Valuable series of commands
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2641 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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cf46e3c85f
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import farm_commands
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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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class CallTarget:
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def __init__(self, name, hetero, minQ = 50, depth = 120, truthGFFName = None, variantEvalArgs = '', otherVCF = None):
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self.name = name
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self.hetero = hetero
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self.minQ = minQ
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self.depth = depth
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if truthGFFName <> None:
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self.truthGFFName = truthGFFName
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else:
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self.truthGFFName = name
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self.variantEvalArgs = variantEvalArgs
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self.otherVCF = otherVCF
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self.unionVCF = None
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if otherVCF != None:
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self.unionVCF = self.name + '.gatk.glftrio.union.filtered.vcf'
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CEU_HET = 0.79e-3
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YRI_HET = 1.0e-3
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targets = [
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CallTarget('NA12878', CEU_HET),
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CallTarget('NA12891', CEU_HET),
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CallTarget('NA12892', CEU_HET),
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CallTarget('NA19238', YRI_HET),
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CallTarget('NA19239', YRI_HET),
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CallTarget('NA19240', YRI_HET),
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CallTarget('NA19240.alltechs', YRI_HET, 50, 120, 'NA19240'),
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CallTarget('NA12878.alltechs', CEU_HET, 50, 120, 'NA12878'),
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CallTarget('ceu.trio', CEU_HET, 50, 360, 'NA12878', '--sampleName NA12878', '/humgen/gsa-hpprojects/1kg/1kg_pilot2/currentBestProjectCalls/CEU_1kg_pilot2.vcf'),
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CallTarget('yri.trio', YRI_HET, 50, 360, 'NA19240', '--sampleName NA19240', '/humgen/gsa-hpprojects/1kg/1kg_pilot2/currentBestProjectCalls/YRI_1kg_pilot2.vcf'),
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]
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sets = ['Intersection', 'filteredInBoth', 'gatk', 'gatk-filteredInOther', 'glftrio', 'glftrio-filteredInOther', 'Intersection', ['gatk-unique', 'gatk.*'], ['glftrio-unique', 'glftrio.*']]
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def main():
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global OPTIONS
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usage = "usage: %prog stage [options]"
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parser = OptionParser(usage=usage)
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# parser.add_option("-q", "--farm", dest="farmQueue",
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# type="string", default=None,
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# help="Farm queue to send processing jobs to")
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parser.add_option("", "--dry", dest="dry",
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action='store_true', default=False,
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help="If provided, nothing actually gets run, just a dry run")
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parser.add_option("-d", "--dir", dest="dir",
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type='string', default="",
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help="If provided, this is the root where files are read and written")
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parser.add_option("-q", "--farm", dest="farmQueue",
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type="string", default=None,
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help="Farm queue to send processing jobs to")
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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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stage = args[0]
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for callTarget in targets:
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target = callTarget.name
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listFile = os.path.join("lists", target + ".list")
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unfilteredVCF = os.path.join(OPTIONS.dir, target + '.gatk.ug.vcf')
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filteredVCF = os.path.join(OPTIONS.dir, target + '.gatk.ug.filtered.vcf')
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tmpdir = os.path.join(OPTIONS.dir, "intermediates", unfilteredVCF + ".scatter")
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if not os.path.exists(tmpdir):
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os.makedirs(tmpdir)
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if stage == 'CALL':
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callSNPs(target, callTarget, listFile, tmpdir)
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if stage == 'MERGE':
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mergeSNPs(target, unfilteredVCF, tmpdir)
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if stage == 'FILTER':
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filterSNPs(target, callTarget.depth, unfilteredVCF, filteredVCF)
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if stage == 'UNION':
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unionSNPs(callTarget, filteredVCF )
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if stage == 'RELEASE':
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dir = '/humgen/gsa-scr1/pub/1000GenomesPilot2'
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subdir = '1000GenomesPilot2SNPs_GATK_glftrio_' + date.today().strftime("%m%d%y")
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releaseSNPs(os.path.join(dir, subdir), callTarget, filteredVCF )
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if stage == 'CLEAN':
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shutil.rmtree("intermediates", True)
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for file in [filteredVCF, unfilteredVCF]:
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if os.path.exists(file): os.remove(file)
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if stage == 'EVAL':
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evalSNPs(callTarget, unfilteredVCF, filteredVCF)
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GATK_STABLE = 'java -ea -Xmx4096m -jar /home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar -l INFO -R /broad/1KG/reference/human_b36_both.fasta '
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GATK_DEV = 'java -ea -Xmx4096m -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -R /broad/1KG/reference/human_b36_both.fasta '
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GATK = GATK_DEV
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def callSNPs(target, callTarget, listFile, tmpdir):
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cmd = "python ./runmeCalls.py -q %s -N 5 -d %s -I %s /broad/1KG/reference/human_b36_both.fasta.fai -e \"-mmq 10 -mbq 10 -pl SOLID --heterozygosity %e\" -Q %s" % (OPTIONS.farmQueue, tmpdir, listFile, callTarget.hetero, callTarget.minQ)
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print 'Enqueuing job for', target, callTarget, listFile, tmpdir
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jobid = farm_commands.cmd(cmd, None, None, just_print_commands = OPTIONS.dry)
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def mergeSNPs(target, snpFile, tmpdir):
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cmd = "python ~/dev/GenomeAnalysisTK/trunk/python/mergeVCFs.py -a -f /broad/1KG/reference/human_b36_both.fasta.fai %s/*.vcf > %s" % (tmpdir, snpFile)
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jobid = farm_commands.cmd(cmd, None, None, just_print_commands = OPTIONS.dry)
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def filterSNPs(target, depth, unfilteredVCF, filteredVCF):
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#expression = "AB > 0.75 || DP > %s" % depth
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expression = "AB > 0.75 || DP > %s || MQ0 > 40 || SB > -0.10" % depth
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cmd = GATK + '-T VariantFiltration -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -B variant,VCF,%s --clusterWindowSize 10 -o %s --filterExpression "%s"' % (unfilteredVCF, filteredVCF, expression)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry)
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def evalSNPs(callTarget, unfilteredVCF, filteredVCF):
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def eval1(vcf, namePostfix = "", args = ""):
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out = os.path.join(OPTIONS.dir, "eval", vcf + namePostfix + ".eval")
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cmd = GATK + "-T VariantEval -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -B 1kg_ceu,VCF,/humgen/gsa-hpprojects/1kg/1kg_pilot1/SNPCalls/Joint/RC1/CEU.2and3_way.annotated.vcf -B 1kg_yri,VCF,/humgen/gsa-hpprojects/1kg/1kg_pilot1/SNPCalls/Joint/RC1/YRI.2and3_way.annotated.vcf -B eval,VCF,%s -G -A -o %s -L %s" % ( vcf, out, '\;'.join(map(str, range(1,23))) )
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hapmap3 = os.path.join("../../hapmap3Genotypes", callTarget.truthGFFName + ".b36.gff")
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if os.path.exists(hapmap3):
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cmd += " -B hapmap-chip,GFF,%s %s %s" % (hapmap3, callTarget.variantEvalArgs, args)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry)
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eval1(filteredVCF)
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eval1(unfilteredVCF)
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if callTarget.unionVCF != None:
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eval1(callTarget.unionVCF, ".union")
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for set in sets:
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if type(set) == list:
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name, selector = set
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else:
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name, selector = set, set
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eval1(callTarget.unionVCF, "." + name, " -vcfInfoSelector set=\"" + selector + "\"")
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def unionSNPs(target, filteredVCF ):
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if target.otherVCF != None:
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cmd = GATK + "-T VCFCombine -B GATK,VCF,%s -B glfTrio,VCF,%s -O %s -type UNION -priority GATK,glfTrio -A" % ( filteredVCF, target.otherVCF, target.unionVCF )
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, None, just_print_commands = OPTIONS.dry)
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def releaseSNPs(dir, callTarget, filteredVCF ):
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if not os.path.exists(dir):
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os.makedirs(dir)
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print dir, filteredVCF
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#shutil.copy(filteredVCF, dir)
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if callTarget.unionVCF != None:
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shutil.copy(callTarget.unionVCF, dir)
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if __name__ == "__main__":
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main()
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# java -Xmx4096m -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T VCFCombine -R /broad/1KG/reference/human_b36_both.fasta -B GATK,VCF,ceu.trio.gatk.ug.filtered.vcf -B glfTrio,VCF,/humgen/gsa-hpprojects/1kg/1kg_pilot2/currentBestProjectCalls/CEU_1kg_pilot2.vcf -O test.vcf -type UNION -priority GATK,glfTrio -l INFO -A
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# java -ea -Xmx4096m -jar /home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -R /broad/1KG/reference/human_b36_both.fasta -T VariantEval -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -B eval,VCF,test.vcf -B hapmap-chip,GFF,../../hapmap3Genotypes/NA12878.b36.gff --sampleName NA12878 -vcfInfoSelector set=gatk-filtered
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# if ( $1 == 3.1 ) then
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# cat ceu.trio.calls.allTechs.mmq10_mbq10_q200.filtered.vcf | cut -f 1-10 > ceu.trio.calls.allTechs.mmq10_mbq10_q200.NA12878only.filtered.vcf
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# endif
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#
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# if ( $1 == 4 ) then
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# foreach callset ( NA12878.allTechs.mmq10_mbq10_q200 ceu.trio.calls.allTechs.mmq10_mbq10_q200.NA12878only )
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# java -Xmx4096m -jar /home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar -T CallsetConcordance -R /broad/1KG/reference/human_b36_both.fasta -B GATK,VCF,$callset.filtered.vcf -B glfTrio,VCF,CEU_1kg_pilot2.na12878.vcf -CT SimpleVenn -CO ${callset}_v_CEU_1kg_pilot2.filtered.vcf -l INFO
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# cat ${callset}_v_CEU_1kg_pilot2.filtered.vcf | awk '$1 ~ "#" || $8 ~ "callset2_only"' > ${callset}_v_CEU_1kg_pilot2.filtered.CEU_1kg_pilot2Unique.vcf
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# cat ${callset}_v_CEU_1kg_pilot2.filtered.vcf | awk '$1 ~ "#" || $8 ~ "callset1_only"' > ${callset}_v_CEU_1kg_pilot2.filtered.${callset}Unique.vcf
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# cat ${callset}_v_CEU_1kg_pilot2.filtered.vcf | awk '$1 ~ "#" || $8 ~ "concordant"' > ${callset}_v_CEU_1kg_pilot2.filtered.concordant.vcf
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# end
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# endif
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#
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# if ( $1 == 5 ) then
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# mkdir /humgen/gsa-scr1/pub/1000Pilot2_010710
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#
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# foreach file ( NA12878.allTechs.mmq10_mbq10_q200.filtered.vcf NA12878.SLX.mmq10_mbq10_q50.filtered.vcf NA12891.calls.mmq10_mbq10_q50.filtered.vcf NA12892.calls.mmq10_mbq10_q50.filtered.vcf ceu.trio.calls.allTechs.mmq10_mbq10_q200.filtered.vcf )
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# echo $file
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# cp $file /humgen/gsa-scr1/pub/1000Pilot2_010710
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# end
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#
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# endif
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