gatk-3.8/python/RecalQual.py

#!/usr/bin/env python

# Executable files.  Please update these to match the installed locations of your tools.
samtools_exe='/seq/dirseq/samtools/current/samtools'
java_exe='/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/bin/java'
R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"

# Any special site-specific arguments to pass the JVM.
jvm_args='-ea -Xmx4096m'

# Where to put the output created as part of recalibration.  
# If editing, please end this variable with a trailing slash.
output_root = './'

# Location of the resource files distributed with the recalibration tool.  
# If editing, please end this variable with a trailing slash.
resources='resources/'

# Where does the reference live?
reference_base = resources + 'human_b36_both'
reference      = reference_base + '.fasta'
reference_dict = reference_base + '.dict'
reference_fai  = reference_base + '.fasta.fai'

# Where does DBSNP live?
dbsnp = resources + 'dbsnp.1kg.rod.out'

# Where are the application files required to run the recalibration?
gatk = resources + 'gatk/GenomeAnalysisTK.jar'
logistic_regression_script = resources + 'logistic_regression.R'
empirical_vs_reported_grapher = resources + 'plot_q_emp_stated_hst.R'

import getopt,glob,os,sys
import LogisticRegressionByReadGroup

def exit(msg,errorcode):
    print msg
    sys.exit(errorcode)

def check_input_file_available(filename,description):
    if not os.access(filename,os.R_OK):
        exit('Unable to access %s %s' % (description,filename),1)

def graph_file(graph_script,graph_data):
    'Graph the given data using the given script.  Leave the data in the output directory.'
    check_input_file_available(graph_script,'%s R graphing script' % graph_script)
    check_input_file_available(graph_data,'%s graphing data' % graph_data)
    result = os.system(' '.join((R_exe,graph_script,graph_data)))
    if result != 0:
        exit('Unable to graph data: %s' % graph_data,1)

def recalibrate():
    'Recalibrate the given bam file'
    # generate the covariates
    print 'generating covariates'
    generate_covariates = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',bam,'-mqs 40','--OUTPUT_FILEROOT',output_dir+'initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
    returncode = os.system(generate_covariates)
    if returncode != 0:
        exit('Unable to generate covariates',1)

    # compute the logistic regression
    print 'computing the logistic regression'
    LogisticRegressionByReadGroup.compute_logistic_regression(output_dir + 'initial.covariate_counts.csv',output_dir + 'linear_regression_results.out',R_exe,logistic_regression_script)

    # apply the logistic regression, writing the output data to calibrated_bam
    print 'applying the correction to the reads'
    apply_logistic_regression = ' '.join((gatk_base_cmdline,'-T LogisticRecalibration','-I',bam,'-logisticParams',output_dir+'linear_regression_results.out','-outputBAM',calibrated_bam))
    returncode = os.system(apply_logistic_regression)
    if returncode != 0:
        exit('Unable to apply logistic regression',1)

    # index the calibrated bam
    print 'indexing the calibrated bam'
    index_calibrated_bamfile = ' '.join((samtools_exe,'index',calibrated_bam))
    returncode = os.system(index_calibrated_bamfile)
    if returncode != 0:
        exit('Unable to index calibrated bamfile',1)

    print 'Recalibration complete!  Calibrated bam is available here: ' + calibrated_bam    

def evaluate():
    'Evaluate recalibration results.'
    print 'Evaluating recalibration results'
    # regenerate the covariates
    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'))
    print 'regenerating covariates'
    returncode = os.system(regenerate_covariates)
    if returncode != 0:
        exit('Unable to regenerate covariates',1)

    print 'graphing initial results'
    for filename in glob.glob(output_dir+'initial.*.empirical_v_reported_quality.csv'):
        graph_file(empirical_vs_reported_grapher,filename)
    print 'graphing final results'
    for filename in glob.glob(output_dir+'recalibrated.*.empirical_v_reported_quality.csv'):
        graph_file(empirical_vs_reported_grapher,filename)

def usage():
    exit('Usage: python RecalQual.py [--recalibrate] [--evaluate] <input bam file> <calibrated output bam file>',1)

# Try to parse the given command-line arguments.
try:
    opts, args = getopt.gnu_getopt(sys.argv[1:],'',['recalibrate','evaluate'])
except getopt.GetoptError, err:
    usage()

# An input and an output file is required.  Fail if left unspecified.
if len(args) < 2:
    usage()

# Determine whether to evaluate / recalibrate.
recalibrate_requested = False
evaluate_requested = False
for opt,arg in opts:
    if opt == '--recalibrate':
        recalibrate_requested = True
    if opt == '--evaluate':
        evaluate_requested = True

# Default to 'recalibrate' unless the user specified only evaluate.
do_recalibration = not (evaluate_requested and not recalibrate_requested)
# Only evaluate if the user specifically requested evaluation.
do_evaluation = evaluate_requested

# check that the input bam file exists, and that the bam is indexed.
bam = args[0]
bam_index = bam + '.bai'

check_input_file_available(bam,'reads file')
check_input_file_available(bam_index,'reads index file')

# parse the user's calibration output file requirements
calibrated_bam = args[1]
calibrated_bam_index = calibrated_bam + '.bai'

# check that the fasta and supporting files are available
check_input_file_available(reference,'reference file')
check_input_file_available(reference_dict,'reference dictionary')
check_input_file_available(reference_fai,'reference index file')

# check that the dbsnp is available
check_input_file_available(dbsnp,'dbsnp file')

# sanity check that the software is available
check_input_file_available(samtools_exe,'samtools')
check_input_file_available(java_exe,'java')
check_input_file_available(R_exe,'R')
check_input_file_available(gatk,'Genome Analysis Toolkit')
check_input_file_available(logistic_regression_script,'logistic regression script')

# make an output directory for temporary files
output_dir=output_root+'output.' + bam[bam.rfind('/')+1:bam.rfind('.bam')] + '/'
if not os.path.isdir(output_dir):
    os.mkdir(output_dir)
if not os.path.isdir(output_dir):
    exit('Unable to create output directory ' + output_dir,1)

# assemble the required program arguments
gatk_base_cmdline = ' '.join((java_exe,jvm_args,'-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))

if do_recalibration:
    recalibrate()

if do_evaluation:
    evaluate()