unspliced should work
authorraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 19:41:13 +0000 (19:41 +0000)
committerraetsch <raetsch@e1793c9e-67f9-0310-80fc-b846ff1f7b36>
Thu, 17 Apr 2008 19:41:13 +0000 (19:41 +0000)
git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@8605 e1793c9e-67f9-0310-80fc-b846ff1f7b36

scripts/PipelineHeuristic.py

index 9d9a6ff..5bb16dc 100644 (file)
@@ -412,35 +412,13 @@ class PipelineHeuristic:
 
       run = self.run
 
-      h = self.h
-      d = self.d
-      a = self.a
-      mmatrix = self.mmatrix
-      qualityPlifs = self.qualityPlifs
-
       # Lets start calculation
       dna, exons, est, original_est, quality, acc_supp, don_supp = alignment
 
-      # Berechne die Parameter des wirklichen Alignments (but with untrained d,a,h ...)    
-      trueSpliceAlign, trueWeightMatch, trueWeightQuality ,dna_calc =\
-      computeSpliceAlignWithQuality(dna, exons, est, original_est,\
-      quality, qualityPlifs, run)
-
-      # Calculate the weights
-      trueWeightDon, trueWeightAcc, trueWeightIntron =\
-      computeSpliceWeights(d, a, h, trueSpliceAlign, don_supp, acc_supp)
-
-      trueWeight = numpy.vstack([trueWeightIntron, trueWeightDon, trueWeightAcc, trueWeightMatch, trueWeightQuality])
-
-      # new alignment score
       score = computeSpliceAlignScoreWithQuality(dna, exons, est, original_est,\
          quality, qualityPlifs, run, self.currentPhi)
       
-      if score!=0.0:
-          print 'diff %f,%f,%f' % ((trueWeight.T * self.currentPhi)[0,0] - score,(trueWeight.T * self.currentPhi)[0,0], score)
-
-      # Calculate w'phi(x,y) the total score of the alignment
-      return (trueWeight.T * self.currentPhi)[0,0]
+      return score 
 
 
 def cpu():