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Cleanup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@931 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-07 20:25:08 +00:00
parent 98396732ba
commit 596773e6c6
2 changed files with 56 additions and 23 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
View File

@ -95,6 +95,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) {
if( readGroup.getAttribute("PL") == null )
Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId()));
if( !isIlluminaReadGroup(readGroup) )
continue;
data.put(readGroup.getReadGroupId(), new RecalData[MAX_READ_LENGTH+1][MAX_QUAL_SCORE+1][NDINUCS]);
for ( int i = 0; i < MAX_READ_LENGTH+1; i++) {
for ( int j = 0; j < MAX_QUAL_SCORE+1; j++) {
@ -117,7 +119,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
for (int i =0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
SAMReadGroupRecord readGroup = read.getHeader().getReadGroup((String)read.getAttribute("RG"));
if ( (readGroup.getAttribute("PL") == null || "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString())) &&
if ( isIlluminaReadGroup(readGroup) &&
!read.getReadNegativeStrandFlag() &&
(READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) &&
(read.getMappingQuality() >= MIN_MAPPING_QUALITY)) {
@ -384,4 +386,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
public CovariateCounterWalker() throws FileNotFoundException {
random_genrator = new Random(123454321); // keep same random seed while debugging
}
private boolean isIlluminaReadGroup( SAMReadGroupRecord readGroup ) {
return (readGroup.getAttribute("PL") == null || "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString()));
}
}

71
python/RecalQual.py
View File

@ -5,6 +5,13 @@ 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/'
@ -18,12 +25,12 @@ reference_fai = reference_base + '.fasta.fai'
# Where does DBSNP live?
dbsnp = resources + 'dbsnp.rod.out'
# Where are the application files required to run the recalibration
# 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 glob,os,sys
import getopt,glob,os,sys
import LogisticRegressionByReadGroup
def exit(msg,errorcode):
@ -46,18 +53,18 @@ 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/initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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/initial.covariate_counts.csv','output/linear_regression_results.out',R_exe,logistic_regression_script)
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/linear_regression_results.out','-outputBAM',calibrated_bam))
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)
@ -75,38 +82,55 @@ 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/recalibrated','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
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/initial.*.empirical_v_reported_quality.csv'):
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/recalibrated.*.empirical_v_reported_quality.csv'):
for filename in glob.glob(output_dir+'recalibrated.*.empirical_v_reported_quality.csv'):
graph_file(empirical_vs_reported_grapher,filename)
if len(sys.argv) < 3:
exit('Usage: python RecalQual.py <input bam file> <calibrated output bam file> [{RECALIBRATE | EVALUATE | RECALIBRATE_AND_EVALUATE}]',1)
def usage():
exit('Usage: python RecalQual.py [--recalibrate] [--evaluate] <input bam file> <calibrated output bam file>',1)
operation = 'RECALIBRATE'
if len(sys.argv) == 4:
operation = sys.argv[3]
# Try to parse the given command-line arguments.
try:
opts, args = getopt.gnu_getopt(sys.argv[1:],'',['recalibrate','evaluate'])
except getopt.GetoptError, err:
usage()
if operation not in ['RECALIBRATE','EVALUATE','RECALIBRATE_AND_EVALUATE']:
exit('Operation %s not recognized. Operation must be RECALIBRATE, EVALUATE, or RECALIBRATE_AND_EVALUATE' % operation,1)
# 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 = sys.argv[1]
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 = sys.argv[2]
calibrated_bam = args[1]
calibrated_bam_index = calibrated_bam + '.bai'
# check that the fasta and supporting files are available
@ -125,14 +149,17 @@ 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
if not os.path.isdir('output'):
os.mkdir('output')
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,'-ea','-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))
gatk_base_cmdline = ' '.join((java_exe,jvm_args,'-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))
if operation.find('RECALIBRATE') != -1:
if do_recalibration:
recalibrate()
if operation.find('EVALUATE') != -1:
if do_evaluation:
evaluate()