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Adding default filter info 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3000 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-15 10:05:46 +00:00
parent 45f70de6df
commit d9b12b468f
1 changed files with 7 additions and 6 deletions
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13
python/getBamFilesFromSpreadsheet.py
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@ -10,18 +10,19 @@ hg18_dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_130_hg18.rod"
b36_dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_130_b36.rod" b36_dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_130_b36.rod"
b36_reference = "/broad/1KG/reference/human_b36_both.fasta" b36_reference = "/broad/1KG/reference/human_b36_both.fasta"
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" 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"
#hg18_intervals = "/humgen/gsa-hpprojects/FHS/indexed/interval_lists/fhs_jhs_pilot.targets.interval_list"
b36_intervals = "" b36_intervals = ""
min_base_q = "10" min_base_q = "10"
min_map_q = "10" min_map_q = "10"
max_reads = "1000000" max_reads = "1000000"
min_conf = "0" min_conf = "50"
variant_expression = "QUAL <= 50.0 || AB > 0.75 || QD < 5.0 || HRun > 3"
spreadsheetPath = sys.argv[3] spreadsheetPath = sys.argv[3]
projectName = sys.argv[2] projectName = sys.argv[2]
groupName = sys.argv[1] groupName = sys.argv[1]
reference = sys.argv[4] reference = sys.argv[4]
filter_name = projectName+"_Initial_Filter"
if ( reference != "hg18" and reference != "b36" ): if ( reference != "hg18" and reference != "b36" ):
raise ValueError("Illegal reference type") raise ValueError("Illegal reference type")
elif ( reference == "hg18" ): elif ( reference == "hg18" ):
@ -36,7 +37,7 @@ else:
fpref = "human_b36" fpref = "human_b36"
outputFile = projectName+"_bam_files.txt" 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"] 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"]
if ( spreadsheetPath.find("/") > -1 ): if ( spreadsheetPath.find("/") > -1 ):
newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv" newSpreadsheet = spreadsheetPath.rsplit("/",1)[1].rsplit(".",1)[0]+"_proper_format.tsv"
@ -74,9 +75,9 @@ for line in project_info.readlines():
version = getNewestVersion(versioningDirectory) version = getNewestVersion(versioningDirectory)
bamfile = versioningDirectory+version+"/"+spline[sample_index]+".bam" bamfile = versioningDirectory+version+"/"+spline[sample_index]+".bam"
fingerprint_path = fingerprint_base+spline[project_index]+"/"+fpref+"/" fingerprint_path = fingerprint_base+spline[project_index]+"/"+fpref+"/"
if ( spline[sample_index]+".fingerprint.geli" in os.listdir(fingerprint_path) ): if ( os.path.isdir(fingerprint_path) and spline[sample_index]+".fingerprint.geli" in os.listdir(fingerprint_path) ):
fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli" fingerprint_file = fingerprint_path+spline[sample_index]+".fingerprint.geli"
else: else:
fingerprint_file = "" fingerprint_file = ""
if ( spline[status_index] == "Complete" ): 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") 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")