def switch_to_codon(alg_fasta_file, kept_columns=None):
# Check conservation of columns. If too many identities,
# switch to codon alignment and make the tree with DNA.
# Mixed models is another possibility.
if kept_columns:
kept_columns = set(map(int, kept_columns))
else:
kept_columns = []
#all_nt_alg = SeqGroup(nt_seed_file)
aa_alg = SeqGroup(alg_fasta_file)
nt_alg = SeqGroup()
for seqname, aaseq, comments in aa_alg.iter_entries():
#ntseq = all_nt_alg.get_seq(seqname).upper()
ntseq = db.get_seq(seqname, "nt").upper()
ntalgseq = []
nt_pos = 0
for pos, ch in enumerate(aaseq):
if ch in GAP_CHARS:
codon = "---"
else:
codon = ntseq[nt_pos:nt_pos+3]
nt_pos += 3
if not kept_columns or pos in kept_columns:
# we trust the sequence in DB, consistency should have been
# checked during the start up
ntalgseq.append(codon)
ntalgseq = "".join(ntalgseq)
nt_alg.set_seq(seqname, ntalgseq)
return nt_alg