comparison gops_merge.py @ 5:dfbbc0291b36 draft default tip

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

4:a2f62c0c0537

#!/usr/bin/env python
"""
Merge overlaping regions.

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -3, --threecol: Output 3 column bed
"""
import fileinput
import sys
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
from bx.intervals.operations.merge import merge
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 )

                    out_file.write( "%s\n" % "\t".join( line.fields ) )
                elif type( line ) is list:
                    out_file.write( "%s\n" % "\t".join( line ) )
                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 __name__ == "__main__":
    main()

5:dfbbc0291b36

#!/usr/bin/env python
"""
Merge overlapping regions.

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -3, --threecol: Output 3 column bed
"""
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.merge import merge
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

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

                    out_file.write( "%s\n" % "\t".join( line.fields ) )
                elif type( line ) is list:
                    out_file.write( "%s\n" % "\t".join( line ) )
                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 __name__ == "__main__":
    main()