comparison gops_concat.py @ 3:32e1c8dac438 draft

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

2:d491589307e7

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 )

        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()

3:32e1c8dac438

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 )

        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()