69 lines
2.7 KiB
Python
69 lines
2.7 KiB
Python
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#!/usr/bin/env python
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# Executable files. Please update these to match the installed locations of your tools.
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samtools_exe='/seq/dirseq/samtools/current/samtools'
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java_exe='/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/bin/java'
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R_exe='/util/bin/R'
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GATK_jar='/humgen/gsa-scr1/hanna/src/StingWorking/dist/GenomeAnalysisTK.jar'
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# Location of the resource files distributed with the recalibration tool.
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resources='resources/'
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# Where does the reference live?
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reference_base = resources + 'Homo_sapiens_assembly18'
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reference = reference_base + '.fasta'
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reference_dict = reference_base + '.dict'
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reference_fai = reference_base + '.fasta.fai'
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# Where does DBSNP live?
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dbsnp = resources + 'dbsnp.rod.out'
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import sys,os
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def exit(msg,errorcode):
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print msg
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sys.exit(errorcode)
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def check_input_file_available(filename,description):
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if not os.access(filename,os.R_OK):
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exit('Unable to access %s %s' % (description,filename),1)
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if len(sys.argv) < 3:
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exit('Usage: python RecalQual.py <input bam file> <calibrated output bam file>',1)
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# check that the input bam file exists, and that the bam is indexed.
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bam = sys.argv[1]
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bam_index = bam + '.bai'
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check_input_file_available(bam,'reads file')
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check_input_file_available(bam_index,'reads index file')
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# parse the user's calibration output file requirements
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calibrated_bam = sys.argv[2]
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calibrated_bam_index = calibrated_bam + '.bai'
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# check that the fasta and supporting files are available
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check_input_file_available(reference,'reference file')
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check_input_file_available(reference_dict,'reference dictionary')
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check_input_file_available(reference_fai,'reference index file')
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# check that the dbsnp is available
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check_input_file_available(dbsnp,'dbsnp file')
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# make an output directory for temporary files
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if not os.path.isdir('output'):
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os.mkdir('output')
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# assemble the required program arguments
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gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',GATK_jar,'-R',reference,'--DBSNP',dbsnp,'-l INFO','-L chrM'))
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generate_covariates = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',bam,'-mqs 40','--OUTPUT_FILEROOT output/output','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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compute_logistic_regression = ' '.join(('python','LogisticRegressionByReadGroup.py','output/output.covariate_counts.csv','output/linear_regression_results.out'))
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apply_logistic_regression = ' '.join((gatk_base_cmdline,'-T LogisticRecalibration','-I',bam,'-logisticParams output/linear_regression_results.out','-outputBAM',calibrated_bam))
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index_calibrated_bamfile = ' '.join((samtools_exe,'index',calibrated_bam))
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os.system(generate_covariates)
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os.system(compute_logistic_regression)
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os.system(apply_logistic_regression)
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os.system(index_calibrated_bamfile)
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