comparison subtract_query.py @ 2:ff3901618482 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

1:960d5d114184

#!/usr/bin/env python
# Greg Von Kuster

"""
Subtract an entire query from another query
usage: %prog in_file_1 in_file_2 begin_col end_col output
    --ignore-empty-end-cols: ignore empty end columns when subtracting
"""
import sys
from bx.cookbook import doc_optparse

# Older py compatibility
try:
    set()

        begin_col = end_col = ''

    try:
        fo = open(out_file, 'w')
    except:
        print >> sys.stderr, "Unable to open output file"
        sys.exit()

    """
    len1 is the number of lines in inp1_file
    lines1 is the set of unique lines in inp1_file

    lines1.difference_update(lines2)
    """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""

    for line in lines1:
        print >> fo, line

    fo.close()

    info_msg = 'Subtracted %d lines. ' % ((len1 - diff1) - len(lines1))

        info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '

    if diff1 > 0:
        info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' % diff1

    print info_msg

if __name__ == "__main__":
    main()

2:ff3901618482

#!/usr/bin/env python
# Greg Von Kuster
"""
Subtract an entire query from another query
usage: %prog in_file_1 in_file_2 begin_col end_col output
    --ignore-empty-end-cols: ignore empty end columns when subtracting
"""
from __future__ import print_function

import sys

from bx.cookbook import doc_optparse

# Older py compatibility
try:
    set()

        begin_col = end_col = ''

    try:
        fo = open(out_file, 'w')
    except:
        print("Unable to open output file", file=sys.stderr)
        sys.exit()

    """
    len1 is the number of lines in inp1_file
    lines1 is the set of unique lines in inp1_file

    lines1.difference_update(lines2)
    """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""

    for line in lines1:
        print(line, file=fo)

    fo.close()

    info_msg = 'Subtracted %d lines. ' % ((len1 - diff1) - len(lines1))

        info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '

    if diff1 > 0:
        info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' % diff1

    print(info_msg)


if __name__ == "__main__":
    main()