git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8645 e1793c9e...
authorraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 21:52:35 +0000 (21:52 +0000)
committerraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 21:52:35 +0000 (21:52 +0000)
scripts/PipelineHeuristic.py

index 9f0221f..8e878e2 100644 (file)
@@ -306,7 +306,7 @@ class PipelineHeuristic:
       effective_len = len(est)
 
       genomicSeq_start  = pos
-      genomicSeq_stop   = pos+self.read_size+1#+self.intron_size*2+self.read_size*2
+      genomicSeq_stop   = pos+1000#self.read_size+1#+self.intron_size*2+self.read_size*2
 
       start = cpu()
       currentDNASeq, currentAcc, currentDon = get_seq_and_scores(chr,strand,genomicSeq_start,genomicSeq_stop,run['dna_flat_files'])
@@ -315,6 +315,8 @@ class PipelineHeuristic:
       dna   = currentDNASeq
 
       alt_don,alt_acc = self.findHighestScoringSpliceSites(currentAcc,currentDon)
+      max_acc=max(currentAcc) ;
+      
       #print alt_don
       #print alt_acc
       
@@ -331,7 +333,7 @@ class PipelineHeuristic:
       # compute dummy scores
       IntronScore = calculatePlif(h, [self.intron_size+1])[0]
       #print IntronScore
-      dummyAcceptorScore = calculatePlif(a, [0.25])[0] 
+      dummyAcceptorScore = calculatePlif(a, [max_acc])[0] 
       dummyDonorScore = calculatePlif(d, [0.25])[0]
       
       _start = cpu()