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"""
Tests for `bx.phylo.phast`.
"""
from io import StringIO
from numpy import (
allclose,
array,
)
from bx.phylo.phast import TreeModel
test_data = """ALPHABET: A C G T -
ORDER: 0
SUBST_MOD: HKY85+Gap
TRAINING_LNL: -178667772.836697
BACKGROUND: 0.227006 0.169993 0.169307 0.227262 0.206432
RATE_MAT:
-0.971735 0.122443 0.465361 0.163692 0.220238
0.163508 -1.130351 0.121949 0.624656 0.220238
0.623952 0.122443 -1.130326 0.163692 0.220238
0.163508 0.467247 0.121949 -0.972942 0.220238
0.242187 0.181362 0.180630 0.242461 -0.846640
TREE: ((((((hg16:0.007738,panTro1:0.008356):0.027141,(baboon:0.009853,rheMac1:0.010187):0.035049):0.103138,galago:0.174770):0.019102,((rn3:0.092633,mm6:0.089667):0.273942,rabbit:0.230839):0.021927):0.023762,(canFam1:0.204637,(elephant:0.123777,tenrec:0.278910):0.085977):0.009439):0.306466,monDom1:0.401151)mammals;
""" # noqa: W291
def test_parser():
tm = TreeModel.from_file(StringIO(test_data))
assert tm.alphabet == ("A", "C", "G", "T", "-")
assert tm.order == 0
assert tm.subst_mod == "HKY85+Gap"
assert allclose(tm.background, [0.227006, 0.169993, 0.169307, 0.227262, 0.206432])
assert allclose(
tm.matrix,
array(
[
[-0.971735, 0.122443, 0.465361, 0.163692, 0.220238],
[0.163508, -1.130351, 0.121949, 0.624656, 0.220238],
[0.623952, 0.122443, -1.130326, 0.163692, 0.220238],
[0.163508, 0.467247, 0.121949, -0.972942, 0.220238],
[0.242187, 0.181362, 0.180630, 0.242461, -0.846640],
]
),
)
assert (
tm.tree
== "((((((hg16:0.007738,panTro1:0.008356):0.027141,(baboon:0.009853,rheMac1:0.010187):0.035049):0.103138,galago:0.174770):0.019102,((rn3:0.092633,mm6:0.089667):0.273942,rabbit:0.230839):0.021927):0.023762,(canFam1:0.204637,(elephant:0.123777,tenrec:0.278910):0.085977):0.009439):0.306466,monDom1:0.401151)mammals;"
)
|
