def test_translate_seqcoll(self):
"""correctly translate a sequence collection"""
seqs = dict(a="ATGAGG", b="ATGTAA")
seqs = make_unaligned_seqs(seqs)
# trim terminal stops
translater = translate_seqs()
aa = translater(seqs)
self.assertEqual(aa.to_dict(), dict(a="MR", b="M"))
self.assertEqual(aa.moltype.label, "protein")
# don't trim terminal stops, returns NotCompleted
translater = translate_seqs(trim_terminal_stop=False)
aa = translater(seqs)
self.assertIsInstance(aa, NotCompleted)
def test_translate_aln(self):
"""correctly translates alignments"""
data = dict(a="ATGAGGCCC", b="ATGTTT---")
# an array alignment
aln = make_aligned_seqs(data)
translater = translate_seqs()
aa = translater(aln)
self.assertEqual(aa.to_dict(), dict(a="MRP", b="MF-"))
self.assertEqual(aa.moltype.label, "protein")
self.assertIsInstance(aa, type(aln))
# Alignment
aln = aln.to_type(array_align=True)
aa = translater(aln)
self.assertEqual(aa.to_dict(), dict(a="MRP", b="MF-"))
self.assertEqual(aa.moltype.label, "protein")
self.assertIsInstance(aa, type(aln))