Mercurial > repos > iuc > spades_metaplasmidspades

view write_tsv_script.py @ 3:b8002c3f7141 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit b7b09cff3ddcdf26f27aabfcf41a8ce0a3985d87"
author iuc
date Wed, 09 Feb 2022 18:58:25 +0000
parents 8d4b90bf9caf
children 21da31ed41a1
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#!/usr/bin/env python

import re
import sys

search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$"

replace_str = r"\1_\2\t\3\t\4"

cmd = re.compile(search_str)

sys.stdout.write("#name\tlength\tcoverage\n")

for i, line in enumerate(sys.stdin):
    if cmd.match(line):
        sys.stdout.write(cmd.sub(replace_str, line))