From b1b9c14c98d44a16d673735b682f0142bee3e35d Mon Sep 17 00:00:00 2001 From: depristo Date: Sat, 26 Feb 2011 15:36:26 +0000 Subject: [PATCH] Minor utility improvements git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5325 348d0f76-0448-11de-a6fe-93d51630548a --- python/Verify1KGArchiveBAMs.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/python/Verify1KGArchiveBAMs.py b/python/Verify1KGArchiveBAMs.py index cf576f96a..394e4eb2b 100644 --- a/python/Verify1KGArchiveBAMs.py +++ b/python/Verify1KGArchiveBAMs.py @@ -200,9 +200,12 @@ def compareAlignmentIndices(remoteAlignmentIndex, alignmentIndex): print ' md5s: local=%s remote=%s' % (raImd5, laImd5) if raImd5 <> laImd5: print ' [FAIL] -- alignment indices do not have the same hash!' - sys.exit(1) + #sys.exit(1) else: print ' [PASS] -- alignment indices are the same' + return remoteAlignmentIndexFile.file + else: + return None def displayChangeLog( changelog ): if changelog <> None: @@ -258,10 +261,14 @@ if __name__ == "__main__": FTPSERVER.login() displayChangeLog(OPTIONS.remoteChangeLog) - compareAlignmentIndices(OPTIONS.remoteAlignmentIndex, OPTIONS.alignmentIndex) + remoteAI = compareAlignmentIndices(OPTIONS.remoteAlignmentIndex, OPTIONS.alignmentIndex) results = dict() - for file in itertools.chain(readAlignmentIndex(OPTIONS.alignmentIndex), filesInLocalPath(root, OPTIONS.scanLocal )): + AIToUse = OPTIONS.alignmentIndex + if remoteAI != None: + AIToUse = remoteAI + print 'Using remote AI', remoteAI, "for comparisons" + for file in itertools.chain(readAlignmentIndex(AIToUse), filesInLocalPath(root, OPTIONS.scanLocal )): #print line #bas = line.split()[6] if file not in results: