def test_align_to_ref_generic_moltype(self):
"""tests when the moltype is generic"""
test_moltypes = ["text", "rna", "protein", "protein_with_stop", "bytes", "ab"]
for test_moltype in test_moltypes:
aligner = align_app.align_to_ref(moltype=test_moltype)
self.assertEqual(aligner._moltype.label, test_moltype)
self.assertEqual(
aligner._kwargs["S"],
make_generic_scoring_dict(10, get_moltype(test_moltype)),
)
def test_pwise_protein(self):
"""works for pairwise protein alignment"""
from cogent3 import PROTEIN
S = make_generic_scoring_dict(1, PROTEIN)
seq1 = PROTEIN.make_seq("MAYPFQLGLQD", "seq1")
seq2 = PROTEIN.make_seq("MAYPFGLQD", "seq2")
a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, local=False)
self.assertEqual(a1.to_dict(),
dict(seq1="MAYPFQLGLQD", seq2="MAYPF--GLQD"))
