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Added absolute path bug fix for Mark. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@949 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-09 02:25:17 +00:00
parent e7f222108d
commit 5fa3f7ed3a
1 changed files with 11 additions and 3 deletions
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14
python/RecalQual.py
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@ -16,6 +16,15 @@ output_root = './'
# If editing, please end this variable with a trailing slash. # If editing, please end this variable with a trailing slash.
resources='resources/' resources='resources/'
import getopt,glob,os,sys
import LogisticRegressionByReadGroup
# if the provided resources path is relative, convert it to a path
# relative to the calling script rather than the cwd.
if not os.path.isabs(resources):
application_path = os.path.dirname(sys.argv[0])
resources = os.path.abspath(application_path) + '/' + resources
# Where does the reference live? # Where does the reference live?
reference_base = resources + 'human_b36_both' reference_base = resources + 'human_b36_both'
reference = reference_base + '.fasta' reference = reference_base + '.fasta'
@ -30,9 +39,6 @@ gatk = resources + 'gatk/GenomeAnalysisTK.jar'
logistic_regression_script = resources + 'logistic_regression.R' logistic_regression_script = resources + 'logistic_regression.R'
empirical_vs_reported_grapher = resources + 'plot_q_emp_stated_hst.R' empirical_vs_reported_grapher = resources + 'plot_q_emp_stated_hst.R'
import getopt,glob,os,sys
import LogisticRegressionByReadGroup
def exit(msg,errorcode): def exit(msg,errorcode):
print msg print msg
sys.exit(errorcode) sys.exit(errorcode)
@ -122,6 +128,8 @@ do_recalibration = not (evaluate_requested and not recalibrate_requested)
# Only evaluate if the user specifically requested evaluation. # Only evaluate if the user specifically requested evaluation.
do_evaluation = evaluate_requested do_evaluation = evaluate_requested
print 'Looking for supplemental files in ' + resources
# check that the input bam file exists, and that the bam is indexed. # check that the input bam file exists, and that the bam is indexed.
bam = args[0] bam = args[0]
bam_index = bam + '.bai' bam_index = bam + '.bai'