git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8653 e1793c9e...
authorfabio <fabio@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Fri, 18 Apr 2008 08:47:29 +0000 (08:47 +0000)
committerfabio <fabio@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Fri, 18 Apr 2008 08:47:29 +0000 (08:47 +0000)
scripts/PipelineHeuristic.py

index 464d49a..4ea1cb9 100644 (file)
@@ -281,7 +281,7 @@ class PipelineHeuristic:
       distal_acc   = []
       for idx in xrange(max_intron_size+read_size, len(currentAcc)):
           if currentAcc[idx]>= splice_thresh:
-            distal_acc.append((idx, currentAcc[idx], DNA[idx:idx+read_size]))
+            distal_acc.append((idx, currentAcc[idx], DNA[idx+1:idx+read_size]))
 
       #distal_acc.sort(lambda x,y: signum(x[1]-y[1])) 
       #distal_acc=distal_acc[-2:]
@@ -296,7 +296,7 @@ class PipelineHeuristic:
       proximal_don=proximal_don[-2:]
 
       distal_don   = []
-      for idx in xrange(max_intron_size, max_intron_size+read_size):
+      for idx in xrange(1, max_intron_size):
          if currentDon[idx] >= splice_thresh:
             distal_don.append((idx, currentDon[idx], DNA[idx-read_size:idx]))
 
@@ -336,13 +336,12 @@ class PipelineHeuristic:
       self.get_time += stop-start
       dna   = currentDNASeq
 
-      proximal_don,proximal_acc,distal_don,distal_acc = self.findHighestScoringSpliceSites(currentAcc,currentDon, max_intron_size)
-
-      #sort_acc=[ elem for elem in enumerate(currentAcc) ] 
-      #sort_acc.sort(lambda x,y: signum(x[1]-y[1]) )
-      
-      #print alt_don
-      #print alt_acc
+      proximal_acc,proximal_don,distal_acc,distal_don = self.findHighestScoringSpliceSites(currentAcc,currentDon, dna, max_intron_size, len(est), splice_thresh)
+       
+      print proximal_acc
+      print proximal_don
+      print distal_acc
+      print distal_don
       
       alternativeScores = []
       
@@ -362,7 +361,7 @@ class PipelineHeuristic:
       dummyDonorScore = calculatePlif(d, [0.25])[0]
       
       _start = cpu()
-      for (don_pos,don_score) in alt_don:
+      for (don_pos,don_score) in proximal_don:
          # remove mismatching positions in the second exon
          original_est_cut=''