1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/217a5c1f12bc/ changeset: 217a5c1f12bc branches: user: jgoecks date: 2011-05-28 01:07:06 summary: Fix bugs in reading and visualizing GFF3 datasets. affected #: 1 file (496 bytes)
--- a/lib/galaxy/datatypes/util/gff_util.py Fri May 27 09:22:27 2011 -0400 +++ b/lib/galaxy/datatypes/util/gff_util.py Sat May 28 01:07:06 2011 +0200 @@ -67,11 +67,18 @@
def name( self ): """ Returns feature's name. """ - name = self.attributes.get( 'transcript_id', None ) - if not name: - name = self.attributes.get( 'id', None ) - if not name: - name = self.attributes.get( 'group', None ) + name = None + # Preference for name: GTF, GFF3, GFF. + for attr_name in [ + # GTF: + 'transcript_id', 'gene_id', + # GFF3: + 'ID', 'id', + # GFF (TODO): + 'group' ]: + name = self.attributes.get( attr_name, None ) + if name is not None: + break return name
def copy( self ): @@ -172,11 +179,14 @@ self.seed_interval = None return return_val
- # Initialize feature name from seed. + # Initialize feature identifier from seed. feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF - feature_id = self.seed_interval.attributes.get( 'ID', None ) # For GFF3 - feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) # For GTF - feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None ) # For GTF + # For GFF3 + feature_id = self.seed_interval.attributes.get( 'ID', None ) + feature_parent_id = self.seed_interval.attributes.get( 'Parent', None ) + # For GTF. + feature_gene_id = self.seed_interval.attributes.get( 'gene_id', None ) + feature_transcript_id = self.seed_interval.attributes.get( 'transcript_id', None )
# Read all intervals associated with seed. feature_intervals = [] @@ -205,8 +215,9 @@ if group and feature_group != group: break # GFF3 test: - parent = interval.attributes.get( 'Parent', None ) - if feature_id and feature_id != parent: + parent_id = interval.attributes.get( 'Parent', None ) + cur_id = interval.attributes.get( 'ID', None ) + if feature_id and parent_id != feature_parent_id and feature_id != cur_id: break # GTF test: gene_id = interval.attributes.get( 'gene_id', None ) @@ -230,7 +241,7 @@ # Convert to BED coords? if self.convert_to_bed_coord: convert_gff_coords_to_bed( feature ) - + return feature
@@ -280,10 +291,11 @@ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: - # Try splitting by space and, if necessary, by '=' sign. - pair = name_value_pair.strip().split(" ") + # Try splitting by '=' (GFF3) first because spaces are allowed in GFF3 + # attribute; next, try double quotes for GTF. + pair = name_value_pair.strip().split("=") if len( pair ) == 1: - pair = name_value_pair.strip().split("=") + pair = name_value_pair.strip().split(""") if len( pair ) == 1: # Could not split for some reason -- raise exception? continue
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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