From f7cbaee1a50ad154b9925a3edbe152e83c8a1233 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 9 May 2016 13:10:46 +0200
Subject: [PATCH] Fix samplenaming in breakdancer
---
.../biopet/extensions/breakdancer/breakdancer2vcf.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
index dac0175e9..262971146 100644
--- a/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
+++ b/public/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
@@ -94,7 +94,7 @@ _tsv_fields = ('Chr1', 'Pos1', 'Orientation1',
-_vcf_fields = ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT')
+_vcf_fields = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT']
TS_NOW = datetime.datetime.now()
@@ -108,6 +108,7 @@ VCF_HEADER = """##fileformat=VCFv4.2
##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
##INFO=<ID=SVEND,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=SVMETHOD,Number=0,Type=String,Description="Program called with">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
@@ -159,7 +160,7 @@ def _format_vcffile(dictreader, vcffile, samplename):
ALT = '.'
SVEND = int(line['Pos2'])
- INFO = 'PROGRAM=breakdancer;SVTYPE={}'.format(line['Type'])
+ INFO = 'SVMETHOD=breakdancer;SVTYPE={}'.format(line['Type'])
if line['Type'] not in ['CTX']:
INFO += ';SVLEN={}'.format(int(line['Size']))
@@ -186,9 +187,9 @@ def _format_vcffile(dictreader, vcffile, samplename):
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--breakdancertsv', dest='breakdancertsv', type=str,
- help='Breakdancer TSV outputfile')
+ help='Breakdancer TSV outputfile')
parser.add_argument('-o', '--outputvcf', dest='outputvcf', type=str,
- help='Output vcf to')
+ help='Output vcf to')
parser.add_argument('-s', '--sample', dest='sample', type=str,
help='sample name')
--
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