changeset 15:743d75da4658 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/breakdancer2vcf.py	Fri Jun 27 08:43:00 2014 -0400
@@ -0,0 +1,127 @@
+#!/usr/bin/env python
+
+__copyright__ = """
+Copyright (C) 2013 - Tim te Beek
+Copyright (C) 2013 - Wai Yi Leung
+Copyright (C) 2013 AllBio (see AUTHORS file)
+"""
+
+__desc__ = """Convert breakdancer output to pseudo .vcf file format."""
+__created__ = "Mar 18, 2013"
+__author__ = "tbeek"
+
+import argparse
+import csv
+import os.path
+import sys
+
+
+def main(tsvfile, vcffile):
+    '''
+:param tsvfile: filename of input file.tsv
+:type tsvfile: string
+:param vcffile: filename of output file.vcf
+:type vcffile: string
+'''
+    with open(tsvfile) as reader:
+        # Parse file
+        dictreader = _parse_tsvfile(reader)
+        print dictreader.fieldnames
+
+        # Write out file
+        _format_vcffile(dictreader, vcffile)
+
+    # Quick output
+    with open(vcffile) as reader:
+        print reader.read(1000)
+
+
+def _parse_tsvfile(readable):
+    '''
+Read readable using csv.Sniffer and csv.DictReader
+:param readable: open file.tsv handle to read with csv.DictReader
+:type readable: file
+'''
+    prev, curr = 0, 0
+    while True:
+        line = readable.readline()
+        if not line.startswith('#'):
+            # lets start from prev # line, without the hash sign
+            readable.seek(prev + 1)
+            break
+        else:
+            prev = curr
+            curr = readable.tell()
+
+    # Determine dialect
+    curr = readable.tell()
+    #dialect = csv.Sniffer().sniff(readable.read(3000))
+    dialect = 'excel-tab'
+    readable.seek(curr)
+
+    # Read file
+    dictreader = csv.DictReader(readable, dialect=dialect)
+    return dictreader
+
+
+_tsv_fields = ('Chr1', 'Pos1', 'Orientation1',
+               'Chr2', 'Pos2', 'Orientation2',
+               'Type', 'Size', 'Score',
+               'num_Reads', 'num_Reads_lib',
+               'ERR031544.sort.bam')
+# 'Chr1': '1',
+# 'Pos1': '269907',
+# 'Orientation1': '39+39-',
+# 'Chr2': '1',
+# 'Pos2': '270919',
+# 'Orientation2': '39+39-',
+# 'Type': 'DEL',
+# 'Size': '99',
+# 'Score': '99',
+# 'num_Reads': '38',
+# 'num_Reads_lib': '/home/allbio/ERR031544.sort.bam|38',
+# 'ERR031544.sort.bam': 'NA'
+
+_vcf_fields = ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO')
+
+
+def _format_vcffile(dictreader, vcffile):
+    '''
+Create a pseudo .vcf file based on values read from DictReader instance.
+:param dictreader: DictReader instance to read data from
+:type dictreader: csv.DictRedaer
+:param vcffile: output file.vcf filename
+:type vcffile: string
+'''
+    with open(vcffile, mode='w') as writer:
+        writer.write('#{}\n'.format('\t'.join(_vcf_fields)))
+        output_vcf = []
+        for line in dictreader:
+            CHROM = line['Chr1']
+            # TODO Figure out whether we have zero or one based positioning
+            POS = int(line['Pos1'])
+            SVEND = int(line['Pos2'])
+            INFO = 'PROGRAM=breakdancer;SVTYPE={};SVLEN={}'.format(line['Type'],
+                                                                   0 - int(line['Size']))
+            if line['Type'] not in ['CTX']:
+                INFO += ";SVEND={}".format(SVEND)
+
+            # Create record
+            output_vcf.append([CHROM, POS, '.', '.', '.', '.', 'PASS', INFO])
+
+        # Sort all results
+        output_vcf.sort()
+        output = "\n".join(["\t".join(map(str,vcf_row)) for vcf_row in output_vcf])
+        # Write record
+        writer.write(output)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-i', '--breakdancertsv', dest='breakdancertsv', type=str,
+            help='Breakdancer TSV outputfile')
+    parser.add_argument('-o', '--outputvcf', dest='outputvcf', type=str,
+            help='Output vcf to')
+
+    args = parser.parse_args()
+    main(args.breakdancertsv, args.outputvcf)