Mercurial > repos > jeremie > pindel_test

comparison pindel.py @ 11:52d89fc2e7fe draft

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Uploaded
author jeremie
date Tue, 08 Jul 2014 05:27:52 -0400
parents accf671c1f3d
children ee3a2e0cc270
comparison
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10:accf671c1f3d 11:52d89fc2e7fe
163 163
164 def getMeanInsertSize(bamFile, tempDir): 164 def getMeanInsertSize(bamFile, tempDir):
165 samFile = tempDir+"/sam" 165 samFile = tempDir+"/sam"
166 histogramFile = tempDir+"/histogram" 166 histogramFile = tempDir+"/histogram"
167 outputFile = tempDir+"/output" 167 outputFile = tempDir+"/output"
168 cmd = "samtools view -h %s %s" % (bamFile, samFile) 168 cmd = "samtools view -h -o %s %s" % (bamFile, samFile)
169 execute(cmd) 169 execute(cmd, )
170 cmd = "picard-tools CollectInsertSizeMetrics H=%s O=%s I=%s" % (histogramFile, outputFile, samFile) 170 cmd = "picard-tools CollectInsertSizeMetrics H=%s O=%s I=%s" % (histogramFile, outputFile, samFile)
171 execute(cmd) 171 execute(cmd)
172 try: 172 try:
173 f = open(outputFile, 'r') 173 f = open(outputFile, 'r')
174 lignes = f.readlines() 174 lignes = f.readlines()