Minor improvements to simple python code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3330 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
504103bd15
commit
d6b036cdab
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@ -0,0 +1,45 @@
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from farm_commands2 import *
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import os.path
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import sys
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from optparse import OptionParser
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from datetime import date
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import glob
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import operator
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import faiReader
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import math
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import shutil
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import string
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from madPipelineUtils import *
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def main():
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global OPTIONS
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usage = "usage: %prog [options] indels.verbose.txt"
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parser = OptionParser(usage=usage)
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parser.add_option("-v", "--verbose", dest="verbose",
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action='store_true', default=False,
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help="")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 1:
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parser.error("incorrect number of arguments")
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indelsFile = args[0]
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print 'event size nReadsWithIndel nReadsWithoutIndel nReadsTotal'
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for line in open(indelsFile):
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try:
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parts = line.split()
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# chr1 30502 30505 -TTT OBS_COUNTS[C/A/T]:5/5/13 AV_MM[C/R]:0.00/0.75 AV_MAPQ[C/R]:37.00/27.13 NQS_MM_RATE[C/R]:0.00/0.01 NQS_AV_QUAL[C/R]:30.90/28.30 STRAND_COUNTS[C/C/R/R]:2/3/6/2
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chr, start, stop = parts[0:3]
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event = parts[3]
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counts = parts[4]
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isInsertion = event[0] == '+'
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size = len(event[1:])
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nConsensusReads, nReadsWithIndel, nReads = map(int, counts.split(':')[1].split('/'))
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nReadsWithoutIndel = nReads - nReadsWithIndel
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print event[0], size, nReadsWithIndel, nReadsWithoutIndel, nReads
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except:
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continue
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if __name__ == "__main__":
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main()
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@ -10,9 +10,9 @@ import math
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import shutil
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import string
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GATK_STABLE = '/home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar'
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GATK_DEV = '/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar'
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GATK = 'java -Xmx%s -Djava.io.tmpdir=/broad/shptmp/depristo/tmp/ -jar ' + GATK_STABLE + ' -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -l INFO '
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GATK_STABLE_JAR = '/home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar'
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GATK_DEV_JAR = '/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar'
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GATK_JAR = GATK_STABLE_JAR
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# add to GATK to enable dbSNP aware cleaning
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# -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod
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@ -23,7 +23,6 @@ GATK = 'java -Xmx%s -Djava.io.tmpdir=/broad/shptmp/depristo/tmp/ -jar ' + GATK_S
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hg18 = ['chr' + str(i) for i in range(1,23)] + ['chrX', 'chrY']
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b36 = [str(i) for i in range(1,23)] + ['X', 'Y']
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HG18_TO_B36 = {
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'hg18' : 'b36',
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'/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta' : '/broad/1KG/reference/human_b36_both.fasta',
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@ -46,17 +45,17 @@ def appendExtension(path, newExt, addExtension = True):
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# return os.path.join(OPTIONS.dir, s)
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class PipelineArgs:
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def __init__( self, GATK = GATK, ref = 'hg18', name = None, memory = '4g' ):
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self.GATK = GATK
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def __init__( self, GATK_JAR = GATK_JAR, ref = 'hg18', name = None, memory = '4g' ):
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self.GATK = 'java -Xmx%s -Djava.io.tmpdir=/broad/shptmp/depristo/tmp/ -jar ' + GATK_JAR + ' -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -l INFO '
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self.ref = ref
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self.name = name
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self.memory = memory
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def convertToB36(self):
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return this.ref == 'b36'
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return self.ref == 'b36'
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def addGATKArg(self, arg):
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if arg[0] != ' ':
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if len(arg) > 0 and arg[0] != ' ':
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arg = ' ' + arg
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self.GATK += arg
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@ -67,8 +66,8 @@ class PipelineArgs:
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return suffix
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def finalizedGATKCommand(self, args):
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cmd = (self.GATK % self.memory) + args
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if self.convertToB36:
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cmd = (self.GATK % self.memory) + ' ' + args
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if self.convertToB36():
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cmd = hg18args_to_b36(cmd)
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return cmd
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@ -83,11 +82,18 @@ def simpleGATKCommand( pargs, name, args, lastJobs ):
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# Takes a simpleGATKCommand and splits it by chromosome, merging output
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#
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def splitGATKCommandByChr( myPipelineArgs, cmd, outputsToParallelize, mergeCommands ):
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if cmd.cmd_str_from_user.find(" -L") != -1:
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sys.exit("Found -L argument in command -- cannot be provided for parallelization by chromosome: " + cmd.cmd_str_from_user)
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def makeChrCmd(chr):
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chrOutputMap = map(lambda x: appendExtension(x, chr), outputsToParallelize)
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chr_cmd_str = cmd.cmd_str_from_user
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chr_cmd_str = cmd.cmd_str_from_user
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chr_cmd_str += ' -L ' + chr
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for x, y in zip(outputsToParallelize, chrOutputMap):
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chr_cmd_str = chr_cmd_str.replace(x, y)
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if myPipelineArgs.convertToB36():
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chr_cmd_str = hg18args_to_b36(chr_cmd_str)
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chrCmd = FarmJob(chr_cmd_str, jobName = cmd.jobName + '.byChr' + chr, dependencies = cmd.dependencies)
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return chrCmd, chrOutputMap
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@ -88,12 +88,12 @@ def main():
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def createTargets( myPipelineArgs, chr, inputBam, outputRoot, args, lastJobs ):
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outputIntervals = outputRoot + ".intervals"
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GATKArgs = '-T RealignerTargetCreator -I %s -o %s -mrl 10000 -L %s' % (inputBam, outputIntervals, chr)
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GATKArgs = '-T RealignerTargetCreator -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -I %s -o %s -mrl 10000 -L %s' % (inputBam, outputIntervals, chr)
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return simpleGATKCommand( myPipelineArgs, 'CreateInterval' + chr, GATKArgs, lastJobs ), outputIntervals
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def realign( myPipelineArgs, chr, inputBam, outputRoot, intervals, lastJobs ):
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outputBAM = outputRoot + ".bam"
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GATKArgs = '-T IndelRealigner -I %s -targetIntervals %s --output %s -sort ON_DISK -mrl 100000 -L %s' % (inputBam, intervals, outputBAM, chr)
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GATKArgs = '-T IndelRealigner -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -I %s -targetIntervals %s --output %s -sort ON_DISK -mrl 100000 -L %s' % (inputBam, intervals, outputBAM, chr)
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return simpleGATKCommand( myPipelineArgs, 'Realign' + chr, GATKArgs, lastJobs ), outputBAM
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def index( myPipelineArgs, chr, inputBam, outputRoot, realignedBam, lastJobs ):
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@ -4,10 +4,10 @@ from optparse import OptionParser
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from vcfReader import *
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if __name__ == "__main__":
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usage = "usage: %prog files.list [options]"
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usage = "usage: %prog [file.vcf | if absent stdin] [options]"
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parser = OptionParser(usage=usage)
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parser.add_option("-f", "--f", dest="fields",
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type='string', default="",
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type='string', default=None,
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help="Comma separated list of fields to exact")
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parser.add_option("-e", "--filter", dest="filter",
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action='store_true', default=False,
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@ -17,13 +17,19 @@ if __name__ == "__main__":
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help="Only print out every 1 / skip records")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 0:
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if len(args) > 1:
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parser.error("incorrect number of arguments")
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counter = OPTIONS.skip
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src = sys.stdin
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if len(args) > 0:
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src = open(args[0])
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if OPTIONS.fields == None:
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sys.exit("Fields argument must be provided")
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fields = OPTIONS.fields.split(',')
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for header, vcf, count in lines2VCF(sys.stdin, extendedOutput = True):
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for header, vcf, count in lines2VCF(src, extendedOutput = True):
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#print vcf, count
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if count == 1 and vcf.hasHeader():
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print '\t'.join(fields)
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