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from io import StringIO
from unittest import TestCase
from numpy.testing import assert_equal
from cogent3.evolve.models import DSO78_freqs, DSO78_matrix
from cogent3.parse.paml_matrix import PamlMatrixParser
data = """
27
98 32
120 0 905
36 23 0 0
89 246 103 134 0
198 1 148 1153 0 716
240 9 139 125 11 28 81
23 240 535 86 28 606 43 10
65 64 77 24 44 18 61 0 7
41 15 34 0 0 73 11 7 44 257
26 464 318 71 0 153 83 27 26 46 18
72 90 1 0 0 114 30 17 0 336 527 243
18 14 14 0 0 0 0 15 48 196 157 0 92
250 103 42 13 19 153 51 34 94 12 32 33 17 11
409 154 495 95 161 56 79 234 35 24 17 96 62 46 245
371 26 229 66 16 53 34 30 22 192 33 136 104 13 78 550
0 201 23 0 0 0 0 0 27 0 46 0 0 76 0 75 0
24 8 95 0 96 0 22 0 127 37 28 13 0 698 0 34 42 61
208 24 15 18 49 35 37 54 44 889 175 10 258 12 48 30 157 0 28
0.087127 0.040904 0.040432 0.046872 0.033474 0.038255 0.049530
0.088612 0.033618 0.036886 0.085357 0.080482 0.014753 0.039772
0.050680 0.069577 0.058542 0.010494 0.029916 0.064718
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
S_ij = S_ji and PI_i for the Dayhoff model, with the rate Q_ij=S_ij*PI_j
The rest of the file is not used.
Prepared by Z. Yang, March 1995.
See the following reference for notation used here:
Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and
applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
"""
class TestParsePamlMatrix(TestCase):
def test_parse(self):
matrix, freqs = PamlMatrixParser(StringIO(data))
assert_equal(DSO78_matrix, matrix)
assert_equal(DSO78_freqs, freqs)
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