Mercurial > repos > miller-lab > genome_diversity

comparison lib/galaxy/datatypes/wsf.py @ 10:9b92372de9f6

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rename snp to gsSnp, sap to gdSap
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 04 Sep 2012 12:49:53 -0400
parents e29f4d801bb0
children
comparison
equal deleted inserted replaced
9:22fe0154fa54 10:9b92372de9f6
137 def set_dataset_dbkey_metadata( self, dataset ): 137 def set_dataset_dbkey_metadata( self, dataset ):
138 value_from_comment_metadata = dataset.metadata.comment_metadata.get( 'dbkey', '?' ) 138 value_from_comment_metadata = dataset.metadata.comment_metadata.get( 'dbkey', '?' )
139 if isinstance( value_from_comment_metadata, basestring ): 139 if isinstance( value_from_comment_metadata, basestring ):
140 dataset.metadata.dbkey = value_from_comment_metadata 140 dataset.metadata.dbkey = value_from_comment_metadata
141 141
142 class SnpFile( Fake ): 142 class GDSnp( Fake ):
143 """ Webb's SNP file format """ 143 """ Webb's SNP file format """
144 file_ext = 'snp' 144 file_ext = 'gdSnp'
145 145
146 MetadataElement( name="individual_names", desc="individual names", visible=False, readonly=True ) 146 MetadataElement( name="individual_names", desc="individual names", visible=False, readonly=True )
147 MetadataElement( name="individual_columns", desc="individual columns", visible=False, readonly=True ) 147 MetadataElement( name="individual_columns", desc="individual columns", visible=False, readonly=True )
148 148
149 def set_dataset_metadata_from_comments( self, dataset ): 149 def set_dataset_metadata_from_comments( self, dataset ):
174 174
175 if individual_names: 175 if individual_names:
176 dataset.metadata.individual_names = individual_names[:] 176 dataset.metadata.individual_names = individual_names[:]
177 dataset.metadata.individual_columns = individual_columns[:] 177 dataset.metadata.individual_columns = individual_columns[:]
178 178
179 class SapFile( Fake ): 179 class GDSap( Fake ):
180 """ Webb's SAP file format """ 180 """ Webb's SAP file format """
181 file_ext = 'sap' 181 file_ext = 'gdSap'
182 182
183 MetadataElement( name="kegg_gene", desc="KEGG gene code column", param=metadata.ColumnParameter, default=0 ) 183 MetadataElement( name="kegg_gene", desc="KEGG gene code column", param=metadata.ColumnParameter, default=0 )
184 MetadataElement( name="kegg_path", desc="KEGG pathway code/name column", param=metadata.ColumnParameter, default=0 ) 184 MetadataElement( name="kegg_path", desc="KEGG pathway code/name column", param=metadata.ColumnParameter, default=0 )
185 185