currentVMatchAlignment = dna, exons, est, original_est, quality,\
currentAcc, currentDon
- vMatchScore = self.calcAlignmentScore(currentVMatchAlignment)
alternativeAlignmentScores = self.calcAlternativeAlignments(location)
- start = cpu()
- # found no alternatives
- #if alternativeAlignmentScores == []:
- # continue
-
if alternativeAlignmentScores == []:
+ # no alignment necessary
maxAlternativeAlignmentScore = -inf
+ vMatchScore = 0.0
else:
maxAlternativeAlignmentScore = max(alternativeAlignmentScores)
+ # compute alignment for vmatch unspliced read
+ vMatchScore = self.calcAlignmentScore(currentVMatchAlignment)
+
+ start = cpu()
+
#print 'vMatchScore/alternativeScore: %f %f ' % (vMatchScore,maxAlternativeAlignmentScore)
#print 'all candidates %s' % str(alternativeAlignmentScores)
jp = os.path.join
run_fname = jp(dir,'run_object.pickle')
- #data_fname = '/fml/ag-raetsch/share/projects/qpalma/solexa/current_data/map.vm_unspliced_1k'
+ data_fname = '/fml/ag-raetsch/share/projects/qpalma/solexa/current_data/map.vm_unspliced_1k'
- data_fname = '/fml/ag-raetsch/share/projects/qpalma/solexa/pipeline_data/map.vm_2k'
+ #data_fname = '/fml/ag-raetsch/share/projects/qpalma/solexa/pipeline_data/map.vm_2k'
#data_fname = '/fml/ag-raetsch/share/projects/qpalma/solexa/pipeline_data/map.vm_100'
param_fname = jp(dir,'param_500.pickle')