view gops_concat.py @ 2:23abefbed3dd draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

#!/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.
"""

import fileinput
import sys
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
from bx.intervals.operations.concat import concat
from bx.cookbook import doc_optparse
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, 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()