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test_dist.py
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test_dist.py
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import os
from unittest import TestCase, main
from numpy.testing import assert_allclose
from cogent3 import DNA, PROTEIN, make_unaligned_seqs
from cogent3.app import align
from cogent3.app import dist as dist_app
from cogent3.app import io, sample
from cogent3.evolve.fast_distance import HammingPair, TN93Pair
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2020, The Cogent Project"
__credits__ = ["Gavin Huttley", "Stephen Ma"]
__license__ = "BSD-3"
__version__ = "2020.7.2a"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Alpha"
_seqs1 = {
"Human": "GCCAGCTCATTACAGCATGAGAACAGCAGTTTATTACTCACT",
"Bandicoot": "NACTCATTAATGCTTGAAACCAGCAGTTTATTGTCCAAC",
"Rhesus": "GCCAGCTCATTACAGCATGAGAACAGTTTGTTACTCACT",
"FlyingFox": "GCCAGCTCTTTACAGCATGAGAACAGTTTATTATACACT",
}
_seqs2 = {
"Human": "ATGCGGCTCGCGGAGGCCGCGCTCGCGGAG",
"Mouse": "ATGCCCGGCGCCAAGGCAGCGCTGGCGGAG",
"Opossum": "ATGCCAGTGAAAGTGGCGGCGGTGGCTGAG",
}
_seqs3 = {
"Human": "ATGCGGCTCGCGGAGGCCGCGCTCGCGGAG",
"Mouse": "ATGCCCGGCGCCAAGGCAGCGCTGGCGGAG",
}
_seqs4 = {
"Human": "ATGCGGCTCGCGGAGGCCGCGCTCGCGGAG",
"Opossum": "ATGCCAGTGAAAGTGGCGGCGGTGGCTGAG",
}
_seqs5 = {"Human": "ASSLQHENSSLLLT", "Bandicoot": "XSLMLETSSLLSN"}
def _get_all_composable_apps():
applications = [
align.align_to_ref(),
align.progressive_align(model="GY94"),
sample.fixed_length(100),
sample.min_length(100),
io.write_seqs(os.getcwd()),
sample.omit_bad_seqs(),
sample.omit_degenerates(),
sample.take_codon_positions(1),
sample.take_named_seqs(),
sample.trim_stop_codons(gc=1),
]
return applications
class FastSlowDistTests(TestCase):
seqs1 = make_unaligned_seqs(_seqs1, moltype=DNA)
seqs2 = make_unaligned_seqs(_seqs2, moltype=DNA)
seqs3 = make_unaligned_seqs(_seqs3, moltype=DNA)
seqs4 = make_unaligned_seqs(_seqs4, moltype=DNA)
seqs5 = make_unaligned_seqs(_seqs5, moltype=PROTEIN)
def test_init(self):
"""tests if fast_slow_dist can be initialised correctly"""
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="hamming", moltype="dna")
self.assertIsInstance(fast_slow_dist.fast_calc, HammingPair)
self.assertIsNone(fast_slow_dist._sm)
fast_slow_dist = dist_app.fast_slow_dist(distance="TN93")
self.assertIsInstance(fast_slow_dist.fast_calc, TN93Pair)
self.assertEqual(fast_slow_dist._sm.name, "TN93")
fast_slow_dist = dist_app.fast_slow_dist(distance="GTR")
self.assertEqual(fast_slow_dist._sm.name, "GTR")
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
self.assertEqual(fast_slow_dist._sm.name, "TN93")
self.assertIsNone(fast_slow_dist.fast_calc)
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(
distance="TN93", fast_calc="TN93", slow_calc="TN93"
)
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="GTR")
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="hamming")
def test_compatible_parameters(self):
"""tests if the input parameters are compatible with fast_slow_dist initialisation"""
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="hamming", moltype="dna")
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="TN93")
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="TN93")
# fails for paralinear or hamming if no moltype
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="hamming")
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="paralinear")
# fails for hamming as slow_calc
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="hamming", moltype="dna")
with self.assertRaises(ValueError):
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="GTR")
def test_composable_apps(self):
"""tests two composable apps"""
composable_apps = _get_all_composable_apps()
fast_slow_dist = dist_app.fast_slow_dist(fast_calc="hamming", moltype="dna")
for app in composable_apps:
# Compose two composable applications, there should not be exceptions.
got = app + fast_slow_dist
self.assertIsInstance(got, dist_app.fast_slow_dist)
self.assertEqual(got._type, "distance")
self.assertIs(got.input, app)
self.assertIs(got.output, None)
self.assertIsInstance(got._input_types, frozenset)
self.assertIsInstance(got._output_types, frozenset)
self.assertIs(got._in, app)
self.assertIs(got._out, None)
app.disconnect()
fast_slow_dist.disconnect()
def test_est_dist_pair_slow(self):
"""tests the distance between seq pairs in aln"""
aligner = align.align_to_ref()
aln3 = aligner(self.seqs3)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(0 <= got[("Mouse", "Human")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(0 <= got[("Mouse", "Human")])
aligner = align.align_to_ref(ref_seq="Human")
aln3 = aligner(self.seqs3)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(0 <= got[("Mouse", "Human")])
aligner = align.align_to_ref(ref_seq="Mouse")
aln3 = aligner(self.seqs3)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Mouse", "Human")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Mouse", "Human")])
aligner = align.align_to_ref()
aln3 = aligner(self.seqs4)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
aligner = align.align_to_ref(ref_seq="Human")
aln3 = aligner(self.seqs4)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
aligner = align.align_to_ref(ref_seq="Opossum")
aln3 = aligner(self.seqs4)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(0 <= got[("Human", "Opossum")])
treestring = "(Human:0.2,Bandicoot:0.2)"
aligner = align.progressive_align(model="WG01", guide_tree=treestring)
_ = aligner(self.seqs5)
if __name__ == "__main__":
main()