Mercurial > repos > iuc > ivar_consensus

view sanitize_bed.py @ 4:78bbd17d0703 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
author iuc
date Mon, 22 Jun 2020 07:31:22 -0400
parents
children e319b5b65879
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#!/usr/bin/env python

import sys


with open(sys.argv[1]) as i:
    bed_data = i.readlines()

sanitized_data = []
try:
    for record in bed_data:
        fields = record.split('\t')
        sanitized_data.append(
            '\t'.join(fields[:4] + ['60'] + fields[5:])
        )
except IndexError:
    pass  # leave column number issue to getmasked
else:
    with open(sys.argv[1], 'w') as o:
        o.writelines(sanitized_data)