annotate snp-filter.py @ 9:41bd2a5793ee
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
| author |
jpayne |
| date |
Tue, 30 Jan 2018 15:55:32 -0500 |
| parents |
eefdd97a6749 |
| children |
|
| rev |
line source |
|
jpayne@0
|
1 from Bio import SeqIO
|
|
jpayne@0
|
2 import vcf
|
|
jpayne@0
|
3
|
|
jpayne@0
|
4
|
|
jpayne@0
|
5 import argparse
|
|
jpayne@0
|
6 import os
|
|
jpayne@0
|
7 import sys
|
|
jpayne@0
|
8
|
|
jpayne@0
|
9 def passes(vcf_feature, contigs, edge_length=500, window_size=1000, max_snps=3):
|
|
jpayne@0
|
10 return True
|
|
jpayne@0
|
11
|
|
jpayne@0
|
12 def main(input_vcf, input_reference, output_included, output_excluded=os.devnull, *args, **kwargs)
|
|
jpayne@0
|
13 contigs = list(SeqIO.parse(input_reference, 'fasta'))
|
|
jpayne@0
|
14 included = vcf.Writer(output_included)
|
|
jpayne@0
|
15 excluded = vcf.Writer(output_excluded)
|
|
jpayne@0
|
16 for feature in vcf.Reader(input_vcf):
|
|
jpayne@0
|
17 if passes(feature, contigs, *args, **kwargs):
|
|
jpayne@0
|
18 included.write(feature)
|
|
jpayne@0
|
19 else:
|
|
jpayne@0
|
20 excluded.write(feature)
|
|
jpayne@0
|
21
|
|
jpayne@0
|
22 if __name__ == '__main__':
|
|
jpayne@0
|
23 parser = argparse.ArgumentParser()
|
|
jpayne@0
|
24 parser.add_argument('input_vcf', type=argparse.FileType())
|
|
jpayne@0
|
25 parser.add_argument('input_reference', type=argparse.FileType())
|
|
jpayne@0
|
26 parser.add_argument('output_included', type=argparse.FileType('w'))
|
|
jpayne@0
|
27 parser.add_argument('--excluded', '-x', dest='output_excluded', type=argparse.FileType('w'), default=os.devnull) |
