94 lines
4.3 KiB
Python
Executable File
94 lines
4.3 KiB
Python
Executable File
#!/usr/bin/env python
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import sys
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import os
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bamfile_base = "/seq/picard_aggregation/"
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fingerprint_base = "/seq/references/reference_genotypes/non-hapmap/"
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hg18_reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
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hg18_dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_130_hg18.rod"
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b36_dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_130_b36.rod"
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b36_reference = "/broad/1KG/reference/human_b36_both.fasta"
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hg18_intervals = "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list"
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#hg18_intervals = "/humgen/gsa-hpprojects/FHS/indexed/interval_lists/fhs_jhs_pilot.targets.interval_list"
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b36_intervals = ""
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min_base_q = "10"
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min_map_q = "10"
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max_reads = "1000000"
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min_conf = "50"
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variant_expression = "QUAL <= 50.0 || AB > 0.75 || QD < 5.0 || HRun > 3"
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spreadsheetPath = sys.argv[3]
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projectName = sys.argv[2]
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groupName = sys.argv[1]
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reference = sys.argv[4]
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filter_name = projectName+"_Initial_Filter"
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if ( reference != "hg18" and reference != "b36" ):
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raise ValueError("Illegal reference type")
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elif ( reference == "hg18" ):
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reference = hg18_reference
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dbsnp = hg18_dbsnp
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intervals = hg18_intervals
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fpref = "Homo_sapiens_assembly18"
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else:
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reference = b36_reference
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dbsnp = b36_dbsnp
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intervals = b36_intervals
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fpref = "human_b36"
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outputFile = projectName+"_bam_files.txt"
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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"]
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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"]
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if ( spreadsheetPath.find("/") > -1 ):
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newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv"
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else:
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newSpreadsheet = spreadsheetPath.rsplit(".",1)[0]+"_proper_format.tsv"
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# convert to proper format
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os.system("sed 's/\\r/\\n/g' "+spreadsheetPath+" > "+newSpreadsheet)
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project_info = open(newSpreadsheet)
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header = project_info.readline().strip().split("\t")
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project_index = header.index("Project")
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sample_index = header.index("Sample")
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status_index = header.index("Sample Status")
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def versionCompare(version1,version2):
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return -int(version1.split("v")[1])+int(version2.split("v")[1])
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def getNewestVersion(baseDir):
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versions = os.listdir(baseDir)
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versions.sort(versionCompare)
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for version in versions:
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if ( "finished.txt" in os.listdir(baseDir+version+"/") ):
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return version
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outputFile = open(outputFile,'w')
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outputFile.write("\t".join(OUTPUT_HEADER)+"\n")
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for line in project_info.readlines():
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if ( not line.startswith("\n") and not line.startswith(" ") and not line.startswith("\t") ):
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spline = line.strip().split("\t")
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versioningDirectory = bamfile_base+spline[project_index]+"/"+spline[sample_index]+"/"
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version = getNewestVersion(versioningDirectory)
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bamfile = versioningDirectory+version+"/"+spline[sample_index]+".bam"
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fingerprint_path = fingerprint_base+spline[project_index]+"/"+fpref+"/"
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if ( os.path.isdir(fingerprint_path) and spline[sample_index]+".fingerprint.geli" in os.listdir(fingerprint_path) ):
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fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli"
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else:
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fingerprint_file = ""
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if ( spline[status_index] == "Complete" ):
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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")
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outputFile.close()
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outputFile = open(projectName+"_Project_Entry.txt",'w')
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outputFile.write("individual_set_id\n")
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outputFile.write(projectName)
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outputFile.close()
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outputFile = open(projectName+"_Population_Entry.txt",'w')
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outputFile.write("individual_id\tindividual_set_id\t"+"\t".join(OUTPUT_HEADER_INDIVIDUAL)+"\n")
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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")
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