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Revert some debug code in RecalQual.py. Make LogisticRegression easier to Ctrl-C out of. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@904 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-05 01:53:48 +00:00
parent 61ae00c7bf
commit 2035d7dfd3
2 changed files with 4 additions and 3 deletions
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5
python/LogisticRegressionByReadGroup.py
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@ -44,8 +44,9 @@ def process_file(source_file,read_group,dinuc,target_file,R_exe,logistic_regress
"Process the contents of an intermediate file. An intermediate file is the specific data arranged per read group, per dinuc."
base = source_file.name[:source_file.name.rfind('.csv')] + '.' + read_group
regression_command = ' '.join((R_exe,logistic_regression_script,base,base,dinuc))
print "Running " + regression_command
os.system(regression_command)
result = os.system(regression_command)
if result != 0:
exit('Unable to run linear regression; command was %s, error code was %d' % (regression_command, result),1)
parameters_filename = '.'.join((base,dinuc,'parameters'))
if not os.access(parameters_filename,os.R_OK):
exit("Unable to read output of R from file " + parameters_filename)

2
python/RecalQual.py
View File

@ -67,7 +67,7 @@ if not os.path.isdir('output'):
os.mkdir('output')
# assemble the required program arguments
gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO','-L chrM'))
gatk_base_cmdline = ' '.join((java_exe,'-ea','-jar',gatk,'-R',reference,'--DBSNP',dbsnp,'-l INFO'))
generate_covariates = ' '.join((gatk_base_cmdline,'-T CountCovariates','-I',bam,'-mqs 40','--OUTPUT_FILEROOT output/initial','--CREATE_TRAINING_DATA','--MIN_MAPPING_QUALITY 1'))
apply_logistic_regression = ' '.join((gatk_base_cmdline,'-T LogisticRecalibration','-I',bam,'-logisticParams output/linear_regression_results.out','-outputBAM',calibrated_bam))
index_calibrated_bamfile = ' '.join((samtools_exe,'index',calibrated_bam))