comparison get_flanks.py @ 5:dd9315a56c09 draft default tip

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

4:0f9775889036

#!/usr/bin/env python
#Done by: Guru

"""
Get Flanking regions.

usage: %prog input out_file size direction region
   -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
   -o, --off=N: Offset
"""

import sys
from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import parse_cols_arg


def stop_err( msg ):

        line = line.strip()
        if line and (not line.startswith( '#' )) and line != '':
            j += 1
            try:
                elems = line.split('\t')
                #if the start and/or end columns are not numbers, skip that line.
                assert int(elems[start_col_1])
                assert int(elems[end_col_1])
                if strand_col_1 != -1:
                    strand = elems[strand_col_1]
                #if the stand value is not + or -, skip that line.
                assert strand in ['+', '-']
                if direction == 'Upstream':
                    if strand == '+':
                        if region == 'end':
                            elems[end_col_1] = str(int(elems[end_col_1]) + offset)

    fo.close()

    if skipped_lines == j:
        stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
    if skipped_lines > 0:
        print 'Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
    print 'Location: %s, Region: %s, Flank-length: %d, Offset: %d ' % ( direction, region, size, offset )

if __name__ == "__main__":
    main()

5:dd9315a56c09

#!/usr/bin/env python
# Done by: Guru
"""
Get Flanking regions.

usage: %prog input out_file size direction region
   -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
   -o, --off=N: Offset
"""
from __future__ import print_function

import sys

from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import parse_cols_arg


def stop_err( msg ):

        line = line.strip()
        if line and (not line.startswith( '#' )) and line != '':
            j += 1
            try:
                elems = line.split('\t')
                # if the start and/or end columns are not numbers, skip that line.
                assert int(elems[start_col_1])
                assert int(elems[end_col_1])
                if strand_col_1 != -1:
                    strand = elems[strand_col_1]
                # if the stand value is not + or -, skip that line.
                assert strand in ['+', '-']
                if direction == 'Upstream':
                    if strand == '+':
                        if region == 'end':
                            elems[end_col_1] = str(int(elems[end_col_1]) + offset)

    fo.close()

    if skipped_lines == j:
        stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
    if skipped_lines > 0:
        print('Skipped %d invalid lines starting with #%dL "%s"' % ( skipped_lines, first_invalid_line, invalid_line ))
    print('Location: %s, Region: %s, Flank-length: %d, Offset: %d ' % ( direction, region, size, offset ))


if __name__ == "__main__":
    main()