def test_trim_stop_codons(self):
"""trims stop codons using the specified genetic code"""
trimmer = sample.trim_stop_codons(gc=1) # standard code
seqs = make_unaligned_seqs(data={
"seq1": "AAATTTCCC",
"seq2": "AAATTTTAA"
},
moltype="dna")
got = trimmer(seqs)
expect = {"seq1": "AAATTTCCC", "seq2": "AAATTT"}
self.assertEqual(got.to_dict(), expect)
trimmer = sample.trim_stop_codons(gc=1) # standard code
aln = make_aligned_seqs(data={
"seq1": "AAATTTCCC",
"seq2": "AAATTTTAA"
},
moltype="dna")
got = trimmer(aln)
expect = {"seq1": "AAATTTCCC", "seq2": "AAATTT---"}
self.assertEqual(got.to_dict(), expect)
# different genetic code
trimmer = sample.trim_stop_codons(gc=2) # mt code
seqs = make_unaligned_seqs(data={
"seq1": "AAATTTCCC",
"seq2": "AAATTTAGA"
},
moltype="dna")
got = trimmer(seqs)
expect = {"seq1": "AAATTTCCC", "seq2": "AAATTT"}
self.assertEqual(got.to_dict(), 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
