Updates

scripts/lpls/rpy_go.py

@@ -38,6 +38,9 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None):
     print "loading GO definitions environment"
     
     gene2terms = {}
+    cc = 0
+    dd = 0
+    ii = 0
     for gene in genelist:
         info = rpy.r('GOENTREZID2GO[["' + str(gene) + '"]]')
         #print info
@@ -50,17 +53,23 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None):
                 if ic.get(term)==None:
                     #print "\nHave no IC on this GO term %s for this gene: %s" %(term,gene)
                     skip=True
+                    ii += 1
                 if desc['Ontology']!=ontology:
                     #print "\nThis GO term %s belongs to: %s:" %(term,desc['Ontology'])
                     skip = True
+                    dd += 1
                 if not skip:
                     if gene2terms.has_key(gene):
                         gene2terms[gene].append(term)
                     else:
                         gene2terms[gene] = [term]
         else:
-           print "\nHave no Annotation on this gene: %s" %gene 
+            cc += 1
 
+    print "\nNumber of genes without annotation: %d" %cc 
+    print "\nNumber of genes not in %s : %d " %(ontology, dd)
+    print "\nNumber of genes with infs : %d " %ii
+    
     return gene2terms
 
 def genego_matrix(goterms, tmat, gene_ids, term_ids, func=max):
@@ -166,7 +175,7 @@ def gene_GO_hypergeo_test(genelist,universe="entrezUniverse",ontology="BP",chip
                        )
     result = rpy.r.summary(rpy.r.hyperGTest(params))
     
-    return rpy.r.summary(result), params
+    return result, params
 
 def data_aff2loc_hgu133a(X, aff_ids, verbose=False):
     aff_ids = scipy.asarray(aff_ids)