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Resnik distances between GO terms work now.

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This commit is contained in:
Einar Ryeng
2007-01-11 22:01:31 +00:00
parent 4b1d16ea78
commit e4d7f8e5a2
2 changed files with 57 additions and 7 deletions
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39
workflows/go_workflow.py
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@@ -118,6 +118,7 @@ class GoWorkflow (workflow.Workflow):
self.add_stage(load)
go = workflow.Stage('go', 'Gene Ontology')
go.add_function(SelectGoTermsFunction(self))
go.add_function(GoDistanceFunction())
self.add_stage(go)
@@ -269,11 +270,36 @@ class NumericDict(dict):
retval = 0.0
return retval
class SelectGoTermsFunction(workflow.Function):
def __init__(self, wf):
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']))
class GoDistanceFunction(workflow.Function):
def __init__(self):
workflow.Function.__init__(self, 'go-dist', 'GO term distance matrix')
self.options = GoDistanceOptions()
def resnik_distance_matrix(self, selection, ic):
size = len(selection['go-terms'])
m = zeros((size, size))
# Create resnik distance matrix
ids = list(selection['go-terms'])
for i, t1 in enumerate(ids):
for j, t2 in enumerate(ids):
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[subsumer['id']] - ic[t1] + ic[subsumer['id']] - ic[t2]
ds = dataset.Dataset(m, (('go-terms', ids), ('_go-terms', ids)), 'Resnik')
return ds
def run(self, x, selection):
global evidence, go
self.options = self.show_gui(self.options)
@@ -288,22 +314,21 @@ class GoDistanceFunction(workflow.Function):
annotations = NumericDict()
ic = NumericDict()
# Insert annotations into dict
for i, v in enumerate(evidence.get_identifiers('go-terms')):
annotations[v] = ann_count_matrix[i]
# Accumulate annotations
for term in reversed(networkx.topological_sort(go)):
for parent in go.in_neighbors(term):
annotations[parent['id']] += annotations[term['id']]
print "%s -> %s (%s)" % (term['id'], parent['id'], annotations[parent['id']])
# print "%s -> %s (%s)" % (term['id'], parent['id'], annotations[parent['id']])
# Create information content dictionary
for i, v in enumerate(evidence.get_identifiers('go-terms')):
annotations[v] = ann_count_matrix[i]
ic[v] = -log(ann_count_matrix[i] / total_ann)
# # Create resnik distance matrix
# for t1 in selection['go-terms']:
# for t2 in selection['go-terms']:
return [self.resnik_distance_matrix(selection, ic)]
def show_gui(self, options, edit=True):
dialog = GoDistanceDialog()