seq_dict[key].append(
textwrap.fill(str(records_dict[key].seq),
width=60)) # formated in fasta
alignments = []
for k in seq_dict:
out_fasta = os.path.join(snakemake.params['TMP_D'], k + '.fa')
out_aln = os.path.join(snakemake.params['TMP_D'], k + '.aln')
alignments.append(out_aln)
with open(out_fasta, 'w') as out_fh:
out_fh.write('\n'.join(seq_dict[k]))
aln = MafftCommandline(quiet=True,
retree=1,
thread=cores,
nuc=True,
globalpair=True,
input=out_fasta)
# print(aln())
with open(out_aln, 'w') as out_fh:
out_fh.write('\n'.join(aln()))
one_big_aln = AlignIO.read(alignments[0], 'fasta')
one_big_aln.sort()
for f in alignments:
aln = AlignIO.read(f, 'fasta')
aln.sort()
one_big_aln = one_big_aln + aln
with open(one_big_aln_f, 'w') as out_fh:
AlignIO.write(one_big_aln, out_fh, 'fasta')
