From 60f05379a709d6af5cd1fb69acfcd8155861c2de Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 10 Feb 2010 21:29:54 +0000 Subject: [PATCH] fix typo. Check explicitly that fingerprint files exist. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2821 348d0f76-0448-11de-a6fe-93d51630548a --- python/getBamFilesFromSpreadsheet.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/python/getBamFilesFromSpreadsheet.py b/python/getBamFilesFromSpreadsheet.py index 89ea62bd3..a0060e8b6 100755 --- a/python/getBamFilesFromSpreadsheet.py +++ b/python/getBamFilesFromSpreadsheet.py @@ -36,7 +36,7 @@ else: fpref = "human_b36" outputFile = projectName+"_bam_files.txt" -OUTPUT_HEADER = ["sample_id","recalbrated_bam_file","individual_id","fingerprint_file","reference_file","dbsnp_file","interval_list","max_reads_at_locus","min_confidence","min_mapping_quality","min_base_quality"] +OUTPUT_HEADER = ["sample_id","recalibrated_bam_file","individual_id","fingerprint_file","reference_file","dbsnp_file","interval_list","max_reads_at_locus","min_confidence","min_mapping_quality","min_base_quality"] if ( spreadsheetPath.find("/") > -1 ): newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv" @@ -72,5 +72,9 @@ for line in project_info.readlines(): versioningDirectory = bamfile_base+spline[project_index]+"/"+spline[sample_index]+"/" version = getNewestVersion(versioningDirectory) bamfile = versioningDirectory+version+"/"+spline[sample_index]+".bam" - fingerprint_file = fingerprint_base+spline[project_index]+"/"+fpref+"/"+spline[sample_index]+".fingerprint.geli" + fingerprint_path = fingerprint_base+spline[project_index]+"/"+fpref+"/" + if ( spline[sample_index]+".fingerprint.geli" in os.listdir(fingerprint_path) ): + 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")