comparison gops_complement.py @ 5:1377a23bc02a draft default tip

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

4:1b2bfb9981b1

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
    -a, --all: Complement all chromosomes (Genome-wide complement)
"""

import sys
import fileinput
from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper
from bx.intervals.operations.complement import complement
from bx.intervals.operations.subtract import subtract
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 interval in generator:
            if type( interval ) is GenomicInterval:
                out_file.write( "%s\n" % "\t".join( interval ) )
            else:
                out_file.write( "%s\n" % interval )
    except ParseError, exc:
        out_file.close()
        fail( "Invalid file format: %s" % str( exc ) )

    out_file.close()

    if g1.skipped > 0:
        print skipped( g1, filedesc="" )

if __name__ == "__main__":
    main()

5:1377a23bc02a

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
    -a, --all: Complement all chromosomes (Genome-wide complement)
"""
from __future__ import print_function

import fileinput
import sys

from bx.cookbook import doc_optparse
from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper
from bx.intervals.operations.complement import complement
from bx.intervals.operations.subtract import subtract
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 interval in generator:
            if type( interval ) is GenomicInterval:
                out_file.write( "%s\n" % "\t".join( interval ) )
            else:
                out_file.write( "%s\n" % interval )
    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="" ))


if __name__ == "__main__":
    main()