def test_translate():
dic = get_transl_table()
codontab = CodonTable(dic)
assert len(test_data['dna']) % 3 == 0
protein = codontab.translate(test_data['dna']).decode('ascii')
print(protein)
print(test_data['protein'])
assert protein[:-1] == test_data['protein']
assert protein[-1] == '*'
def render(cls, args, outfile):
dic = translate.get_transl_table(args.table)
tab = CodonTable(dic)
for fn in args.filenames:
for rec in fasta.read(fn, args.concise):
if len(rec.seq) % 3:
if not args.quiet:
msg = 'warning: lenth of seq not a multiple of 3\n'
msg += '^debug:\t{}\t{}\t{}'.format(len(rec.seq), fn, rec.cmt)
print(msg, file=sys.stderr)
if args.skip:
continue
l = len(rec.seq)
rec.seq = rec.seq[:int(l - l % 3)]
rec.seq = tab.translate(rec.seq)
fasta.write(outfile, rec)