def load_weighted_msa(work_msa):
"""
The given multiple sequence alignment (MSA) should contain the reference
sequence. The reference will be removed from the alignment and returned
separately. The alignment will also be changed such that "." is used to
indicate terminal deletions while "-" is used to indicate internal
deletions.
"""
msa_with_ref = AlignIO.read(work_msa.output_aln, 'clustal')
ref = None
msa = MultipleSeqAlignment([])
for record in msa_with_ref:
# Use "." to indicate terminal mismatches, and "-" to indicate internal
# mismatches.
to_dots = lambda m: '.' * (m.end() - m.start())
record.seq = Seq(
re.sub('^-+|-+$', to_dots, str(record.seq)),
record.seq.alphabet,
)
if record.id == work_msa.shared.target_id:
ref = record
else:
msa.append(record)
msa.ref = ref
msa.ref_ungapped = remove_gaps(ref.seq)
weight_alignments(msa)
return msa
