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Check to ensure sample status is "Complete" before writing out the bam file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2844 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-16 15:36:42 +00:00
parent 37fa1bf0cc
commit 0e4b5ad9c6
1 changed files with 3 additions and 1 deletions
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4
python/getBamFilesFromSpreadsheet.py
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@ -52,6 +52,7 @@ header = project_info.readline().strip().split("\t")
project_index = header.index("Project") project_index = header.index("Project")
sample_index = header.index("Sample") sample_index = header.index("Sample")
status_index = header.index("Sample Status")
def versionCompare(version1,version2): def versionCompare(version1,version2):
return -int(version1.split("v")[1])+int(version2.split("v")[1]) return -int(version1.split("v")[1])+int(version2.split("v")[1])
@ -77,4 +78,5 @@ for line in project_info.readlines():
fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli" fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli"
else: else:
fingerprint_file = "" fingerprint_file = ""
outputFile.write(projectName+"_"+spline[sample_index]+"\t"+bamfile+"\t"+groupName+"\t"+fingerprint_file+"\t"+reference+"\t"+dbsnp+"\t"+intervals+"\t"+max_reads+"\t"+min_conf+"\t"+min_map_q+"\t"+min_base_q+"\n") if ( spline[status_index] == "Complete" ):
outputFile.write(projectName+"_"+spline[sample_index]+"\t"+bamfile+"\t"+groupName+"\t"+fingerprint_file+"\t"+reference+"\t"+dbsnp+"\t"+intervals+"\t"+max_reads+"\t"+min_conf+"\t"+min_map_q+"\t"+min_base_q+"\n")