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1 from Bio import SeqIO
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2 import vcf
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3
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4
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5 import argparse
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6 import os
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7 import sys
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8
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9 def passes(vcf_feature, contigs, edge_length=500, window_size=1000, max_snps=3):
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10 return True
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11
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12 def main(input_vcf, input_reference, output_included, output_excluded=os.devnull, *args, **kwargs)
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13 contigs = list(SeqIO.parse(input_reference, 'fasta'))
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14 included = vcf.Writer(output_included)
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15 excluded = vcf.Writer(output_excluded)
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16 for feature in vcf.Reader(input_vcf):
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17 if passes(feature, contigs, *args, **kwargs):
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18 included.write(feature)
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19 else:
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20 excluded.write(feature)
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21
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22 if __name__ == '__main__':
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23 parser = argparse.ArgumentParser()
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24 parser.add_argument('input_vcf', type=argparse.FileType())
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25 parser.add_argument('input_reference', type=argparse.FileType())
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26 parser.add_argument('output_included', type=argparse.FileType('w'))
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27 parser.add_argument('--excluded', '-x', dest='output_excluded', type=argparse.FileType('w'), default=os.devnull) |
