1. biolab
  2. Untitled project
  3. orange-bioinformatics

Commits

Marko Toplak  committed 1a49add

Fixed updateGO to work with the updated go module.

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  • Parent commits 8f100ab
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File server_update/updateGO.py

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 if web_ontology_mtime() > sf_ontology_mtime():
+    print "donwloading ontology"
     filename = os.path.join(tmp_path, "gene_ontology_edit.obo.tar.gz")
     obiGO.Ontology.DownloadOntology(filename)
 
 
 
 for org in list_available_organisms():
+
     if org in exclude or org not in commonOrgs:
         continue
 
         # Skip update
         continue
 
+    print "Updating", org
+
     filename = os.path.join(tmp_path, "gene_association." + org + ".tar.gz")
     obiGO.Annotations.DownloadAnnotations(org, filename)
 
     ## Load the annotations to test them and collect all taxon ids from them
+    print filename
     a = obiGO.Annotations(filename, genematcher=obiGene.GMDirect())
-    taxons = set([ann.taxon for ann in a.annotations])
+    taxons = set([ann.Taxon for ann in a.annotations])
     ## exclude taxons with cardinality 2
     taxons = [tax for tax in taxons if "|" not in tax]
     for tax in taxons: