def test_msa_pop(self):
msa = MultipleSequenceAlignment.from_fasta(string=self.fasta)
pop_seq = msa.pop('A')
self.assertEqual(pop_seq.header, 'A')
self.assertEqual(pop_seq.sequence, 'ABC')
self.assertNotIn('A', msa.headers)
self.assertNotIn('ABC', msa.sequences)
def test_trailing_newline_msa(self):
fasta = f'{self.fasta}\n'
seq = MultipleSequenceAlignment.from_fasta(string=fasta)
self.assertEqual(seq.to_fasta(), fasta[:-1])
def test_sequence_iter_msa(self):
for _ in MultipleSequenceAlignment.from_fasta(string=self.fasta):
pass
def test_json_parsing_msa(self):
MultipleSequenceAlignment.from_json(string=self.json)
def test_fasta_input_output_msa(self):
seq = MultipleSequenceAlignment.from_fasta(string=self.fasta)
self.assertEqual(seq.to_fasta(), self.fasta)
def test_fasta_parsing_msa(self):
MultipleSequenceAlignment.from_fasta(string=self.fasta)
def test_empty_init_msa(self):
MultipleSequenceAlignment()
def test_msa_batch_rename(self):
msa = MultipleSequenceAlignment.from_fasta(string=self.fasta)
msa.batch_rename(self.rename_func)
self.assertEqual(msa.headers, ['A.test', 'B.test'])