def test_open_reading_frames(self):
dna = DNASeq(example_dna)
orf = list(dna.open_reading_frames())
self.assertEqual(6, len(orf))
self.assertEqual(
"[['MKL_', 'MSLS_'], [], ['MNEPQLKHRASDYAQTQTQHYSEC_'], [], [], []]",
str(orf))
def test_codon_usage(self):
dna = DNASeq("GCTGCTGCTGCCGCCGCAGCAGCGGCGGCG")
self.assertDictEqual({
'GCA': 0.2,
'GCC': 0.2,
'GCG': 0.3,
'GCU': 0.3
}, dna.codon_usage("A"))
def test_align(self):
m = MSA(sm2, -1)
seqs = [DNASeq("ATAGC"), DNASeq("AACC")]
c, aligned = m.align(seqs)
self.assertEqual("ATACC", str(c))
self.assertEqual(len(aligned), 2)
seqs = [DNASeq("ATAGC"), DNASeq("AACC"), DNASeq("ATGAC")]
c, aligned = m.align(seqs)
self.assertEqual("ATGACC", str(c))
self.assertEqual(len(aligned), 3)
def test_constructor(self):
s = DNASeq("ATATATCGCG")
self.assertIsInstance(s, DNASeq)
self.assertEqual("ATATATCGCG", s.sequence)
self.assertEqual("DNA", s.seq_type)
def test_translation(self):
dna = DNASeq("GCTGCCTGTATTTAG")
pro = dna.translation()
self.assertEqual("AACI_", pro.sequence)
self.assertEqual("PROTEIN", pro.seq_type)
self.assertIsInstance(pro, ProteinSeq)
self.assertEqual(
"AACI_",
dna.translation(0).sequence) # expecting the same as the default
self.assertEqual("ACI_",
dna.translation(3).sequence) # skip the first codon
dna = DNASeq("AGCTGCCTGTATTTAG")
self.assertEqual("AACI_",
dna.translation(1).sequence) # test different start
dna = DNASeq("AAGCTGCCTGTATTTAG")
self.assertEqual("AACI_",
dna.translation(2).sequence) # test different start
def test_transcription(self):
dna = DNASeq("ATCG")
rna = dna.transcription()
self.assertEqual("AUCG", rna.sequence)
self.assertEqual("RNA", rna.seq_type)
self.assertIsInstance(rna, RNASeq)
def test_reverse_complement(self):
s = DNASeq("ATCG")
self.assertEqual("CGAT", s.reverse_complement())
def test_custom_assert_valid(self):
x = DNASeq("ATATATCGCG")
self.assertRaises(Exception, DNASeq, "ATATATCGCGU")
x.sequence = "ATATATCGCGU"
self.assertRaises(Exception, x._assert_valid_sequence)
self.assertRaises(Exception, x._assert_valid_sequence_regex)
def test_get_col(self):
m = MSA(sm2, -1)
seqs = [DNASeq("ATAGC"), DNASeq("A_ACC")]
self.assertEqual(m.get_col(seqs, 0), ["A", "A"])
self.assertEqual(m.get_col(seqs, 1), ["T", "_"])
def test_consensus(self):
m = MSA(sm2, -1)
c = m.consensus([DNASeq("ATAGC"), DNASeq("A_ACC")], DNASeq)
self.assertEqual(type(c), bioseq.dnaseq.DNASeq)
self.assertEqual(str(c), "ATACC")