Lots of cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@903 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
9689bb3331
commit
61ae00c7bf
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@ -2,9 +2,6 @@
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import os,sys
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R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"
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logistic_regression_script="/humgen/gsa-scr1/hanna/src/StingWorking/R/logistic_regression.R"
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def exit(msg,errorlevel):
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"Exit the program with the specified message and error code."
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print msg
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@ -25,7 +22,7 @@ def read_header(source_file):
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exit("Input file is in invalid format. First two columns should be <read group>,<dinucleotide>",1)
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return header
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def create_intermediate_file(source_file,read_group,dinuc):
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def create_intermediate_file(source_file,header,read_group,dinuc):
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"Create an intermediate file for a particular read group / dinuc from a given source file"
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base = source_file.name[:source_file.name.rfind('.csv')]
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intermediate_filename = "%s.%s.%s.csv" % (base,read_group,dinuc)
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@ -43,7 +40,8 @@ def open_target_file(target_filename):
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target_file.write("\n")
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return target_file
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def process_file(source_file,read_group,dinuc,target_file):
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def process_file(source_file,read_group,dinuc,target_file,R_exe,logistic_regression_script):
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"Process the contents of an intermediate file. An intermediate file is the specific data arranged per read group, per dinuc."
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base = source_file.name[:source_file.name.rfind('.csv')] + '.' + read_group
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regression_command = ' '.join((R_exe,logistic_regression_script,base,base,dinuc))
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print "Running " + regression_command
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@ -54,37 +52,47 @@ def process_file(source_file,read_group,dinuc,target_file):
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parameters_file = open(parameters_filename,'r')
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parameters = ' '.join([line.rstrip('\n') for line in parameters_file]).split(' ')
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target_file.write('\t'.join([read_group,dinuc]+parameters)+'\n')
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os.remove('.'.join((base,dinuc,'csv')))
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os.remove('.'.join((base,dinuc,'parameters')))
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# optionally remove the input and output files. For now, keep them around for debugging purposes.
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# os.remove('.'.join((base,dinuc,'csv')))
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# os.remove('.'.join((base,dinuc,'parameters')))
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if len(sys.argv) < 3:
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exit("Usage: logistic_regression <covariate count input csv> <parameters csv>",1)
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def compute_logistic_regression(source_filename,target_filename,R_exe,logistic_regression_script):
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"Do the heavy lifting. Group covariant data into individual output files, compute the logistic regression, and format the results."
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source_file = open_source_file(source_filename)
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target_file = open_target_file(target_filename)
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source_file = open_source_file(sys.argv[1])
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target_file = open_target_file(sys.argv[2])
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header = read_header(source_file)
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header = read_header(source_file)
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intermediate_file = None
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read_group = None
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dinuc = None
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intermediate_file = None
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read_group = None
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dinuc = None
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for data_line in source_file:
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data_line = data_line.strip()
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if len(data_line) == 0:
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continue
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data = data_line.split(',')
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if read_group != data[0] or dinuc != data[1]:
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if intermediate_file:
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intermediate_file.close()
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process_file(source_file,read_group,dinuc,target_file,R_exe,logistic_regression_script)
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read_group,dinuc = data[0:2]
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intermediate_file = create_intermediate_file(source_file,header,read_group,dinuc)
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intermediate_file.write(','.join(data[2:])+'\n')
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for data_line in source_file:
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data_line = data_line.strip()
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if len(data_line) == 0:
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continue
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data = data_line.split(',')
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if read_group != data[0] or dinuc != data[1]:
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if intermediate_file:
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intermediate_file.close()
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process_file(source_file,read_group,dinuc,target_file)
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read_group,dinuc = data[0:2]
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intermediate_file = create_intermediate_file(source_file,read_group,dinuc)
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intermediate_file.write(','.join(data[2:])+'\n')
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if intermediate_file:
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intermediate_file.close()
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process_file(source_file,read_group,dinuc,target_file,R_exe,logistic_regression_script)
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if intermediate_file:
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intermediate_file.close()
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process_file(source_file,read_group,dinuc,target_file)
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source_file.close()
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target_file.close()
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source_file.close()
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target_file.close()
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if __name__ == "__main__":
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# set up sensible defaults for the locations of R and the logistic regression script
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R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"
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logistic_regression_script="resources/logistic_regression.R"
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if len(sys.argv) < 3:
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exit("Usage: logistic_regression <covariate count input csv> <parameters csv>",1)
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compute_logistic_regression(sys.argv[1],sys.argv[2],R_exe,logistic_regression_script)
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@ -3,10 +3,10 @@
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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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R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"
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# Location of the resource files distributed with the recalibration tool.
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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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# Where does the reference live?
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@ -18,7 +18,12 @@ 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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# 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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import sys,os
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import LogisticRegressionByReadGroup
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def exit(msg,errorcode):
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print msg
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@ -50,19 +55,43 @@ 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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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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gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',gatk,'-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/initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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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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# generate the covariates
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print 'generating covariates'
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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/initial.covariate_counts.csv','output/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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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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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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