From 4bdc3b2784c68ae7da681c886a47a6e0af01622c Mon Sep 17 00:00:00 2001 From: chartl Date: Mon, 15 Mar 2010 10:36:33 +0000 Subject: [PATCH] automatic generation of individual and individual set import files git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3001 348d0f76-0448-11de-a6fe-93d51630548a --- python/getBamFilesFromSpreadsheet.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/python/getBamFilesFromSpreadsheet.py b/python/getBamFilesFromSpreadsheet.py index 0627a6356..8ae95b2df 100755 --- a/python/getBamFilesFromSpreadsheet.py +++ b/python/getBamFilesFromSpreadsheet.py @@ -38,6 +38,7 @@ else: outputFile = projectName+"_bam_files.txt" 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","variant_filter_expression","variant_filter_name"] +OUTPUT_HEADER_INDIVIDUAL = ["reference_file","dbsnp_file","interval_list","max_reads_at_locus","min_confidence","min_mapping_quality","min_base_quality","variant_filter_expression","variant_filter_name"] if ( spreadsheetPath.find("/") > -1 ): newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv" @@ -81,3 +82,12 @@ for line in project_info.readlines(): fingerprint_file = "" 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+"\t"+variant_expression+"\t"+filter_name+"\n") + +outputFile.close() +outputFile = open(projectName+"_Project_Entry.txt",'w') +outputFile.write("individual_set_id\n") +outputFile.write(projectName) +outputFile.close() +outputFile = open(projectName+"_Population_Entry.txt",'w') +outputFile.write("individual_id\tindividual_set_id\t"+"\t".join(OUTPUT_HEADER_INDIVIDUAL)+"\n") +outputFile.write(groupName+"\t"+projectName+"\t"+reference+"\t"+dbsnp+"\t"+intervals+"\t"+max_reads+"\t"+min_conf+"\t"+min_base_q+"\t"+variant_expression+"\t"+filter_name+"\n")