def test_progress_with_guide_tree(self):
"""progressive align works with provided guide tree"""
tree = make_tree(treestring=self.treestring)
aligner = align_app.progressive_align(model="nucleotide",
guide_tree=self.treestring)
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
aligner = align_app.progressive_align(model="nucleotide",
guide_tree=tree)
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
# even if it has underscores in name
treestring = ("(Bandicoot:0.4,FlyingFox:0.05,(Rhesus_macaque:0.06,"
"Human:0.0):0.04);")
aligner = align_app.progressive_align(model="nucleotide",
guide_tree=treestring)
data = self.seqs.to_dict()
data["Rhesus macaque"] = data.pop("Rhesus")
seqs = make_unaligned_seqs(data)
aln = aligner(seqs)
self.assertEqual(len(aln), 42)
# guide tree with no lengths raises value error
with self.assertRaises(ValueError):
_ = align_app.progressive_align(
model="nucleotide",
guide_tree="(Bandicoot,FlyingFox,(Rhesus_macaque,Human));",
)
def test_progressive_align_codon(self):
"""progressive alignment with codon models"""
aligner = align_app.progressive_align(model="GY94")
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
aligner = align_app.progressive_align(model="codon")
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
def test_progressive_align_protein(self):
"""progressive alignment with protein models"""
seqs = self.seqs.get_translation()
aligner = align_app.progressive_align(model="WG01",
guide_tree=self.treestring)
aln = aligner(seqs)
self.assertEqual(len(aln), 14)
aligner = align_app.progressive_align(model="protein",
guide_tree=self.treestring)
aln = aligner(seqs)
self.assertEqual(len(aln), 14)
def test_with_genetic_code(self):
"""handles genetic code argument"""
aligner = align_app.progressive_align(model="GY94", gc="2")
# the 'TGA' codon is a sense codon in vertebrate mitochondrial
self.assertTrue("TGA" in aligner._model.get_motifs())
aligner = align_app.progressive_align(model="codon")
# but a stop codon in the standard nuclear
self.assertTrue("TGA" not in aligner._model.get_motifs())
# try using a nuclear
with self.assertRaises(TypeError):
aligner = align_app.progressive_align(model="nucleotide", gc="2")
def test_progress_with_guide_tree(self):
"""progressive align works with provided guide tree"""
tree = make_tree(treestring=self.treestring)
aligner = align_app.progressive_align(
model="nucleotide", guide_tree=self.treestring
)
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
aligner = align_app.progressive_align(model="nucleotide", guide_tree=tree)
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
def test_progressive_align_protein_moltype(self):
"""tests guide_tree is None and moltype is protein"""
from cogent3 import load_aligned_seqs
seqs = load_aligned_seqs("data/nexus_aa.nxs", moltype="protein")
seqs = seqs.degap()
seqs = seqs.take_seqs(["Rat", "Cow", "Human", "Mouse", "Whale"])
aligner = align_app.progressive_align(model="WG01")
got = aligner(seqs)
self.assertNotIsInstance(got, NotCompleted)
aligner = align_app.progressive_align(model="protein")
got = aligner(seqs)
self.assertNotIsInstance(got, NotCompleted)
def _get_all_composables(tmp_dir_name):
test_model1 = evo.model("HKY85")
test_model2 = evo.model("GN")
test_hyp = evo.hypothesis(test_model1, test_model2)
test_num_reps = 100
applications = [
align.align_to_ref(),
align.progressive_align(model="GY94"),
evo.ancestral_states(),
evo.bootstrap(hyp=test_hyp, num_reps=test_num_reps),
evo.hypothesis(test_model1, test_model2),
evo.model("GN"),
evo.tabulate_stats(),
sample.fixed_length(100),
sample.min_length(100),
io.write_db(tmp_dir_name, create=True),
io.write_json(tmp_dir_name, create=True),
io.write_seqs(tmp_dir_name, create=True),
sample.omit_bad_seqs(),
sample.omit_degenerates(),
sample.omit_duplicated(),
sample.take_codon_positions(1),
sample.take_named_seqs(),
sample.trim_stop_codons(gc=1),
translate.select_translatable(),
tree.quick_tree(),
tree.scale_branches(),
tree.uniformize_tree(),
]
return applications
def test_pickle_progressive_align(self):
"""test progressive_align is picklable"""
from pickle import dumps, loads
aligner = align_app.progressive_align(model="codon")
aln = aligner(self.seqs)
got = loads(dumps(aln))
self.assertTrue(got)
def test_progressive_align_nuc(self):
"""progressive alignment with nuc models"""
aligner = align_app.progressive_align(model="TN93", distance="TN93")
aln = aligner(self.seqs)
expect = {
"Rhesus": "GCCAGCTCATTACAGCATGAGAACAG---TTTGTTACTCACT",
"Human": "GCCAGCTCATTACAGCATGAGAACAGCAGTTTATTACTCACT",
"Bandicoot": "NACTCATTAATGCTTGAAACCAGCAG---TTTATTGTCCAAC",
"FlyingFox": "GCCAGCTCTTTACAGCATGAGAACAG---TTTATTATACACT",
}
got = aln.to_dict()
self.assertEqual(got, expect)
# using default
aligner = align_app.progressive_align(model="TN93", distance="TN93")
aln = aligner(self.seqs)
self.assertEqual(len(aln), 42)
self.assertEqual(aln.moltype, aligner._moltype)
def test_progressive_fails(self):
"""should return NotCompletedResult along with message"""
# Bandicoot has an inf-frame stop codon
seqs = make_unaligned_seqs(
data={"Human": "GCCTCA", "Rhesus": "GCCAGCTCA", "Bandicoot": "TGATCATTA"},
moltype="dna",
)
aligner = align_app.progressive_align(model="codon")
got = aligner(seqs)
self.assertTrue(type(got), NotCompleted)
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
def test_composite_pickleable(self):
"""composable functions should be pickleable"""
from pickle import dumps
from cogent3.app import io, sample, evo, tree, translate, align
read = io.load_aligned(moltype="dna")
dumps(read)
trans = translate.select_translatable()
dumps(trans)
aln = align.progressive_align("nucleotide")
dumps(aln)
just_nucs = sample.omit_degenerates(moltype="dna")
dumps(just_nucs)
limit = sample.fixed_length(1000, random=True)
dumps(limit)
mod = evo.model("HKY85")
dumps(mod)
qt = tree.quick_tree()
dumps(qt)
proc = read + trans + aln + just_nucs + limit + mod
dumps(proc)
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)
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(got[("Mouse", "Human")] >= 0)
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(got[("Mouse", "Human")] >= 0)
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(got[("Mouse", "Human")] >= 0)
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(got[("Mouse", "Human")] >= 0)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Mouse", "Human")] >= 0)
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(got[("Human", "Opossum")] >= 0)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
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(got[("Human", "Opossum")] >= 0)
fast_slow_dist = dist_app.fast_slow_dist(slow_calc="TN93")
got = fast_slow_dist(aln3).to_dict()
self.assertTrue(got[("Human", "Opossum")] >= 0)
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(got[("Human", "Opossum")] >= 0)
fast_slow_dist = dist_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 = align.align_to_ref() + dist_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 = align.progressive_align(model="WG01", guide_tree=treestring)
_ = aligner(self.seqs5)
