174 lines
6.9 KiB
Python
Executable File
174 lines
6.9 KiB
Python
Executable File
#!/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="/broad/tools/apps/R-2.6.0/bin/Rscript"
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# Any special site-specific arguments to pass the JVM.
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jvm_args='-ea -Xmx4096m'
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# Where to put the output created as part of recalibration.
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# If editing, please end this variable with a trailing slash.
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output_root = './'
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# Location of the resource files distributed with the recalibration tool.
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# If editing, please end this variable with a trailing slash.
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resources='resources/'
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import getopt,glob,os,sys
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import LogisticRegressionByReadGroup
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# if the provided resources path is relative, convert it to a path
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# relative to the calling script rather than the cwd.
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if not os.path.isabs(resources):
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application_path = os.path.dirname(sys.argv[0])
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resources = os.path.abspath(application_path) + '/' + resources
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# Where does the reference live?
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reference_base = resources + 'human_b36_both'
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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.1kg.rod.out'
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# Where are the application files required to run the recalibration?
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gatk = resources + 'gatk/GenomeAnalysisTK.jar'
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logistic_regression_script = resources + 'logistic_regression.R'
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empirical_vs_reported_grapher = resources + 'plot_q_emp_stated_hst.R'
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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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def graph_file(graph_script,graph_data):
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'Graph the given data using the given script. Leave the data in the output directory.'
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check_input_file_available(graph_script,'%s R graphing script' % graph_script)
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check_input_file_available(graph_data,'%s graphing data' % graph_data)
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result = os.system(' '.join((R_exe,graph_script,graph_data)))
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if result != 0:
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exit('Unable to graph data: %s' % graph_data,1)
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def recalibrate():
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'Recalibrate the given bam file'
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# generate the covariates
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print 'generating covariates'
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generate_covariates = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',bam,'-mqs 40','--OUTPUT_FILEROOT',output_dir+'initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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returncode = os.system(generate_covariates)
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if returncode != 0:
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exit('Unable to generate covariates',1)
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# compute the logistic regression
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print 'computing the logistic regression'
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LogisticRegressionByReadGroup.compute_logistic_regression(output_dir + 'initial.covariate_counts.csv',output_dir + 'linear_regression_results.out',R_exe,logistic_regression_script)
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# apply the logistic regression, writing the output data to calibrated_bam
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print 'applying the correction to the reads'
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apply_logistic_regression = ' '.join((gatk_base_cmdline,'-T LogisticRecalibration','-I',bam,'-logisticParams',output_dir+'linear_regression_results.out','-outputBAM',calibrated_bam))
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returncode = os.system(apply_logistic_regression)
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if returncode != 0:
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exit('Unable to apply logistic regression',1)
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# index the calibrated bam
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print 'indexing the calibrated bam'
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index_calibrated_bamfile = ' '.join((samtools_exe,'index',calibrated_bam))
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returncode = os.system(index_calibrated_bamfile)
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if returncode != 0:
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exit('Unable to index calibrated bamfile',1)
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print 'Recalibration complete! Calibrated bam is available here: ' + calibrated_bam
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def evaluate():
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'Evaluate recalibration results.'
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print 'Evaluating recalibration results'
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# regenerate the covariates
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regenerate_covariates = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',calibrated_bam,'-mqs 40','--OUTPUT_FILEROOT',output_dir+'recalibrated','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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print 'regenerating covariates'
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returncode = os.system(regenerate_covariates)
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if returncode != 0:
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exit('Unable to regenerate covariates',1)
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print 'graphing initial results'
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for filename in glob.glob(output_dir+'initial.*.empirical_v_reported_quality.csv'):
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graph_file(empirical_vs_reported_grapher,filename)
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print 'graphing final results'
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for filename in glob.glob(output_dir+'recalibrated.*.empirical_v_reported_quality.csv'):
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graph_file(empirical_vs_reported_grapher,filename)
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def usage():
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exit('Usage: python RecalQual.py [--recalibrate] [--evaluate] <input bam file> <calibrated output bam file>',1)
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# Try to parse the given command-line arguments.
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try:
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opts, args = getopt.gnu_getopt(sys.argv[1:],'',['recalibrate','evaluate'])
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except getopt.GetoptError, err:
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usage()
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# An input and an output file is required. Fail if left unspecified.
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if len(args) < 2:
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usage()
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# Determine whether to evaluate / recalibrate.
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recalibrate_requested = False
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evaluate_requested = False
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for opt,arg in opts:
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if opt == '--recalibrate':
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recalibrate_requested = True
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if opt == '--evaluate':
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evaluate_requested = True
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# Default to 'recalibrate' unless the user specified only evaluate.
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do_recalibration = not (evaluate_requested and not recalibrate_requested)
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# Only evaluate if the user specifically requested evaluation.
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do_evaluation = evaluate_requested
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print 'Looking for supplemental files in ' + resources
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# check that the input bam file exists, and that the bam is indexed.
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bam = args[0]
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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 = args[1]
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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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# sanity check that the software is available
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check_input_file_available(samtools_exe,'samtools')
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check_input_file_available(java_exe,'java')
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check_input_file_available(R_exe,'R')
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check_input_file_available(gatk,'Genome Analysis Toolkit')
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check_input_file_available(logistic_regression_script,'logistic regression script')
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# make an output directory for temporary files
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output_dir=output_root+'output.' + bam[bam.rfind('/')+1:bam.rfind('.bam')] + '/'
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if not os.path.isdir(output_dir):
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os.mkdir(output_dir)
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if not os.path.isdir(output_dir):
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exit('Unable to create output directory ' + output_dir,1)
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# assemble the required program arguments
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gatk_base_cmdline = ' '.join((java_exe,jvm_args,'-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))
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if do_recalibration:
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recalibrate()
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if do_evaluation:
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evaluate()
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