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_write_db(self):
"""writing with overwrite in MPI should reset db"""
dstore = io_app.get_data_store("data", suffix="fasta")
members = dstore.filtered(
callback=lambda x: "brca1.fasta" not in x.split("/"))
reader = io_app.load_unaligned()
aligner = align_app.align_to_ref()
writer = write_db("delme.tinydb", create=True, if_exists="overwrite")
process = reader + aligner + writer
r = process.apply_to(
members,
logger=False,
show_progress=False,
parallel=True,
par_kw=dict(use_mpi=True),
)
expect = [str(m) for m in process.data_store]
process.data_store.close()
# now get read only and check what's in there
result = io_app.get_data_store("delme.tinydb")
got = [str(m) for m in result]
assert got == expect
def test_align_to_ref_generic_moltype(self):
"""tests when the moltype is generic"""
test_moltypes = ["text", "rna", "protein", "protein_with_stop", "bytes", "ab"]
for test_moltype in test_moltypes:
aligner = align_app.align_to_ref(moltype=test_moltype)
self.assertEqual(aligner._moltype.label, test_moltype)
self.assertEqual(
aligner._kwargs["S"],
make_generic_scoring_dict(10, get_moltype(test_moltype)),
)
def test_align_to_ref(self):
"""correctly aligns to a reference"""
aligner = align_app.align_to_ref(ref_seq="Human")
aln = aligner(self.seqs)
expect = {
"Bandicoot": "---NACTCATTAATGCTTGAAACCAGCAGTTTATTGTCCAAC",
"FlyingFox": "GCCAGCTCTTTACAGCATGAGAACAG---TTTATTATACACT",
"Human": "GCCAGCTCATTACAGCATGAGAACAGCAGTTTATTACTCACT",
"Rhesus": "GCCAGCTCATTACAGCATGAGAAC---AGTTTGTTACTCACT",
}
self.assertEqual(aln.to_dict(), expect)
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_aln_to_ref_known(self):
"""correctly recapitulates known case"""
orig = make_aligned_seqs(
{
"Ref": "CAG---GAGAACAGAAACCCAT--TACTCACT",
"Qu1": "CAG---GAGAACAG---CCCGTGTTACTCACT",
"Qu2": "CAGCATGAGAACAGAAACCCGT--TA---ACT",
"Qu3": "CAGCATGAGAACAGAAACCCGT----CTCACT",
"Qu4": "CAGCATGAGAACAGAAACCCGTGTTACTCACT",
"Qu5": "CAG---GAGAACAG---CCCAT--TACTCACT",
"Qu6": "CAG---GA-AACAG---CCCAT--TACTCACT",
"Qu7": "CAG---GA--ACAGA--CCCGT--TA---ACT",
},
moltype="dna",
)
expect = orig.to_dict()
aligner = align_app.align_to_ref(ref_seq="Ref")
aln = aligner(orig.degap())
self.assertEqual(aln.to_dict(), expect)
def test_align_to_ref_result_has_moltype(self):
"""aligned object has correct moltype"""
aligner = align_app.align_to_ref(moltype="dna")
got = aligner(self.seqs)
self.assertEqual(got.moltype.label, "dna")
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)
