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Minor utility improvements 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5325 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-26 15:36:26 +00:00
parent aaecc271e8
commit b1b9c14c98
1 changed files with 10 additions and 3 deletions
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13
python/Verify1KGArchiveBAMs.py
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@ -200,9 +200,12 @@ def compareAlignmentIndices(remoteAlignmentIndex, alignmentIndex):
print ' md5s: local=%s remote=%s' % (raImd5, laImd5) print ' md5s: local=%s remote=%s' % (raImd5, laImd5)
if raImd5 <> laImd5: if raImd5 <> laImd5:
print ' [FAIL] -- alignment indices do not have the same hash!' print ' [FAIL] -- alignment indices do not have the same hash!'
sys.exit(1) #sys.exit(1)
else: else:
print ' [PASS] -- alignment indices are the same' print ' [PASS] -- alignment indices are the same'
return remoteAlignmentIndexFile.file
else:
return None
def displayChangeLog( changelog ): def displayChangeLog( changelog ):
if changelog <> None: if changelog <> None:
@ -258,10 +261,14 @@ if __name__ == "__main__":
FTPSERVER.login() FTPSERVER.login()
displayChangeLog(OPTIONS.remoteChangeLog) displayChangeLog(OPTIONS.remoteChangeLog)
compareAlignmentIndices(OPTIONS.remoteAlignmentIndex, OPTIONS.alignmentIndex) remoteAI = compareAlignmentIndices(OPTIONS.remoteAlignmentIndex, OPTIONS.alignmentIndex)
results = dict() 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 #print line
#bas = line.split()[6] #bas = line.split()[6]
if file not in results: if file not in results: