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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
This commit is contained in:
chartl 2010-03-15 10:36:33 +00:00
parent d9b12b468f
commit 4bdc3b2784
1 changed files with 10 additions and 0 deletions
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10
python/getBamFilesFromSpreadsheet.py
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@ -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")