1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5a73d78e0a47/ Changeset: 5a73d78e0a47 User: dannon Date: 2013-07-01 11:57:51 Summary: Fix converter imports -- resolves failing unit tests Affected #: 2 files
diff -r 6673bd3bf4571c4134797077ca85350a6319e444 -r 5a73d78e0a4782d9c57d8c1d6cea167e4f4671b6 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -11,15 +11,13 @@
from __future__ import division
-import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes
def main(): - + # Read options, args. parser = optparse.OptionParser() parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 ) @@ -27,12 +25,12 @@ parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 ) (options, args) = parser.parse_args() input_fname, output_fname = args - + # Make column indices 0-based. options.chrom_col -= 1 options.start_col -= 1 options.end_col -= 1 - + # Do conversion. index = Indexes() offset = 0 @@ -46,9 +44,9 @@ chrom_end = int( feature[ options.end_col ] ) index.add( chrom, chrom_start, chrom_end, offset ) offset += len(line) - + index.write( open(output_fname, "w") )
-if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file +
diff -r 6673bd3bf4571c4134797077ca85350a6319e444 -r 5a73d78e0a4782d9c57d8c1d6cea167e4f4671b6 lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -8,20 +8,18 @@
from __future__ import division
-import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes
def main(): - + # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args - + # Do conversion. index = Indexes() offset = 0 @@ -31,9 +29,9 @@ start = int( start ) - 1 index.add( chrom, start, start + 1, offset ) offset += len( line ) - + index.write( open(output_fname, "w") )
-if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file +
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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