def test_take_named(self):
"""returns collections containing named seqs"""
select = sample.take_named_seqs("a", "b")
alns = [
make_aligned_seqs(data=[
("a", "GCAAGCGTTTAT"),
("b", "GCTTTTGTCAAT"),
("c", "GC--GCGTTTAT"),
("d", "GCAAGCNNTTAT"),
]),
make_aligned_seqs(data=[
("a", "GGAAGCGTTTAT"),
("b", "GCTTTTGTCAAT"),
("c", "GC--GCGTTTAT"),
("d", "GCAAGCNNTTAT"),
]),
]
got = [aln.to_dict() for aln in map(select, alns) if aln]
expected = [
dict((("a", "GCAAGCGTTTAT"), ("b", "GCTTTTGTCAAT"))),
dict((("a", "GGAAGCGTTTAT"), ("b", "GCTTTTGTCAAT"))),
]
self.assertEqual(got, expected)
# return False if a named seq absent
aln = make_aligned_seqs(data=[("c",
"GC--GCGTTTAT"), ("d", "GCAAGCNNTTAT")])
got = select(aln)
self.assertFalse(got)
self.assertTrue(type(got) == composable.NotCompleted)
# using negate
select = sample.take_named_seqs("c", negate=True)
alns = [
make_aligned_seqs(data=[("a", "GCAAGCGTTTAT"), ("b",
"GCTTTTGTCAAT")]),
make_aligned_seqs(data=[
("a", "GGAAGCGTTTAT"),
("b", "GCTTTTGTCAAT"),
("c", "GC--GCGTTTAT"),
]),
]
got = [aln.to_dict() for aln in map(select, alns) if aln]
expect = [
dict(d) for d in [
[("a", "GCAAGCGTTTAT"), ("b", "GCTTTTGTCAAT")],
[("a", "GGAAGCGTTTAT"), ("b", "GCTTTTGTCAAT")],
]
]
self.assertEqual(got, expect)
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
