1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4426265b87be/ changeset: r5112:4426265b87be user: jgoecks date: 2011-02-23 16:40:30 summary: Enhance GFF reader to handle headers and comments. affected #: 1 file (308 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Tue Feb 22 18:49:57 2011 -0500 +++ b/lib/galaxy/datatypes/util/gff_util.py Wed Feb 23 10:40:30 2011 -0500 @@ -3,6 +3,7 @@ """ import pkg_resources; pkg_resources.require( "bx-python" ) from bx.intervals.io import * +from bx.tabular.io import Header, Comment class GFFInterval( GenomicInterval ): """ @@ -148,6 +149,12 @@ self.seed_interval = GenomicIntervalReader.next( self ) except ParseError, e: handle_parse_error( e ) + + # If header or comment, clear seed interval and return it. + if isinstance( self.seed_interval, ( Header, Comment ) ): + return_val = self.seed_interval + self.seed_interval = None + return return_val # Initialize feature name from seed. feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.