SelectGoTermsFunction(workflow.Function):
workflow.Function.__init__(self, 'go-select', 'Select GO Terms')
self.wf = wf
def run(self):
self.wf.project.set_selection('go-terms', set(['GO:0007582', 'GO:0008150', 'GO:0051704', 'GO:0044419']))
def run(self, ds):
terms = [x['id'] for x in networkx.paths.bfs(go, go.get_bp())]
self.wf.project.set_selection('go-terms', set(terms[:100]))
# self.wf.project.set_selection('go-terms', set(['GO:0007582', 'GO:0008150', 'GO:0051704', 'GO:0044419']))
class GoDistanceFunction(workflow.Function):
@@ -296,8 +299,12 @@ class GoDistanceFunction(workflow.Function):
term1 = go.by_id[t1]
term2 = go.by_id[t2]
subsumer = go.subsumer(term1, term2)
print "%s - %s - %s" % (t1, subsumer['id'], t2)
m[i, j] = ic[t1] + ic[t2] - 2.0 * ic[subsumer['id']]
if subsumer == None:
m[i, j] = 1000
else:
# print "%s - %s - %s" % (t1, subsumer['id'], t2)
m[i, j] = ic[t1] + ic[t2] - 2.0 * ic[subsumer['id']]
ds = dataset.Dataset(m, (('go-terms', ids), ('_go-terms', ids)), 'Resnik')
return ds