def multiple_sequence_alignment(seqs_fp):
"""Perform multiple sequence alignment on FASTA file using MAFFT
Parameters
----------
seqs_fp: string
filepath to FASTA file for multiple sequence alignment
Returns
-------
Alignment object
The aligned sequences.
See Also
--------
skbio.Alignment
"""
return align_unaligned_seqs(seqs_fp)
def multiple_sequence_alignment(seqs_fp):
"""Perform multiple sequence alignment on FASTA file using MAFFT
Parameters
----------
seqs_fp: string
filepath to FASTA file for multiple sequence alignment
Returns
-------
Alignment object
The aligned sequences.
See Also
--------
skbio.Alignment
"""
return align_unaligned_seqs(seqs_fp)
def multiple_sequence_alignment(seqs_fp, threads=1):
"""Perform multiple sequence alignment on FASTA file using MAFFT.
Parameters
----------
seqs_fp: string
filepath to FASTA file for multiple sequence alignment
threads: integer, optional
number of threads to use
Returns
-------
Alignment object
The aligned sequences.
See Also
--------
skbio.Alignment
"""
return align_unaligned_seqs(seqs_fp=seqs_fp, params={'--thread': threads})
def test_align_unaligned_seqs(self):
"""align_unaligned_seqs should work as expected"""
res = align_unaligned_seqs(self.seqs1_fp, RNA)
self.assertEqual(res.toFasta(), self.seqs1_aln)
