def test_codon_positions_4fold_degen(self):
"""codon_positions correctly return fourfold degenerate bases"""
# **4---**4---
aln = make_aligned_seqs(data=[("a", "GCAAGCGTTTAT"),
("b", "GCTTTTGTCAAT")],
moltype=DNA)
expect = dict([("a", "AT"), ("b", "TC")])
ffold = sample.take_codon_positions(fourfold_degenerate=True)
got = ffold(aln)
self.assertEqual(got.to_dict(), expect)
# error if no moltype
with self.assertRaises(AssertionError):
_ = sample.take_codon_positions(moltype=None)
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 _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 _codon_positions(self, array_align):
"""correctly return codon positions"""
aln = make_aligned_seqs(data=[("a", "ACGACGACG"), ("b", "GATGATGAT")],
array_align=array_align)
one = sample.take_codon_positions(1)
got = one(aln)
self.assertEqual(got.to_dict(), {"a": "AAA", "b": "GGG"})
two = sample.take_codon_positions(2)
got = two(aln)
self.assertEqual(got.to_dict(), {"a": "CCC", "b": "AAA"})
three = sample.take_codon_positions(3)
got = three(aln)
self.assertEqual(got.to_dict(), {"a": "GGG", "b": "TTT"})
one_two = sample.take_codon_positions(1, 2)
got = one_two(aln)
self.assertEqual(got.to_dict(), {"a": "ACACAC", "b": "GAGAGA"})
one_three = sample.take_codon_positions(1, 3)
got = one_three(aln)
self.assertEqual(got.to_dict(), {"a": "AGAGAG", "b": "GTGTGT"})
two_three = sample.take_codon_positions(2, 3)
got = two_three(aln)
self.assertEqual(got.to_dict(), {"a": "CGCGCG", "b": "ATATAT"})
