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Better validation scripts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@458 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-16 23:18:00 +00:00
parent 01be8f09e3
commit e842b543c9
2 changed files with 12 additions and 4 deletions
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10
python/ValidateGATK.py
View File

@ -32,6 +32,11 @@ def main():
parser.add_option("-a", "--rebuildAllFiles", dest="rebuildAllFiles", parser.add_option("-a", "--rebuildAllFiles", dest="rebuildAllFiles",
action='store_true', default=False, action='store_true', default=False,
help="If provided, all intermediate files (BAM and pileups) will be regenerated") help="If provided, all intermediate files (BAM and pileups) will be regenerated")
parser.add_option("-p", "--justPrint", dest="justPrint",
action='store_true', default=False,
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:
@ -69,7 +74,7 @@ def main():
filebase = os.path.splitext(read_filename)[0] filebase = os.path.splitext(read_filename)[0]
reads = os.path.join(OPTIONS.dataDir, read_filename) reads = os.path.join(OPTIONS.dataDir, read_filename)
readsIndex = os.path.join(OPTIONS.dataDir, filebase + '.selected.bam.bai') readsIndex = reads + '.bai'
subBAM = os.path.join(OPTIONS.dataDir, filebase + '.selected.bam') subBAM = os.path.join(OPTIONS.dataDir, filebase + '.selected.bam')
pileup = os.path.join(OPTIONS.dataDir, filebase + '.selected.pileup') pileup = os.path.join(OPTIONS.dataDir, filebase + '.selected.pileup')
validationOutput = os.path.join(OPTIONS.outputDir, filebase + '.validate.output') validationOutput = os.path.join(OPTIONS.outputDir, filebase + '.validate.output')
@ -88,6 +93,7 @@ def main():
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)
indexBAM(subBAM)
if not os.path.exists(pileup) or OPTIONS.rebuildAllFiles: if not os.path.exists(pileup) or OPTIONS.rebuildAllFiles:
cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup
@ -97,7 +103,7 @@ def main():
analysis = "ValidatingPileup" analysis = "ValidatingPileup"
cmd = "java -ea -Xmx1024m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U -B pileup SAMPileup " + pileup cmd = "java -ea -Xmx1024m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U -B pileup SAMPileup " + pileup
print cmd print cmd
farm_commands.cmd(cmd, OPTIONS.farmQueue, outputFile=validationOutput) farm_commands.cmd(cmd, OPTIONS.farmQueue, outputFile=validationOutput, just_print_commands=OPTIONS.justPrint)
if __name__ == "__main__": if __name__ == "__main__":
main() main()

6
testdata/ValidatingPileupTargets.list vendored
View File

@ -14,10 +14,12 @@
/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta * /broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
# anthony PCR lane # anthony PCR lane
/seq/dirseq/aphilipp/combo/sequences/pcr/samfiles/10035.5.clean.sam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta * # samtools import /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/pcr/samfiles/10035.5.clean.sam 10035.5.clean.bam
/humgen/gsa-scr1/GATK_Data/Validation_Data/10035.5.clean.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
# anthony HS lane # anthony HS lane
/seq/dirseq/aphilipp/combo/sequences/hs/samfiles/30CLA.5.clean.sam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta * # samtools import /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/hs/samfiles/30CLA.5.clean.sam 30CLA.5.clean.bam
/humgen/gsa-scr1/GATK_Data/Validation_Data/30CLA.5.clean.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
# WGS tumor -- figure it out # WGS tumor -- figure it out
#/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta * #/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *