Mercurial > repos > in_silico > cravat_annotate_mutations

comparison cravat_convert/cravat_convert.py @ 12:4b860b1f92fa draft

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author in_silico
date Tue, 12 Jun 2018 12:04:06 -0400
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11:a9299c08850e 12:4b860b1f92fa
1 '''
2 Convert a VCF format file to Cravat format file
3 '''
4
5 import os
6 import argparse
7 from vcf_converter import CravatConverter
8
9 # File read/write configuration variables
10 vcf_sep = '\t'
11 cr_sep = '\t'
12 cr_newline = '\n'
13
14 # VCF Headers mapped to their index position in a row of VCF values
15 vcf_mapping = {
16 'CHROM': 0,
17 'POS': 1,
18 'ID': 2,
19 'REF': 3,
20 'ALT': 4,
21 'QUAL': 5,
22 'FILTER': 6,
23 'INFO': 7,
24 'FORMAT': 8,
25 'NA00001': 9,
26 'NA00002': 10,
27 'NA00003': 11
28 }
29
30
31 def get_args():
32 parser = argparse.ArgumentParser()
33 parser.add_argument('--input',
34 '-i',
35 required = True,
36 help='Input path to a VCF file for conversion',)
37 parser.add_argument('--output',
38 '-o',
39 default = os.path.join(os.getcwd(), "cravat_converted.txt"),
40 help = 'Output path to write the cravat file to')
41 return parser.parse_args()
42
43
44 def convert(in_path, out_path=None):
45 if not out_path:
46 base, _ = os.path.split(in_path)
47 out_path = os.path.join(base, "cravat_converted.txt")
48
49 with open(in_path, 'r') as in_file, \
50 open(out_path, 'w') as out_file:
51
52 # cr_count will be used to generate the 'TR' field of the cravat rows (first header)
53 cr_count = 0
54 # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute
55 strand = '+'
56 # VCF converter. Adjusts position, reference, and alternate for Cravat formatting.
57 converter = CravatConverter()
58
59 for line in in_file:
60 if line.startswith("#"):
61 continue
62 line = line.strip().split(vcf_sep)
63 # row is dict of VCF headers mapped to corresponding values of this line
64 row = { header: line[index] for header, index in vcf_mapping.items() }
65 for alt in row["ALT"].split(","):
66 new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt)
67 new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt)
68 cr_line = cr_sep.join([
69 'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID']
70 ])
71 out_file.write(cr_line + cr_newline)
72 cr_count += 1
73
74
75 if __name__ == "__main__":
76 cli_args = get_args()
77 convert(cli_args.input, cli_args.output)