annotate gops_concat.py @ 5:73ca13a7ec5f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9

#!/usr/bin/env python
"""
Concatenate two bed files.  The concatenated files are returned in the
same format as the first.  If --sameformat is specified, then all
columns will be treated as the same, and all fields will be saved,
although the output will be trimmed to match the primary input.  In
addition, if --sameformat is specified, missing fields will be padded
with a period(.).

usage: %prog in_file_1 in_file_2 out_file
    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file
    -s, --sameformat: All files are precisely the same format.
"""
from __future__ import print_function

import fileinput
import sys

from bx.cookbook import doc_optparse
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
from bx.intervals.operations.concat import concat
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

assert sys.version_info[:2] >= ( 2, 4 )


def main():
    sameformat = False

    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
        if options.sameformat:
            sameformat = True
        in_file_1, in_file_2, out_fname = args
    except:
        doc_optparse.exception()

    g1 = NiceReaderWrapper( fileinput.FileInput( in_file_1 ),
                            chrom_col=chr_col_1,
                            start_col=start_col_1,
                            end_col=end_col_1,
                            strand_col=strand_col_1,
                            fix_strand=True )

    g2 = NiceReaderWrapper( fileinput.FileInput( in_file_2 ),
                            chrom_col=chr_col_2,
                            start_col=start_col_2,
                            end_col=end_col_2,
                            strand_col=strand_col_2,
                            fix_strand=True )

    out_file = open( out_fname, "w" )

    try:
        for line in concat( [g1, g2], sameformat=sameformat ):
            if type( line ) is GenomicInterval:
                out_file.write( "%s\n" % "\t".join( line.fields ) )
            else:
                out_file.write( "%s\n" % line )
    except ParseError as exc:
        out_file.close()
        fail( "Invalid file format: %s" % str( exc ) )

    out_file.close()

    if g1.skipped > 0:
        print(skipped( g1, filedesc=" of 1st dataset" ))
    if g2.skipped > 0:
        print(skipped( g2, filedesc=" of 2nd dataset" ))


if __name__ == "__main__":
    main()