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import os
from tempfile import TemporaryDirectory
from unittest import TestCase, main
from numpy.testing import assert_allclose
from cogent3 import DNA, PROTEIN, get_app, make_unaligned_seqs, open_data_store
from cogent3.app.composable import WRITER
from cogent3.evolve.fast_distance import HammingPair, TN93Pair
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Gavin Huttley", "Stephen Ma", "Nick Shahmaras"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__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():
return [
get_app("align_to_ref"),
get_app("progressive_align", model="GY94"),
get_app("fixed_length", 100),
get_app("sample.min_length", 100),
get_app("write_seqs", os.getcwd()),
get_app(
"omit_bad_seqs",
),
get_app(
"omit_degenerates",
),
get_app("take_codon_positions", 1),
get_app(
"take_named_seqs",
),
get_app("trim_stop_codons", gc=1),
]
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 = get_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 = get_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 = get_app("fast_slow_dist", distance="GTR")
self.assertEqual(fast_slow_dist._sm.name, "GTR")
fast_slow_dist = get_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 = get_app(
"fast_slow_dist", distance="TN93", fast_calc="TN93", slow_calc="TN93"
)
with self.assertRaises(ValueError):
fast_slow_dist = get_app("fast_slow_dist", fast_calc="GTR")
with self.assertRaises(ValueError):
fast_slow_dist = get_app("fast_slow_dist", slow_calc="hamming")
def test_compatible_parameters(self):
"""tests if the input parameters are compatible with fast_slow_dist initialisation"""
for kwargs in (
dict(fast_calc="hamming", moltype="dna"),
dict(fast_calc="TN93"),
dict(slow_calc="GTR"),
dict(fast_calc="TN93"),
):
_ = get_app("fast_slow_dist", **kwargs)
def test_incompatible_parameters(self):
"""tests incompatible input parameters with fast_slow_dist initialisation"""
for kwargs in (
dict(fast_calc="hamming"),
dict(slow_calc="paralinear"),
dict(fast_calc="GTR"),
dict(slow_calc="hamming", moltype="dna"),
):
with self.assertRaises(ValueError):
_ = get_app("fast_slow_dist", **kwargs)
def test_composable_apps(self):
"""tests two composable apps"""
composable_apps = _get_all_composable_apps()
calc_dist = get_app("fast_slow_dist", fast_calc="hamming", moltype="dna")
for app in composable_apps:
if app.app_type is WRITER:
# cannot have a WRITER before a GENERIC
continue
# Compose two composable applications, there should not be exceptions.
got = app + calc_dist
self.assertIsInstance(got, type(calc_dist))
self.assertIs(got.input, app)
self.assertIsInstance(got._data_types, frozenset)
self.assertIsInstance(got._return_types, frozenset)
self.assertIs(got.input, app)
app.disconnect()
calc_dist.disconnect()
def test_est_dist_pair_slow(self):
"""tests the distance between seq pairs in aln"""
aligner = get_app(
"align_to_ref",
)
aln3 = aligner(self.seqs3)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(got[("Mouse", "Human")] >= 0)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(got[("Mouse", "Human")] >= 0)
aligner = get_app("align_to_ref", ref_seq="Human")
aln3 = aligner(self.seqs3)
fast_slow_dist = get_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 = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
assert_allclose(got[("Human", "Mouse")], got[("Mouse", "Human")])
self.assertTrue(got[("Mouse", "Human")] >= 0)
aligner = get_app("align_to_ref", ref_seq="Mouse")
aln3 = aligner(self.seqs3)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Mouse", "Human")] >= 0)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Mouse", "Human")] >= 0)
aligner = get_app(
"align_to_ref",
)
aln3 = aligner(self.seqs4)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
aligner = get_app("align_to_ref", ref_seq="Human")
aln3 = aligner(self.seqs4)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
aligner = get_app("align_to_ref", ref_seq="Opossum")
aln3 = aligner(self.seqs4)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="GTR")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
fast_slow_dist = get_app("fast_slow_dist", slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
# now as a process
proc = (
get_app(
"align_to_ref",
)
+ get_app("fast_slow_dist", fast_calc="hamming", moltype="dna")
)
got = proc(self.seqs1)
self.assertEqual(got[("Human", "Rhesus")], 1)
treestring = "(Human:0.2,Bandicoot:0.2)"
aligner = get_app("progressive_align", model="WG01", guide_tree=treestring)
_ = aligner(self.seqs5)
def test_composes_with_write_tabular(self):
"""correctly links to tabular"""
with TemporaryDirectory(dir=".") as dirname:
out_dstore = open_data_store(dirname, suffix="tsv", mode="w")
writer = get_app("write_tabular", out_dstore)
dist_calc = get_app("fast_slow_dist", distance="hamming", moltype="protein")
_ = dist_calc + writer
def test_functions_as_composable(self):
"""works as a composable app"""
from pathlib import Path
loader = get_app("load_aligned", moltype="dna", format="paml")
dist = get_app("fast_slow_dist", "hamming", moltype="dna")
with TemporaryDirectory(dir=".") as dirname:
dirname = Path(dirname)
out_dstore = open_data_store(dirname, suffix="tsv", mode="w")
writer = get_app("write_tabular", out_dstore)
proc = loader + dist + writer
_ = proc("data/brca1_5.paml")
output = dirname / "brca1_5.tsv"
self.assertTrue(output.exists())
if __name__ == "__main__":
main()
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