From 0e4b5ad9c6ab63adac85f4b4d40bebbcee60e481 Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 16 Feb 2010 15:36:42 +0000 Subject: [PATCH] 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 --- python/getBamFilesFromSpreadsheet.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/getBamFilesFromSpreadsheet.py b/python/getBamFilesFromSpreadsheet.py index a0060e8b6..17ade7b7d 100755 --- a/python/getBamFilesFromSpreadsheet.py +++ b/python/getBamFilesFromSpreadsheet.py @@ -52,6 +52,7 @@ header = project_info.readline().strip().split("\t") project_index = header.index("Project") sample_index = header.index("Sample") +status_index = header.index("Sample Status") def versionCompare(version1,version2): 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" else: 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")