def test_inter(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.CustomStreamExample(self.ins), fi).pull()
f = fi.get_features_for_seqid('ctg123')
dfi = gt.FeatureNodeIteratorDepthFirst(f[0])
f = dfi.next()
types = set([])
while f:
types.update([f.type])
f = dfi.next()
self.assertTrue('bar' in types, types)
def test_depth_first(self):
dfi = gt.FeatureNodeIteratorDepthFirst(self.feature)
found = dfi.next()
self.assertEqual(found.get_attribute("ID"), "gene12")
self.assertEqual(found.type, "gene")
found = dfi.next()
self.assertEqual(found.type, 'exon')
found = dfi.next()
self.assertEqual(found.type, 'five_prime_cis_splice_site')
found = dfi.next()
found = dfi.next()
self.assertEqual(found.type, 'exon')
def test_dup(self):
fi = gt.FeatureIndexMemory()
gt.FeatureStream(gt.DuplicateFeatureStream(self.ins, "intron", "exon"),
fi).pull()
f = fi.get_features_for_seqid('ctg123')
dfi = gt.FeatureNodeIteratorDepthFirst(f[0])
f = dfi.next()
types = set([])
while f:
types.update([f.type])
f = dfi.next()
self.assertTrue('intron' in types, types)