+ extended test cases
[qpalma.git] / qpalma / Lookup.py
index 5d3b7df..2c7fd35 100644 (file)
@@ -83,13 +83,14 @@ class LookupTable:
       """
       assert chromo in self.chromo_list
 
+      
       genomicSeq_start  = 0
       genomicSeq_stop   = self.seqInfo.getFragmentSize(chromo)
 
       print 'lt total_size %d' % self.seqInfo.getFragmentSize(chromo)
 
       strand = '+'
-      genomicSeq,currentAcc,currentDon = self.seqInfo.get_seq_and_scores(chromo,strand,genomicSeq_start,genomicSeq_stop,False,False)
+      genomicSeq,currentAcc,currentDon = self.seqInfo.get_seq_and_scores(chromo,strand,genomicSeq_start,genomicSeq_stop)
       #print len(currentAcc),len(currentDon)
       genomicSeq = genomicSeq.lower()
 
@@ -99,19 +100,19 @@ class LookupTable:
       self.acceptorScoresPos[chromo_idx]   = currentAcc
       self.donorScoresPos[chromo_idx]      = currentDon
 
-
       strand = '-'
-      genomicSeq,currentAcc,currentDon = self.seqInfo.get_seq_and_scores(chromo,strand,genomicSeq_start,genomicSeq_stop,False,False)
-      #print len(currentAcc),len(currentDon)
+      genomicSeq,currentAcc,currentDon = self.seqInfo.get_seq_and_scores(chromo,strand,genomicSeq_start,genomicSeq_stop)
+
       genomicSeq = genomicSeq.lower()
 
       newCurrentAcc = [-inf] 
       newCurrentAcc.extend(currentAcc[:-1])
       currentAcc = newCurrentAcc
+
       newCurrentDon = [-inf] 
       newCurrentDon.extend(currentDon[:-1])
+      #pdb.set_trace()
       currentDon = newCurrentDon
 
       self.acceptorScoresNeg[chromo_idx]   = currentAcc
       self.donorScoresNeg[chromo_idx]      = currentDon
-