def test_detect(self):
"""Test tta.detect()"""
self.assertEqual(
len(self.record.get_cds_features()) +
len(self.record.get_protoclusters()), 3)
options = get_simple_options(tta, ["--tta-threshold", "0"])
detected = tta.detect(self.record, options)
self.assertEqual(len(detected), 2)
# make sure features not added yet
features = self.record.get_generics()
self.assertEqual(len(features), 0)
# add to record and make sure they're there
detected.add_to_record(self.record)
features = self.record.get_generics()
self.assertEqual(len(features), 2)
for feature in features:
assert feature.type == "misc_feature"
fw_tta, rv_tta = features[0], features[1]
self.assertEqual(fw_tta.location.start, 3)
self.assertEqual(fw_tta.location.end, 6)
self.assertEqual(fw_tta.strand, 1)
self.assertEqual(rv_tta.location.start, 15)
self.assertEqual(rv_tta.location.end, 18)
self.assertEqual(rv_tta.strand, -1)
def setUp(self):
self.options = update_config(
get_simple_options(genefinding, [
'--taxon', 'fungi', '--genefinding-tool', 'glimmerhmm',
'--cpus', '1'
]))
self.data_location = get_full_path(__file__, "data")
def setUp(self):
self.config = get_simple_options(None, [])
self.config.genefinding_gff3 = path.get_full_path(__file__, "data", "test_gff.gff")
self.single_entry = False
contig1 = DummyRecord(seq="A"*2000)
contig1.id = "CONTIG_1"
contig2 = DummyRecord(seq="A"*2000)
contig2.id = "CONTIG_2"
self.sequences = [contig1, contig2]
def setUp(self):
self.options = update_config(
get_simple_options(
genefinding,
['--genefinding-tool', 'prodigal', '--cpus', '1']))