comparison unsorted_uniq.py @ 0:ec66f9d90ef0 draft

initial uploaded

0:ec66f9d90ef0

import sys
import subprocess

"""
    We only need that file because galaxy do not understand the -t $'\t' term.
    Otherwise that would be the right XML-only solution:
    sort -u 
        $ignore_case
        $is_numeric
        -t \$'\t'
        #if $adv_opts.adv_opts_selector=="advanced":
            -k$adv_opts.column_start,$adv_opts.column_end
        #end if
        -o $outfile
        $input
"""

if sys.argv[1].strip() != 'false':
    ignore_case = sys.argv[1]
else:
    ignore_case = ''

if sys.argv[2].strip() != 'false':
    is_numeric = sys.argv[2]
else:
    is_numeric = ''

try:
    col_start = sys.argv[3]
    col_end = sys.argv[4]
    com = "sort -u %s %s -t '	' -k%s,%s -o %s %s" % (is_numeric, ignore_case, col_start, col_end, sys.argv[5], sys.argv[6])
except:
    # no advanced options selected
    com = "sort -u %s %s -t '	' -o %s %s" % (is_numeric, ignore_case, sys.argv[3], sys.argv[4])

subprocess.call(com, shell=True)