def test_training_info_deallocation(self):
p = Pyrodigal(meta=False)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p.train(str(self.record.seq))
genes = p.find_genes(str(self.record.seq))
del p # normally should not deallocate training info since it's RC
self.assertEqual(genes[0].translate(), str(self.proteins[0].seq))
def test_empty_sequence(self):
p = Pyrodigal(meta=False)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p.train(str(self.record.seq[:20000]))
genes = p.find_genes("")
self.assertEqual(len(genes), 0)
self.assertRaises(StopIteration, next, iter(genes))
def test_short_sequences(self):
seq = "AATGTAGGAAAAACAGCATTTTCATTTCGCCATTTT"
p = Pyrodigal(meta=False)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p.train(str(self.record.seq[:20000]))
for i in range(1, len(seq)):
genes = p.find_genes(seq[:i])
self.assertEqual(len(genes), 0)
self.assertRaises(StopIteration, next, iter(genes))
def find_genes(cls, seq):
p = Pyrodigal(meta=False)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p.train(seq)
return p.find_genes(seq)