def test_short_sequences(self):
seq = "AATGTAGGAAAAACAGCATTTTCATTTCGCCATTTT"
p = Pyrodigal(meta=True)
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 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 run_prodigal(seqrecord):
id = seqrecord.id
nuclen = len(str(seqrecord.seq))
p = Pyrodigal(meta=True)
#p.train(str(seqrecord.seq))
genes = p.find_genes(str(seqrecord.seq))
table_11 = [gene.translate(translation_table=11) for gene in genes]
table_4 = [gene.translate(translation_table=4) for gene in genes]
table_15 = [gene.translate(translation_table=15) for gene in genes]
#Chooses best translation table (highest coding density)
all_lens = find_max(table_4, table_11, table_15)
table_densities = [float(x) / float(nuclen) for x in all_lens]
return [id] + table_densities
def setUpClass(cls):
data = os.path.realpath(os.path.join(__file__, "..", "data"))
fna = os.path.join(data, "SRR492066.fna.gz")
meta_faa = os.path.join(data, "SRR492066.meta.faa.gz")
with gzip.open(fna, "rt") as f:
cls.record = next(Bio.SeqIO.parse(f, "fasta"))
cls.p = Pyrodigal(meta=True)
cls.genes = cls.p.find_genes(str(cls.record.seq))
def test_overflow(self):
# > 180195.SAMN03785337.LFLS01000089
seq = """
AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAAC
AGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATC
GCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACG
GTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTG
ACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACC
AACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGC
AATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGC
GTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCT
GGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACC
ACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTG
ACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACC
GTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAAC
CTGAGC
"""
p = Pyrodigal(meta=True, closed=False)
genes = p.find_genes(textwrap.dedent(seq).replace("\n", ""))
self.assertEqual(len(genes), 1)
self.assertEqual(genes[0].start_type, "Edge")
self.assertTrue(genes[0].partial_begin)
self.assertTrue(genes[0].partial_end)
def find_genes(cls, seq):
p = Pyrodigal(meta=True)
return p.find_genes(seq)
def test_train(self):
p = Pyrodigal(meta=True)
self.assertRaises(RuntimeError, p.train, str(self.record.seq))
def test_train_not_called(self):
p = Pyrodigal(meta=False)
self.assertRaises(RuntimeError, p.find_genes, str(self.record.seq))
def find_genes(cls, seq):
p = Pyrodigal(meta=False)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p.train(seq)
return p.find_genes(seq)
def test_empty_sequence(self):
p = Pyrodigal(meta=True)
genes = p.find_genes("")
self.assertEqual(len(genes), 0)
self.assertRaises(StopIteration, next, iter(genes))