def test_multiple_sequence_alignment(self):
"""Test multiple sequence alignment.
"""
seqs = [DNA('caccggcggcccggtggtggccattattattgggtctaaag',
metadata={'id': 'seq_1'}, lowercase=True),
DNA('caccggcggcccgagtggtggccattattattgggtcaagg',
metadata={'id': 'seq_2'}, lowercase=True),
DNA('caccggcggcccgagtgatggccattattattgggtctaaag',
metadata={'id': 'seq_3'}, lowercase=True),
DNA('aaccggcggcccaagtggtggccattattattgggtctaaag',
metadata={'id': 'seq_4'}, lowercase=True),
DNA('caccgggcccgagtggtggccattattattgggtctaaag',
metadata={'id': 'seq_5'}, lowercase=True)]
seqs_fp = join(self.working_dir, "seqs.fna")
with open(seqs_fp, 'w') as o:
for seq in seqs:
seq.write(o, format='fasta')
alignment_file = multiple_sequence_alignment(seqs_fp)
aligned_seqs = [DNA(item[1], metadata={'id': item[0]}, lowercase=True)
for item in sequence_generator(alignment_file)]
align_exp = [
DNA('caccggcggcccg-gtggtggccattattattgggtctaaag',
lowercase=True, metadata={'id': 'seq_1'}),
DNA('caccggcggcccgagtggtggccattattattgggtcaagg-',
lowercase=True, metadata={'id': 'seq_2'}),
DNA('caccggcggcccgagtgatggccattattattgggtctaaag',
lowercase=True, metadata={'id': 'seq_3'}),
DNA('aaccggcggcccaagtggtggccattattattgggtctaaag',
lowercase=True, metadata={'id': 'seq_4'}),
DNA('caccg--ggcccgagtggtggccattattattgggtctaaag',
lowercase=True, metadata={'id': 'seq_5'})]
self.assertEqual(aligned_seqs, align_exp)
def test_multiple_sequence_alignment(self):
"""Test multiple sequence alignment.
"""
seqs = [
DNA('caccggcggcccggtggtggccattattattgggtctaaag', id='seq_1'),
DNA('caccggcggcccgagtggtggccattattattgggtcaagg', id='seq_2'),
DNA('caccggcggcccgagtgatggccattattattgggtctaaag', id='seq_3'),
DNA('aaccggcggcccaagtggtggccattattattgggtctaaag', id='seq_4'),
DNA('caccgggcccgagtggtggccattattattgggtctaaag', id='seq_5')
]
seqs_col = SequenceCollection(seqs)
seqs_fp = join(self.working_dir, "seqs.fna")
with open(seqs_fp, 'w') as o:
o.write(seqs_col.to_fasta())
alignment = multiple_sequence_alignment(seqs_fp)
align_exp = [
DNA('caccggcggcccg-gtggtggccattattattgggtctaaag', id='seq_1'),
DNA('caccggcggcccgagtggtggccattattattgggtcaagg-', id='seq_2'),
DNA('caccggcggcccgagtgatggccattattattgggtctaaag', id='seq_3'),
DNA('aaccggcggcccaagtggtggccattattattgggtctaaag', id='seq_4'),
DNA('caccg--ggcccgagtggtggccattattattgggtctaaag', id='seq_5')
]
self.assertItemsEqual(alignment, align_exp)