comparison gops_join.py @ 4:a10f49d9218a draft

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

3:ffbd1de29c28

    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -f, --fill=N: none, right, left, both
"""
import fileinput
import sys
from bx.intervals.io import NiceReaderWrapper
from bx.intervals.operations.join import join
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 outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill):
            if type( outfields ) is list:
                out_file.write( "%s\n" % "\t".join( outfields ) )
            else:
                out_file.write( "%s\n" % outfields )
    except ParseError, exc:
        out_file.close()
        fail( "Invalid file format: %s" % str( exc ) )
    except MemoryError:
        out_file.close()
        fail( "Input datasets were too large to complete the join operation." )

    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()

4:a10f49d9218a

    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -f, --fill=N: none, right, left, both
"""
from __future__ import print_function

import fileinput
import sys

from bx.cookbook import doc_optparse
from bx.intervals.io import NiceReaderWrapper
from bx.intervals.operations.join import join
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 outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill):
            if type( outfields ) is list:
                out_file.write( "%s\n" % "\t".join( outfields ) )
            else:
                out_file.write( "%s\n" % outfields )
    except ParseError as exc:
        out_file.close()
        fail( "Invalid file format: %s" % str( exc ) )
    except MemoryError:
        out_file.close()
        fail( "Input datasets were too large to complete the join operation." )

    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()