Mercurial > repos > artbio > lumpy_smoove

annotate vcf2hrdetect.py @ 11:5a326a6fa105 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
author artbio
date Fri, 17 Oct 2025 17:21:17 +0000
parents 7dcf61950215
children
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11
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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1 #!/usr/bin/env python
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2 import argparse
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3 import re
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ad8853ee9909 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
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4 import sys
ad8853ee9909 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
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5
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6
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7 def create_arg_parser():
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8 """Creates and returns the argument parser."""
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9 parser = argparse.ArgumentParser(
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10 description=(
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11 "Convert a VCF file from lumpy-smoove to a tabular format "
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12 "compatible with the HRDetect pipeline."
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13 )
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14 )
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15 parser.add_argument(
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16 'vcf_file',
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17 help='Path to the input VCF file.'
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18 )
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19 parser.add_argument(
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20 'output_file',
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21 help='Path to the output tabular file.'
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22 )
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23 return parser
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26 def parse_breakend_alt(alt_field):
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27 """
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28 Parses the ALT field for a breakend and returns chromosome and position.
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30 Args:
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31 alt_field (str): The ALT field (column 5) of a VCF line.
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33 Returns:
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34 tuple: A tuple containing (chromosome, position) or (None, None)
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35 if parsing fails.
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36 """
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37 # Search for patterns ]chr:pos] or [chr:pos[
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38 pattern = (
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39 r"\](?P<chrom1>[^:]+):(?P<pos1>\d+)\]|"
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40 r"\[(?P<chrom2>[^:]+):(?P<pos2>\d+)\["
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41 )
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42 match = re.search(pattern, alt_field)
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43
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44 if not match:
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45 return None, None
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47 groups = match.groupdict()
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48 chrom = groups['chrom1'] or groups['chrom2']
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49 pos = groups['pos1'] or groups['pos2']
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50 return chrom, pos
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53 def process_vcf(vcf_path, output_path):
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54 """
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55 Reads a VCF file, converts it, and writes the result to a tabular file.
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56
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57 Args:
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58 vcf_path (str): Path to the input VCF file.
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59 output_path (str): Path to the output tabular file.
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60 """
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61 header = ["chr1", "pos1", "chr2", "pos2", "type"]
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62 try:
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63 with open(vcf_path, 'r') as infile, open(output_path, 'w') as outfile:
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64 outfile.write("\t".join(header) + "\n")
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65
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66 for line in infile:
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67 if line.startswith('#'):
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68 continue
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70 fields = line.strip().split('\t')
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71 if len(fields) < 8:
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72 continue
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74 chrom1 = fields[0]
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75 pos1 = fields[1]
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76 info = fields[7]
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78 # Attempt to extract the structural variant type from the info
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79 svtype_match = re.search(r'SVTYPE=([^;]+)', info)
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80 if not svtype_match:
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81 continue # Skip lines without SVTYPE tag
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82 svtype = svtype_match.group(1)
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84 if svtype == "BND": # Breakend (INV or TRA)
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85 alt_field = fields[4]
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86 chrom2, pos2 = parse_breakend_alt(alt_field)
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87 if not (chrom2 and pos2):
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88 continue
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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89 event_type = "INV" if chrom1 == chrom2 else "TRA"
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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90 row = [chrom1, pos1, chrom2, pos2, event_type]
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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91 outfile.write("\t".join(row) + "\n")
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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92
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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93 else: # Other SV types (DEL, DUP, etc.)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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94 end_match = re.search(r'END=([^;]+)', info)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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95 if not end_match:
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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96 continue
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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97 pos2 = end_match.group(1)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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98 chrom2 = chrom1
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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99 row = [chrom1, pos1, chrom2, pos2, svtype]
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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100 outfile.write("\t".join(row) + "\n")
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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101
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102 except FileNotFoundError:
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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103 print(f"Error: File '{vcf_path}' not found.",
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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104 file=sys.stderr)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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105 sys.exit(1)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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106 except IOError as e:
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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107 print(f"IO Error: {e}", file=sys.stderr)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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108 sys.exit(1)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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109
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110
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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111 def main():
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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112 """Main function of the script."""
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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113 parser = create_arg_parser()
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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114 args = parser.parse_args()
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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115 process_vcf(args.vcf_file, args.output_file)
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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116
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117
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118 if __name__ == '__main__':
5a326a6fa105 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 8b10e8fc832f8ca7c32479e20d5edbd62088a3aa
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119 main()