jpayne@0: from Bio import SeqIO
jpayne@0: import vcf
jpayne@0: 
jpayne@0: 
jpayne@0: import argparse
jpayne@0: import os
jpayne@0: import sys
jpayne@0: 
jpayne@0: def passes(vcf_feature, contigs, edge_length=500, window_size=1000, max_snps=3):
jpayne@0: 	return True
jpayne@0: 
jpayne@0: def main(input_vcf, input_reference, output_included, output_excluded=os.devnull, *args, **kwargs)
jpayne@0: 	contigs = list(SeqIO.parse(input_reference, 'fasta'))
jpayne@0: 	included = vcf.Writer(output_included)
jpayne@0: 	excluded = vcf.Writer(output_excluded)
jpayne@0: 	for feature in vcf.Reader(input_vcf):
jpayne@0: 		if passes(feature, contigs, *args, **kwargs):
jpayne@0: 			included.write(feature)
jpayne@0: 		else:
jpayne@0: 			excluded.write(feature)
jpayne@0: 
jpayne@0: if __name__ == '__main__':
jpayne@0: 	parser = argparse.ArgumentParser()
jpayne@0: 	parser.add_argument('input_vcf', type=argparse.FileType())
jpayne@0: 	parser.add_argument('input_reference', type=argparse.FileType())
jpayne@0: 	parser.add_argument('output_included', type=argparse.FileType('w'))
jpayne@0: 	parser.add_argument('--excluded', '-x', dest='output_excluded', type=argparse.FileType('w'), default=os.devnull)