Many generalization improvements - parameters, files as options - to script that runs pieces for predicting SNP calling performance for given SNP calling coverage
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1619 348d0f76-0448-11de-a6fe-93d51630548a
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andrewk
parent
7eb21e55c1
commit
e06e31d99f
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@ -1,4 +1,4 @@
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#!/usr/bin/python
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#!/usr/bin/env python
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import sys, os
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from farm_commands import cmd
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@ -17,75 +17,117 @@ class OptionParser (OptionParser):
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def exists_and_non_zero(file):
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return os.path.exists(file) and os.path.getsize(file) != 0
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# Global files
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gatk_exe = "java -Xmx8192m -jar ~/dev/Sting/trunk/dist/GenomeAnalysisTK.jar "
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ref = " -R /broad/1KG/reference/human_b36_both.fasta"
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parser = OptionParser()
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parser.add_option("-b", "--bam-file", help="Input BAM filename", dest="bam_file", default=None)
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(options, args) = parser.parse_args()
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parser.check_required(("-b",))
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output_base = os.path.splitext(options.bam_file)[0]
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print "Input BAM file:",options.bam_file
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# Assure that hapmap chip file is here
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hapmapchip_file = output_base+".hapmapchip.gff"
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if not exists_and_non_zero(hapmapchip_file):
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sys.exit("Expected to find "+hapmapchip_file+" but it's not around")
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# Run SSG calls
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ssg_outfile = output_base+".SSG.calls"
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if not exists_and_non_zero(ssg_outfile):
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print "Running SingleSampleGenotyper"
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Cmd = gatk_exe + ref + " -T SingleSampleGenotyper"+\
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" -I "+options.bam_file+\
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" -varout "+ssg_outfile+\
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" -L 1"+\
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" -fmq0 -l INFO "
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cmd(Cmd)
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# Run VariantEval on SSG calls
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varianteval_outdir = "VariantEval"
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varianteval_outbase = "VariantEval/"+output_base
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varianteval_outfile = "VariantEval/"+output_base+".all.genotype_concordance"
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if not exists_and_non_zero(varianteval_outfile):
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print "Running VarianteEval with output to "+varianteval_outbase
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if not os.path.exists(varianteval_outdir):
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os.mkdir(varianteval_outdir)
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Cmd = gatk_exe + ref + "-T VariantEval"+\
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" -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\
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" -B eval,Variants,"+ssg_outfile+\
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" -hc "+hapmapchip_file+\
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" -o "+varianteval_outbase+\
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" -L /humgen/gsa-scr1/andrewk/coverage/b36.hapmap_intervals.chr1"+\
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" -evalContainsGenotypes"+\
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" -minDiscoveryQ 5"+\
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" -fmq0 -l INFO"
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cmd(Cmd)
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# Run CoverageHist on BAM file
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hist_outfile = output_base+".hapmap.coverage_hist"
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if not exists_and_non_zero(hist_outfile):
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print "Running CoverageHist on "+options.bam_file
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Cmd = gatk_exe + ref + "-T CoverageHistogram"+\
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" -I "+options.bam_file+\
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" -o "+hist_outfile+\
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" -L /humgen/gsa-scr1/andrewk/coverage/b36.hapmap_intervals.chr1"+\
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" -fmq0 -l INFO"
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#" -hc ~/coverage/NA12878.b36.gff"+\
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#" -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\
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cmd(Cmd)#,"gsa", output_base)
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# Now show CoverageEval predictions
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Cmd = "CoverageEval.py -e"+\
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" -s /humgen/gsa-scr1/projects/1kg_pilot2/coverage_eval/fixed_stats/NA12878.CLEANED.chr1.full.hapmap.stats"+\
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" -g "+hist_outfile
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cmd(Cmd)
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def process_bam(bam_file):
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gatk_exe = "java -Xmx8192m -jar ~/dev/Sting/trunk/dist/GenomeAnalysisTK.jar "
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output_basepath = os.path.splitext(bam_file)[0]
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output_basefile = os.path.basename(output_basepath)
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print "Input BAM file:",bam_file
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using_hapmapchip = None
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if False:
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# Config for chr1 of pilot 2 people
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ref = " -R /broad/1KG/reference/human_b36_both.fasta"
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#interval_string = "1"
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# Assure existance of intervals file
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intervals_file = output_basepath+".hapmap.intervals.chr1"
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if not exists_and_non_zero(intervals_file):
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Cmd = "awk -F' ' '{ if ($1 == \""+interval_string+"\") {print $1 \":\" $4} }' "+hapmapchip_file+" > "+intervals_file
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cmd(Cmd, die_on_fail = True)
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# Setup hapmapchip GFFs; assure that hapmap chip file is here
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using_hapmapchip = True
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hapmapchip_file = output_basepath+".hapmapchip.gff"
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if not exists_and_non_zero(hapmapchip_file):
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sys.exit("Expected to find "+hapmapchip_file+" but it's not around")
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else:
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# Config for pilot 3
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ref = " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
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intervals_file = "/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.targets.interval_list"
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# Assure that BAM index exists
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bam_index_file = output_basepath+".bam.bai"
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if not exists_and_non_zero(bam_index_file):
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Cmd = "samtools index "+bam_file
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cmd(Cmd, die_on_fail = True)
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# Run SSG calls
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ssg_outfile = output_basepath+".SSG.calls"
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if not exists_and_non_zero(ssg_outfile):
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print "Running SingleSampleGenotyper"
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Cmd = gatk_exe + ref + " -T SingleSampleGenotyper"+\
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" -I "+bam_file+\
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" -varout "+ssg_outfile+\
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" -L "+intervals_file+\
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" -fmq0 -l INFO "
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#" --genotype -lod 5"
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#+interval_string+\
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cmd(Cmd, die_on_fail=True)
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# Run VariantEval on SSG calls
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varianteval_outdir = output_basepath+".VariantEval"
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varianteval_outbase = output_basepath+".VariantEval/"+output_basepath
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varianteval_outfile = output_basepath+".VariantEval/"+output_basepath #+".all.genotype_concordance"
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if not exists_and_non_zero(varianteval_outfile):
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print "Running VariantEval with output to "+varianteval_outbase
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if not os.path.exists(varianteval_outdir):
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os.mkdir(varianteval_outdir)
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Cmd = gatk_exe + ref + " -T VariantEval"+\
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" -B dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod"+\
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" -B eval,Variants,"+ssg_outfile+\
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" -o "+varianteval_outbase+\
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" -L "+intervals_file+\
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" --evalContainsGenotypes"+\
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" -minConfidenceScore 5"+\
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" -fmq0 -l INFO"
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if using_hapmapchip:
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Cmd = Cmd + " -hc "+hapmapchip_file
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cmd(Cmd, die_on_fail=True)
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# Run CoverageHist on BAM file
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hist_outfile = output_basepath+".hapmap.coverage_hist"
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if not exists_and_non_zero(hist_outfile):
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print "Running CoverageHist on "+bam_file
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Cmd = gatk_exe + ref + " -T CoverageHistogram"+\
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" -I "+bam_file+\
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" -o "+hist_outfile+\
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" -L "+intervals_file+\
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" -fmq0 -l INFO"
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cmd(Cmd, die_on_fail=True)#,"gsa", output_basepath)
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# Now do CoverageEval predictions if they haven't been done
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oneline_stats_file = output_basepath+".oneline_stats"
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if not exists_and_non_zero(oneline_stats_file):
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Cmd = "CoverageEval.py -e"+\
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" -s /humgen/gsa-scr1/projects/1kg_pilot2/coverage_eval/fixed_stats/current/NA12878.chr1.full.stats"+\
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" -g "+hist_outfile+\
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" -v "+varianteval_outfile+\
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" -o "+oneline_stats_file
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cmd(Cmd, die_on_fail=True)
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if __name__ == "__main__":
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parser = OptionParser()
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parser.add_option("-b", "--bam-file", help="Input BAM filename", dest="bam_file", default=None)
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parser.add_option("-a", "--all_bams", help="Process all BAMs in current directory", default=False, dest="all_bams", action="store_true")
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(options, args) = parser.parse_args()
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if not options.all_bams:
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parser.check_required(("-b",))
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process_bam(options.bam_file)
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else:
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bams = [f for f in os.listdir(".") if f.endswith(".bam")]
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print bams
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for bam in bams:
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process_bam(bam)
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#print
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