Mercurial > repos > pitagora > gatk_1_6_pitagora
changeset 3:1a95dea5a2f0
commit
| author | pitagora <ryota.yamanaka@riken.jp> |
|---|---|
| date | Wed, 15 Apr 2015 19:24:28 +0900 |
| parents | 855b279dbdaf |
| children | 2f7daeeaf4aa |
| files | GATKRealignerTargetCreator.py GATKRealignerTargetCreator.xml |
| diffstat | 2 files changed, 38 insertions(+), 37 deletions(-) [+] |
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--- a/GATKRealignerTargetCreator.py Wed Apr 15 18:52:30 2015 +0900 +++ b/GATKRealignerTargetCreator.py Wed Apr 15 19:24:28 2015 +0900 @@ -6,40 +6,41 @@ import traceback def __main__(): - try: - descr = "GATKRealignerTargetCreator.py: version 1.0. kick a GATK Realigner Target Creator command. \n" - parser = argparse.ArgumentParser(description=descr) - parser.add_argument( '-I', '--I', help='input file' ) - parser.add_argument( '-O', '--O', help='output file' ) - parser.add_argument( '-L', '--L', help='bed file' ) - parser.add_argument( '-R', '--R', help='reference genome file' ) - parser.add_argument( '-nt', '--nt', help='process count' ) - parser.add_argument( '-log', '--log', help='log' ) - args = parser.parse_args() - - target_dir = os.getcwd() - gatk_filename = os.path.join( target_dir, "gatk_file.bam" ) - os.symlink( args.I, gatk_filename ) - - cmd1 = "samtools index " + gatk_filename - print "The cmd is %s" % cmd1 - - proc1 = subprocess.Popen( args=cmd1, shell=True ) - rtncode1 = proc1.wait() - - if rtncode1 != 0: - raise Exception - - cmd2 = "java -Xmx2g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R " + args.R + " -nt " + args.nt + " -I " + gatk_filename + " -L " + args.L + " -log " + args.log + " -o " + args.O - print "The cmd is %s" % cmd2 - - proc2 = subprocess.Popen( args=cmd2, shell=True ) - rtncode2 = proc2.wait() - - if rtncode2 != 0: - raise Exception - except Exception: - err = traceback.format_exc(None) - print err + try: + descr = "GATKRealignerTargetCreator.py: version 1.0. kick a GATK Realigner Target Creator command. \n" + parser = argparse.ArgumentParser(description=descr) + parser.add_argument( '-J', '--J', help='java jar path' ) + parser.add_argument( '-I', '--I', help='input file' ) + parser.add_argument( '-O', '--O', help='output file' ) + parser.add_argument( '-L', '--L', help='bed file' ) + parser.add_argument( '-R', '--R', help='reference genome file' ) + parser.add_argument( '-nt', '--nt', help='process count' ) + parser.add_argument( '-log', '--log', help='log' ) + args = parser.parse_args() + + target_dir = os.getcwd() + gatk_filename = os.path.join( target_dir, "gatk_file.bam" ) + os.symlink( args.I, gatk_filename ) + + cmd1 = "samtools index " + gatk_filename + print "The cmd is %s" % cmd1 + + proc1 = subprocess.Popen( args=cmd1, shell=True ) + rtncode1 = proc1.wait() + + if rtncode1 != 0: + raise Exception + + cmd2 = "java -Xmx2g -jar " + arg.P + "/GenomeAnalysisTK.jar -T RealignerTargetCreator -R " + args.R + " -nt " + args.nt + " -I " + gatk_filename + " -L " + args.L + " -log " + args.log + " -o " + args.O + print "The cmd is %s" % cmd2 + + proc2 = subprocess.Popen( args=cmd2, shell=True ) + rtncode2 = proc2.wait() + + if rtncode2 != 0: + raise Exception + except Exception: + err = traceback.format_exc(None) + print err if __name__=="__main__": __main__()
--- a/GATKRealignerTargetCreator.xml Wed Apr 15 18:52:30 2015 +0900 +++ b/GATKRealignerTargetCreator.xml Wed Apr 15 19:24:28 2015 +0900 @@ -1,7 +1,8 @@ <tool id="GATK_realigner_target_creator" name="GATK Realigner Target Creator" version="1.6.13"> - <description>for pitagora</description> + <description></description> <command interpreter="python"> GATKRealignerTargetCreator.py + --J $JAVA_JAR_PATH --I $input --O $output --L $db_beds @@ -28,7 +29,6 @@ <data format="txt" name="log" /> </outputs> <help> - help </help> </tool>