git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8595 e1793c9e...
authorraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 19:23:55 +0000 (19:23 +0000)
committerraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 19:23:55 +0000 (19:23 +0000)
qpalma/computeSpliceAlignWithQuality.py

index 03f2ec7..5ffc725 100644 (file)
@@ -219,7 +219,7 @@ def  computeSpliceAlignScoreWithQuality(dna, exons, est, original_est, quality,
                dnaletter=original_est[ptr+2][ptr]
                estletter=dnaletter
                ptr+=1
-           if estletter=='-':
+           if estletter==0:# '-':
                score+= mmatrixP[dna_letter]
                dna_ptr+=1 
            else:
@@ -248,9 +248,9 @@ def  computeSpliceAlignScoreWithQuality(dna, exons, est, original_est, quality,
                    score += numqP[(estletter-1)*6*numQualSuppPoints + dnaletter*numQualSuppPoints+Upper]*weightup ;
                    score += numqP[(estletter-1)*6*numQualSuppPoints + dnaletter*numQualSuppPoints+Lower]*weightlow ;
                                   
-           if estletter=='-':
+           if estletter==0:# '-':
                dna_ptr+=1 
-           elif dnaletter=='-':
+           elif dnaletter==0:#'-':
                est_ptr+=1
            else:
                dna_ptr+=1