def test_validate(self):
dna = BioSeq.create_bio_seq("ACTG")
rna = BioSeq.create_bio_seq("ACUG", "rna")
self.assertTrue(dna.validate())
self.assertTrue(rna.validate())
# seq.csv contains a DNA sequence
rna.read_sequence('tests/files/seq.csv')
self.assertFalse(rna.validate())
def test_save_load(self):
seq = BioSeq.create_bio_seq("ACTGTCATAT")
seq.save('tests/files/test_save_load.csv')
loaded_seq = BioSeq.load('tests/files/test_save_load.csv')
self.assertEqual(seq.get_seq(), loaded_seq.get_seq())
self.assertEqual(seq.get_genetic_code(), loaded_seq.get_genetic_code())
self.assertEqual(seq.__class__.__name__, loaded_seq.__class__.__name__)
def test_read_write(self):
seq = BioSeq.create_bio_seq("ACTGTCATAT")
len_bwr = len(seq)
seq.write_sequence('tests/files/test_write.csv')
seq.read_sequence('tests/files/seq.csv')
self.assertGreater(len(seq), len_bwr)
self.assertEqual(2591, len(seq))
seq.read_sequence('tests/files/test_write.csv')
self.assertEqual(len_bwr, len(seq))
def test_freq(self):
seq = BioSeq.create_bio_seq("ACTGTCATAT")
self.assertEqual(seq.freq_symbols(), {"T": 4, "A": 3, "C": 2, "G": 1})
def test_basics(self):
seq = BioSeq.create_bio_seq("ACTGTCATGAT")
self.assertEqual(seq.get_seq(), "ACTGTCATGAT")
self.assertEqual(len(seq), len("ACTGTCATGAT"))
def test_rev_complement(self):
self.assertEqual(
BioSeq.create_bio_seq("ACGGTA").reverse_complement(), "TACCGT")
self.assertEqual(
BioSeq.create_bio_seq("ACGUUA", "rna").reverse_complement(),
"UAACGU")
def test_gc_percent(self):
dna = BioSeq.create_bio_seq("ACGG")
self.assertEqual(dna.gc_percent(), 0.75)
self.assertEqual(dna.gc_percent_sub_seq(2), [0.5, 1])