def test_annotate_geneclusters_overlaps(self):
"Test clusterfinder.annotate_geneclusters() with overlaps"
mock("antismash.utils.get_pfam_features",
tracker=self.tt,
returns=self.fake_features)
self.config.clusternr_offset = 1
seq_record = Mock('seq_record', tracker=self.tt)
seq_record.seq = Seq("X" * 2000, IUPAC.protein)
seq_record.features = [
_make_fake_feature(10, 40, type_='cluster'),
_make_fake_feature(1040, 1050, type_='cluster'),
_make_fake_feature(110, 400, type_='cluster'),
]
clusterfinder.annotate_geneclusters(seq_record, self.config)
self.assertEqual(3, len(seq_record.features))
self.assertEqual(10, int(seq_record.features[0].location.start))
self.assertEqual(120, int(seq_record.features[0].location.end))
self.assertAlmostEqual(
0.6429, float(seq_record.features[0].qualifiers['probability'][0]))
self.assertEqual(1030, int(seq_record.features[1].location.start))
self.assertEqual(1120, int(seq_record.features[1].location.end))
self.assertAlmostEqual(
0.6429, float(seq_record.features[1].qualifiers['probability'][0]))
self.assertEqual(30, int(seq_record.features[2].location.start))
self.assertEqual(400, int(seq_record.features[2].location.end))
self.assertAlmostEqual(
0.6429, float(seq_record.features[2].qualifiers['probability'][0]))
def test_find_nr_cds(self):
"Test clusterfinder.find_nr_cds"
seq_record = Mock('seq_record', tracker=self.tt)
seq_record.features = []
seq_record.seq = Seq("X" * 2000, IUPAC.protein)
left = (0, 5)
newpos, num = clusterfinder.find_nr_cds(left, seq_record)
self.assertEqual(left, newpos)
self.assertEqual(0, num)
right = (150, 160)
newpos, num = clusterfinder.find_nr_cds(right, seq_record)
self.assertEqual(right, newpos)
self.assertEqual(0, num)
middle = (35, 115)
newpos, num = clusterfinder.find_nr_cds(middle, seq_record)
self.assertEqual([30, 120], newpos)
self.assertEqual(7, num)
small = (501, 504)
newpos, num = clusterfinder.find_nr_cds(small, seq_record)
self.assertEqual([500, 505], newpos)
self.assertEqual(1, num)
def test_annotate_geneclusters_no_overlaps(self):
"Test clusterfinder.annotate_geneclusters() without overlaps"
mock("antismash.utils.get_pfam_features",
tracker=self.tt,
returns=self.fake_features)
self.config.clusternr_offset = 1
self.config.next_clusternr = -5
seq_record = Mock('seq_record', tracker=self.tt)
seq_record.features = []
seq_record.seq = Seq("X" * 2000, IUPAC.protein)
clusterfinder.annotate_geneclusters(seq_record, self.config)
self.assertEqual(3, self.config.next_clusternr)
self.assertEqual(2, len(seq_record.features))
cluster1, cluster2 = seq_record.features
self.assertIn('probability', cluster1.qualifiers.keys())
self.assertAlmostEqual(0.6429,
float(cluster1.qualifiers['probability'][0]))
self.assertIn('probability', cluster2.qualifiers.keys())
self.assertAlmostEqual(0.6429,
float(cluster2.qualifiers['probability'][0]))
