comparison gops_intersect.py @ 5:33b3f3688db4 draft

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

4:8ddabc73af92

    -m, --mincols=N: Require this much overlap (default 1bp)
    -p, --pieces: just print pieces of second set (after padding)
    -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
    -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
"""
import fileinput
import sys
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
from bx.intervals.operations.intersect import intersect
from bx.cookbook import doc_optparse
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff

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


def main():

                    out_file.write( "%s\n" % "\t".join( interval.fields ) )
            elif isinstance( feature, GenomicInterval ):
                out_file.write( "%s\n" % "\t".join( feature.fields ) )
            else:
                out_file.write( "%s\n" % feature )
    except ParseError, e:
        out_file.close()
        fail( "Invalid file format: %s" % str( e ) )

    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()

5:33b3f3688db4

    -m, --mincols=N: Require this much overlap (default 1bp)
    -p, --pieces: just print pieces of second set (after padding)
    -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
    -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
"""
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.intersect import intersect
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

from utils.gff_util import convert_bed_coords_to_gff, GFFFeature, GFFReaderWrapper

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


def main():

                    out_file.write( "%s\n" % "\t".join( interval.fields ) )
            elif isinstance( feature, GenomicInterval ):
                out_file.write( "%s\n" % "\t".join( feature.fields ) )
            else:
                out_file.write( "%s\n" % feature )
    except ParseError as e:
        out_file.close()
        fail( "Invalid file format: %s" % str( e ) )

    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()