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1 #!/usr/bin/env python
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2
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3 __copyright__ = """
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4 Copyright (C) 2013 - Tim te Beek
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5 Copyright (C) 2013 - Wai Yi Leung
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6 Copyright (C) 2013 AllBio (see AUTHORS file)
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7 """
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8
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9 __desc__ = """Convert breakdancer output to pseudo .vcf file format."""
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10 __created__ = "Mar 18, 2013"
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11 __author__ = "tbeek"
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12
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13 import argparse
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14 import csv
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15 import os.path
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16 import sys
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17
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18
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19 def main(tsvfile, vcffile):
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20 '''
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21 :param tsvfile: filename of input file.tsv
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22 :type tsvfile: string
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23 :param vcffile: filename of output file.vcf
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24 :type vcffile: string
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25 '''
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26 with open(tsvfile) as reader:
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27 # Parse file
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28 dictreader = _parse_tsvfile(reader)
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29 print dictreader.fieldnames
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30
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31 # Write out file
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32 _format_vcffile(dictreader, vcffile)
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33
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34 # Quick output
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35 with open(vcffile) as reader:
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36 print reader.read(1000)
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37
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38
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39 def _parse_tsvfile(readable):
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40 '''
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41 Read readable using csv.Sniffer and csv.DictReader
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42 :param readable: open file.tsv handle to read with csv.DictReader
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43 :type readable: file
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44 '''
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45 prev, curr = 0, 0
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46 while True:
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47 line = readable.readline()
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48 if not line.startswith('#'):
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49 # lets start from prev # line, without the hash sign
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50 readable.seek(prev + 1)
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51 break
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52 else:
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53 prev = curr
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54 curr = readable.tell()
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55
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56 # Determine dialect
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57 curr = readable.tell()
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58 #dialect = csv.Sniffer().sniff(readable.read(3000))
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59 dialect = 'excel-tab'
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60 readable.seek(curr)
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61
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62 # Read file
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63 dictreader = csv.DictReader(readable, dialect=dialect)
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64 return dictreader
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65
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66
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67 _tsv_fields = ('Chr1', 'Pos1', 'Orientation1',
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68 'Chr2', 'Pos2', 'Orientation2',
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69 'Type', 'Size', 'Score',
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70 'num_Reads', 'num_Reads_lib',
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71 'ERR031544.sort.bam')
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72 # 'Chr1': '1',
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73 # 'Pos1': '269907',
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74 # 'Orientation1': '39+39-',
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75 # 'Chr2': '1',
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76 # 'Pos2': '270919',
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77 # 'Orientation2': '39+39-',
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78 # 'Type': 'DEL',
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79 # 'Size': '99',
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80 # 'Score': '99',
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81 # 'num_Reads': '38',
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82 # 'num_Reads_lib': '/home/allbio/ERR031544.sort.bam|38',
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83 # 'ERR031544.sort.bam': 'NA'
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84
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85 _vcf_fields = ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO')
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86
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87
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88 def _format_vcffile(dictreader, vcffile):
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89 '''
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90 Create a pseudo .vcf file based on values read from DictReader instance.
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91 :param dictreader: DictReader instance to read data from
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92 :type dictreader: csv.DictRedaer
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93 :param vcffile: output file.vcf filename
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94 :type vcffile: string
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95 '''
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96 with open(vcffile, mode='w') as writer:
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97 writer.write('#{}\n'.format('\t'.join(_vcf_fields)))
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98 output_vcf = []
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99 for line in dictreader:
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100 CHROM = line['Chr1']
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101 # TODO Figure out whether we have zero or one based positioning
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102 POS = int(line['Pos1'])
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103 SVEND = int(line['Pos2'])
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104 INFO = 'PROGRAM=breakdancer;SVTYPE={};SVLEN={}'.format(line['Type'],
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105 0 - int(line['Size']))
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106 if line['Type'] not in ['CTX']:
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107 INFO += ";SVEND={}".format(SVEND)
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108
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109 # Create record
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110 output_vcf.append([CHROM, POS, '.', '.', '.', '.', 'PASS', INFO])
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111
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112 # Sort all results
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113 output_vcf.sort()
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114 output = "\n".join(["\t".join(map(str,vcf_row)) for vcf_row in output_vcf])
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115 # Write record
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116 writer.write(output)
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117
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118
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119 if __name__ == '__main__':
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120 parser = argparse.ArgumentParser()
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121 parser.add_argument('-i', '--breakdancertsv', dest='breakdancertsv', type=str,
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122 help='Breakdancer TSV outputfile')
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123 parser.add_argument('-o', '--outputvcf', dest='outputvcf', type=str,
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124 help='Output vcf to')
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125
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126 args = parser.parse_args()
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127 main(args.breakdancertsv, args.outputvcf)
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