def test_paralinear_for_determinant_lte_zero(self):
"""returns distance of None if the determinant is <= 0"""
data = dict(
seq1="AGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT",
seq2="TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC",
)
aln = make_aligned_seqs(data=data, moltype=DNA)
paralinear_calc = ParalinearPair(moltype=DNA, alignment=aln)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.get_pairwise_distances().to_dict()
self.assertTrue(numpy.isnan(list(dists.values())[0]))
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.get_pairwise_distances().to_dict()
self.assertTrue(numpy.isnan(list(dists.values())[0]))
def test_paralinear_pair_aa(self):
"""paralinear shouldn't fail to produce distances for aa seqs"""
aln = load_aligned_seqs("data/brca1_5.paml", moltype=DNA)
aln = aln.get_translation()
paralinear_calc = ParalinearPair(moltype=PROTEIN, alignment=aln)
paralinear_calc.run(show_progress=False)
dists = paralinear_calc.get_pairwise_distances()