comparison gops_cluster.py @ 5:2108e2dc3d32 draft default tip

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

4:3231f921ba4f

    -d, --distance=N: Maximum distance between clustered intervals
    -v, --overlap=N: Minimum overlap require (negative distance)
    -m, --minregions=N: Minimum regions per cluster
    -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
"""
import fileinput
import sys
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
from bx.intervals.operations.find_clusters import find_clusters
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 )

                            fix_strand=True )

    # Get the cluster tree
    try:
        clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
    except ParseError, exc:
        fail( "Invalid file format: %s" % str( exc ) )

    f1 = open( in_fname, "r" )
    out_file = open( out_fname, "w" )

                                                            g1.start_col,
                                                            g1.end_col,
                                                            g1.strand_col,
                                                            g1.default_strand,
                                                            g1.fix_strand )
                    except Exception, exc:
                        print >> sys.stderr, str( exc )
                        f1.close()
                        sys.exit()
                    interval_size = cluster_interval.end - cluster_interval.start
                    if outsize == -1 or \
                       ( outsize > interval_size and output == 4 ) or \

    f1.close()
    out_file.close()

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

if __name__ == "__main__":
    main()

5:2108e2dc3d32

    -d, --distance=N: Maximum distance between clustered intervals
    -v, --overlap=N: Minimum overlap require (negative distance)
    -m, --minregions=N: Minimum regions per cluster
    -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
"""
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.find_clusters import find_clusters
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

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

                            fix_strand=True )

    # Get the cluster tree
    try:
        clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
    except ParseError as exc:
        fail( "Invalid file format: %s" % str( exc ) )

    f1 = open( in_fname, "r" )
    out_file = open( out_fname, "w" )

                                                            g1.start_col,
                                                            g1.end_col,
                                                            g1.strand_col,
                                                            g1.default_strand,
                                                            g1.fix_strand )
                    except Exception as exc:
                        print(str( exc ), file=sys.stderr)
                        f1.close()
                        sys.exit()
                    interval_size = cluster_interval.end - cluster_interval.start
                    if outsize == -1 or \
                       ( outsize > interval_size and output == 4 ) or \

    f1.close()
    out_file.close()

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


if __name__ == "__main__":
    main()