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()