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_seqs(self):
"""correctly writes sequences out"""
fasta_paths = list(io_app.findall(self.basedir, suffix=".fasta", limit=2))
fasta_loader = io_app.load_aligned(format="fasta")
alns = list(map(fasta_loader, fasta_paths))
with TemporaryDirectory(dir=".") as dirname:
writer = io_app.write_seqs(dirname, if_exists="ignore")
wrote = list(map(writer, alns))
written = list(io_app.findall(dirname, suffix="fasta"))
for i, wrote in enumerate(written):
self.assertEqual(alns[i].info.stored, join(dirname, wrote))
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_checkpointable(self):
"""chained funcs should be be able to apply a checkpoint"""
path = "data" + os.sep + "brca1.fasta"
reader = io_app.load_aligned(moltype="dna")
omit_degens = sample_app.omit_degenerates(moltype="dna")
with TemporaryDirectory(dir=".") as dirname:
writer = io_app.write_seqs(dirname)
aln = reader(path)
outpath = writer(aln)
read_write = reader + writer
got = read_write(path) # should skip reading and return path
self.assertEqual(got, outpath)
read_write.disconnect() # allows us to reuse bits
read_write_degen = reader + writer + omit_degens
# should return an alignment instance
got = read_write_degen(path)
self.assertIsInstance(got, ArrayAlignment)
self.assertTrue(len(got) > 1000)
