def __call__(self,
seq_path,
result_path=None,
log_path=None,
failure_path=None):
# load candidate sequences
seq_file = open(seq_path, 'U')
candidate_sequences = parse_fasta(seq_file)
# load template sequences
template_alignment = []
template_alignment_fp = self.Params['template_filepath']
for seq_id, seq in parse_fasta(open(template_alignment_fp)):
# replace '.' characters with '-' characters
template_alignment.append((seq_id, seq.replace('.', '-').upper()))
template_alignment = Alignment.from_fasta_records(template_alignment,
DNASequence,
validate=True)
# initialize_logger
logger = NastLogger(log_path)
# get function for pairwise alignment method
pairwise_alignment_f = pairwise_alignment_methods[
self.Params['pairwise_alignment_method']]
pynast_aligned, pynast_failed = pynast_seqs(
candidate_sequences,
template_alignment,
min_pct=self.Params['min_pct'],
min_len=self.Params['min_len'],
align_unaligned_seqs_f=pairwise_alignment_f,
logger=logger,
temp_dir=get_qiime_temp_dir())
logger.record(str(self))
for i, seq in enumerate(pynast_failed):
skb_seq = DNASequence(str(seq), id=seq.Name)
pynast_failed[i] = skb_seq
pynast_failed = SequenceCollection(pynast_failed)
for i, seq in enumerate(pynast_aligned):
skb_seq = DNASequence(str(seq), id=seq.Name)
pynast_aligned[i] = skb_seq
pynast_aligned = Alignment(pynast_aligned)
if failure_path is not None:
fail_file = open(failure_path, 'w')
fail_file.write(pynast_failed.to_fasta())
fail_file.close()
if result_path is not None:
result_file = open(result_path, 'w')
result_file.write(pynast_aligned.to_fasta())
result_file.close()
return None
else:
return pynast_aligned
def __call__(self, seq_path, result_path=None, log_path=None,
failure_path=None):
# load candidate sequences
seq_file = open(seq_path, 'U')
candidate_sequences = parse_fasta(seq_file)
# load template sequences
template_alignment = []
template_alignment_fp = self.Params['template_filepath']
for seq_id, seq in parse_fasta(open(template_alignment_fp)):
# replace '.' characters with '-' characters
template_alignment.append((seq_id, seq.replace('.', '-').upper()))
template_alignment = Alignment.from_fasta_records(
template_alignment, DNASequence, validate=True)
# initialize_logger
logger = NastLogger(log_path)
# get function for pairwise alignment method
pairwise_alignment_f = pairwise_alignment_methods[
self.Params['pairwise_alignment_method']]
pynast_aligned, pynast_failed = pynast_seqs(
candidate_sequences,
template_alignment,
min_pct=self.Params['min_pct'],
min_len=self.Params['min_len'],
align_unaligned_seqs_f=pairwise_alignment_f,
logger=logger,
temp_dir=get_qiime_temp_dir())
logger.record(str(self))
for i, seq in enumerate(pynast_failed):
skb_seq = DNASequence(str(seq), id=seq.Name)
pynast_failed[i] = skb_seq
pynast_failed = SequenceCollection(pynast_failed)
for i, seq in enumerate(pynast_aligned):
skb_seq = DNASequence(str(seq), id=seq.Name)
pynast_aligned[i] = skb_seq
pynast_aligned = Alignment(pynast_aligned)
if failure_path is not None:
fail_file = open(failure_path, 'w')
fail_file.write(pynast_failed.to_fasta())
fail_file.close()
if result_path is not None:
result_file = open(result_path, 'w')
result_file.write(pynast_aligned.to_fasta())
result_file.close()
return None
else:
return pynast_aligned
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)