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gatk-3.8
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Actually listens to justPrint now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1253 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-15 16:52:46 +00:00
parent d36e232ed3
commit 702cdd087f
1 changed files with 6 additions and 8 deletions
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14
python/ValidateGATK.py
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@ -8,7 +8,7 @@ defaultCommands = ['CountReads', 'Pileup']
def indexBAM(reads, queue=None): def indexBAM(reads, queue=None):
cmd = "samtools index " + reads cmd = "samtools index " + reads
farm_commands.cmd(cmd, queue, None) farm_commands.cmd(cmd, queue, None, just_print_commands=OPTIONS.justPrint)
def readIntervalFile(file): def readIntervalFile(file):
def notHeaderP(line): def notHeaderP(line):
@ -112,8 +112,6 @@ def main():
action='store_true', default=False, action='store_true', default=False,
help="Don't actually run GATK, just setup data files") help="Don't actually run GATK, just setup data files")
(OPTIONS, args) = parser.parse_args() (OPTIONS, args) = parser.parse_args()
if len(args) != 0: if len(args) != 0:
parser.error("incorrect number of arguments") parser.error("incorrect number of arguments")
@ -157,22 +155,22 @@ def main():
#print 'reads', reads #print 'reads', reads
if not os.path.exists(reads) or OPTIONS.rebuildAllFiles: if not os.path.exists(reads) or OPTIONS.rebuildAllFiles:
farm_commands.cmd("ln -s " + os.path.abspath(originalReads) + " " + reads) farm_commands.cmd("ln -s " + os.path.abspath(originalReads) + " " + reads, just_print_commands=OPTIONS.justPrint)
if not os.path.exists(readsIndex) or OPTIONS.rebuildAllFiles: if not os.path.exists(readsIndex) or OPTIONS.rebuildAllFiles:
indexBAM(reads) indexBAM(reads)
if not os.path.exists(subBAM) or OPTIONS.rebuildAllFiles: if not os.path.exists(subBAM) or OPTIONS.rebuildAllFiles:
if region == '*' or isIntervalFile(region): if region == '*' or isIntervalFile(region):
farm_commands.cmd("ln -s " + os.path.abspath(reads) + " " + subBAM) farm_commands.cmd("ln -s " + os.path.abspath(reads) + " " + subBAM, just_print_commands=OPTIONS.justPrint)
else: else:
cmd = "samtools view -b " + reads + " " + region + " > " + subBAM cmd = "samtools view -b " + reads + " " + region + " > " + subBAM
farm_commands.cmd(cmd, None, None) farm_commands.cmd(cmd, None, None, just_print_commands=OPTIONS.justPrint)
subBAMIndex = subBAM+'.bai' subBAMIndex = subBAM+'.bai'
if not os.path.exists(subBAMIndex) or OPTIONS.rebuildAllFiles: if not os.path.exists(subBAMIndex) or OPTIONS.rebuildAllFiles:
if region == '*' or isIntervalFile(region): if region == '*' or isIntervalFile(region):
farm_commands.cmd("ln -s " + os.path.abspath(readsIndex) + " " + subBAMIndex) farm_commands.cmd("ln -s " + os.path.abspath(readsIndex) + " " + subBAMIndex, just_print_commands=OPTIONS.justPrint)
else: else:
indexBAM(subBAM) indexBAM(subBAM)
@ -185,7 +183,7 @@ def main():
filterByInterval(readIntervalFile(region), filteredPileup, pileup) filterByInterval(readIntervalFile(region), filteredPileup, pileup)
else: else:
cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup
farm_commands.cmd(cmd, None, None) farm_commands.cmd(cmd, None, None, just_print_commands=OPTIONS.justPrint)
if not OPTIONS.dontValidate and (not os.path.exists(validationOutput) or OPTIONS.ignoreExistingFiles): if not OPTIONS.dontValidate and (not os.path.exists(validationOutput) or OPTIONS.ignoreExistingFiles):
print validationOutput, 'does not exist' print validationOutput, 'does not exist'