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bed2fa.py
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bed2fa.py
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#!/usr/bin/env python
"""
convert bed8 to fasta
bed8 is the output of extract_ins.py
bed8: bed6 + {length} + {seq}
"""
import os
import sys
def bed2fa(x, out=None):
"""
bed8: (last column store sequence)
bed: column-4 => name
bed: last column => seq
"""
if isinstance(x, str):
if out is None:
out = x.replace('.bed', '.fa')
# run
with open(x) as r, open(out, 'wt') as w:
for line in r:
p = line.strip().split('\t')
w.write('>{}\n{}\n'.format(p[3], p[-1]))
def main():
if len(sys.argv) < 2:
print('Usage: bed2fa.py in.bed [out.fa]')
sys.exit(1)
in_bed = sys.argv[1]
out_fa = sys.argv[2] if len(sys.argv) > 2 else None
bed2fa(in_bed, out_fa)
if __name__ == '__main__':
main()
# EOF