def testWorkspaceGTFIntergenic1( self ):
workspace = annotator_distance.readWorkspace( open( self.workspace ),
workspace_builder = "gtf-intergenic",
label = "none" )
self.assertEqual( workspace, {'chr1': [(4000, 10000, ( ('X', ), ('X', ))), (14000, 20000, ( ('X',) , ('X',)))]} )
def testWorkspaceGFF( self ):
workspace = annotator_distance.readWorkspace( open( self.workspace ),
workspace_builder = "gff",
label = "none" )
self.assertEqual( workspace, {'chr1': [(0, 1000), (3000, 4000), (10000, 11000), (13000, 14000), (20000, 21000), (23000, 24000)]} )
def testWorkspaceGTFIntronic2( self ):
workspace = annotator_distance.readWorkspace( open( self.workspace ),
workspace_builder = "gtf-intronic",
label = "direction" )
self.assertEqual( workspace, {'chr1': [(100, 1000, (('3',), ('5',))), (1100, 2000, (('3',), ('5',))), (10100, 11000, (('5',), ('3',))), (11100, 12000, (('5',), ('3',)))]} )
