Whatnot

scripts/lpls/rpy_go.py

@@ -4,7 +4,7 @@ import rpy
 silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
 import collections
 
-def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
+def goterms_from_gene(genelist, ontology='BP', garbage=['IEA'], ic_cutoff=2.0, verbose=False):
     """ Returns the go-terms from a specified genelist (Entrez id).
 
     Recalculates the information content if needed based on selected evidence codes.
@@ -30,10 +30,17 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
     ddef = False
     if ontology=='BP' and garbage!=None:
         # This is for ont=BP and garbage =['IEA', 'ISS', 'ND']
-        rpy.r.load("ICsBPIMP_IGI_IPI_ISS_IDA_IEP_TAS_NAS_IC.rda")
+        rpy.r.load("ICsBP_small.rda") # Excludes IEA
         ic = rpy.r.assign("IC",rpy.r.IC, envir=rpy.r.GOSimEnv)
-        print len(ic)
+        max_val = 0
+        for key, val in ic.items():
+            if val != scipy.inf:
+                if val>max_val:
+                    max_val = val
+        for key, val in ic.items():
+            ic[key] = val/max_val
     else:
+        # NB! this IC is just for BP
         ic = rpy.r('get("IC", envir=GOSimEnv)')
     print "loading GO definitions environment"
     
@@ -42,25 +49,57 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
     dd = 0
     ii = 0
     jj = 0
-    all = rpy.r.mget(gene_ids, rpy.r.GOENTREZID2GO,ifnotfound="NA")
+    kk = 0
+    all = rpy.r.mget(genelist, rpy.r.GOENTREZID2GO,ifnotfound="NA")
+    n_ic = len(ic)
+    print "Number of terms with IC: %d" %n_ic
+    stopp = False
     for gene, terms in all.items():
+        if verbose:
+            print "\n\n ======ITEM========\n"
+            print "Gene: " + str(gene)
+            print "Number of terms: %d " %len(terms)
+            print terms
+            print "---\n"
+            if stopp:
+                1/0
         if terms!="NA":
-            for term,desc in terms.items():
-                if desc['Ontology'].lower() == ontology and term in ic:
-                    if ic[term]>.88:
+            for term, desc in terms.items():
+                if verbose:
+                    print "\nChecking term: " + str(term)
+                    print "With description: " + str(desc)
+                if desc['Ontology'].lower() == ontology.lower() and term in ic:
+                    if ic[term]>ic_cutoff:
+                        #print ic[term]
                         jj+=1
+                        if verbose:
+                            print "too high" + str((gene, term))
+                            stopp = True
                         continue
-                    cc+=1
+                    cc += 1
+                    if verbose:
+                        print "accepted" + str((gene, term))
                     gene2terms[gene].append(term)
                 else:
-                    dd+=1
+                    if verbose:
+                        print "Not accepted: " + str((gene, term))
+                    if term not in ic:
+                        if verbose:
+                            print "Not in IC: "  + str((gene, term))
+                        kk+=1
+                    if desc['Ontology'].lower() != ontology:
+                        if verbose:
+                            print "Not in Ontology" + str((gene, term))
+                        dd+=1
         else:
             ii+=1
                     
-        
-    print "\nNumber of genes without annotation: %d" %ii 
-    print "\nNumber of genes not in %s : %d " %(ontology, dd)
-    print "\nNumber of genes with too high IC : %d " %jj
+    print "Number of genes total: %d" %len(all)
+    print "\nNumber of genes without annotation: (%d (NA))" %ii
+    print "\nNumber of terms with annoation but no IC: %d" %kk
+    print "\nNumber of terms not in %s : %d " %(ontology, dd)
+    print "\nNumber of terms with too high IC : %d " %jj
+    print "\n Number of accepted terms: %d" %cc
     
     return gene2terms
 
@@ -156,7 +195,7 @@ def parents_dag(go_terms, ontology=['BP']):
 def gene_GO_hypergeo_test(genelist,universe="entrezUniverse",ontology="BP",chip = "hgu133a",pval_cutoff=0.01,cond=False,test_direction="over"):
     
     #assert(scipy.alltrue([True for i in genelist if i in universe]))
-    universeGeneIds=universe
+    universeGeneIds = universe
     params = rpy.r.new("GOHyperGParams",
                        geneIds=genelist,
                        annotation="hgu133a",
@@ -222,5 +261,3 @@ def R_PLS(x,y,ncomp=3, validation='"LOO"'):
     result = rpy.r(callstr)
     return result
 
-
-def gogene()