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_composable_apps(self):
"""checks the ability of these two apps(fast_slow_dist and quick_tree) to communicate"""
path = os.path.join(data_path, "brca1_5.paml")
aln1 = load_aligned_seqs(path, moltype=DNA)
fast_slow_dist = dist.fast_slow_dist(fast_calc="hamming", moltype="dna")
quick = tree_app.quick_tree(drop_invalid=False)
proc = fast_slow_dist + quick
self.assertEqual(
str(proc),
"fast_slow_dist(type='distance', distance=None, moltype='dna',\n"
"fast_calc='hamming', slow_calc=None) + quick_tree(type='tree',\n"
"drop_invalid=False)",
)
self.assertIsInstance(proc, tree_app.quick_tree)
self.assertEqual(proc._type, "tree")
self.assertIsInstance(proc.input, dist.fast_slow_dist)
self.assertIs(proc.output, None)
self.assertIsInstance(proc._input_types, frozenset)
self.assertIsInstance(proc._output_types, frozenset)
self.assertIsInstance(proc._in, dist.fast_slow_dist)
self.assertIs(proc._out, None)
tree1 = proc(aln1)
self.assertIsInstance(tree1, PhyloNode)
self.assertIsNotNone(tree1.children)
self.assertEqual(set(tree1.get_tip_names()), set(aln1.names))
# tests when distances contain None
data = dict(
seq1="AGGGGGGGGGGCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGCGGTTTTTTTTTTTTTTTTTT",
seq2="TAAAAAAAAAAGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCC",
)
aln2 = make_aligned_seqs(data=data, moltype=DNA)
tree2 = proc(aln2)
self.assertIsInstance(tree2, NotCompleted)
def test_quick_tree(self):
"""correctly calc a nj tree"""
path = os.path.join(data_path, "brca1_5.paml")
aln = load_aligned_seqs(path, moltype=DNA)
fast_slow_dist = dist.fast_slow_dist(fast_calc="hamming", moltype="dna")
dist_matrix = fast_slow_dist(aln)
quick1 = tree_app.quick_tree()
tree1 = quick1.quick_tree(dist_matrix)
self.assertEqual(set(tree1.get_tip_names()), set(aln.names))
def test_composite_pickleable(self):
"""composable functions should be pickleable"""
from pickle import dumps
from cogent3.app import io, sample, evo, tree, translate, align
read = io.load_aligned(moltype="dna")
dumps(read)
trans = translate.select_translatable()
dumps(trans)
aln = align.progressive_align("nucleotide")
dumps(aln)
just_nucs = sample.omit_degenerates(moltype="dna")
dumps(just_nucs)
limit = sample.fixed_length(1000, random=True)
dumps(limit)
mod = evo.model("HKY85")
dumps(mod)
qt = tree.quick_tree()
dumps(qt)
proc = read + trans + aln + just_nucs + limit + mod
dumps(proc)
def test_str(self):
"""str representation correctly represents parameterisations"""
func = select_translatable()
got = str(func)
self.assertEqual(
got,
"select_translatable(type='sequences', "
"moltype='dna', gc='Standard Nuclear', "
"allow_rc=False, trim_terminal_stop=True)",
)
func = select_translatable(allow_rc=True)
got = str(func)
self.assertEqual(
got,
"select_translatable(type='sequences', "
"moltype='dna', gc='Standard Nuclear', "
"allow_rc=True, trim_terminal_stop=True)",
)
nodegen = omit_degenerates()
got = str(nodegen)
self.assertEqual(
got,
"omit_degenerates(type='aligned', moltype=None, "
"gap_is_degen=True, motif_length=1)",
)
ml = min_length(100)
got = str(ml)
self.assertEqual(
got,
"min_length(type='sequences', length=100, "
"motif_length=1, subtract_degen=True, "
"moltype=None)",
)
qt = quick_tree()
self.assertEqual(str(qt),
"quick_tree(type='tree', drop_invalid=False)")
def test_quick_tree_taking_distance_matrix(self):
"""quick_tree should take a distance matrix"""
quick_tree = tree_app.quick_tree()
data = {
("ABAYE2984", "Avin_42730"): 0.638,
("Atu3667", "Avin_42730"): 2.368,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
tree = quick_tree.quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(set(tree.get_tip_names()),
set.union(*(set(tup) for tup in data.keys())))
data = {
("DogFaced", "FlyingFox"): 0.05,
("DogFaced", "FreeTaile"): 0.14,
("DogFaced", "LittleBro"): 0.16,
("DogFaced", "TombBat"): 0.15,
("FlyingFox", "DogFaced"): 0.05,
("FlyingFox", "FreeTaile"): 0.12,
("FlyingFox", "LittleBro"): 0.13,
("FlyingFox", "TombBat"): 0.14,
("FreeTaile", "DogFaced"): 0.14,
("FreeTaile", "FlyingFox"): 0.12,
("FreeTaile", "LittleBro"): 0.09,
("FreeTaile", "TombBat"): 0.1,
("LittleBro", "DogFaced"): 0.16,
("LittleBro", "FlyingFox"): 0.13,
("LittleBro", "FreeTaile"): 0.09,
("LittleBro", "TombBat"): 0.12,
("TombBat", "DogFaced"): 0.15,
("TombBat", "FlyingFox"): 0.14,
("TombBat", "FreeTaile"): 0.1,
("TombBat", "LittleBro"): 0.12,
}
darr = DistanceMatrix(data)
tree = quick_tree.quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(set(tree.get_tip_names()),
set.union(*(set(tup) for tup in data.keys())))
data = {
("ABAYE2984", "Atu3667"): 0.25,
("ABAYE2984", "Avin_42730"): 0.638,
("ABAYE2984", "BAA10469"): None,
("Atu3667", "ABAYE2984"): 0.25,
("Atu3667", "Avin_42730"): 2.368,
("Atu3667", "BAA10469"): 0.25,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "ABAYE2984"): 0.25,
("BAA10469", "Atu3667"): 0.25,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
tree = quick_tree.quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(set(tree.get_tip_names()),
set.union(*(set(tup) for tup in data.keys())))
data = {
("ABAYE2984", "Atu3667"): None,
("ABAYE2984", "Avin_42730"): 0.638,
("ABAYE2984", "BAA10469"): None,
("Atu3667", "ABAYE2984"): None,
("Atu3667", "Avin_42730"): 2.368,
("Atu3667", "BAA10469"): None,
("Avin_42730", "ABAYE2984"): 0.638,
("Avin_42730", "Atu3667"): 2.368,
("Avin_42730", "BAA10469"): 1.85,
("BAA10469", "ABAYE2984"): None,
("BAA10469", "Atu3667"): None,
("BAA10469", "Avin_42730"): 1.85,
}
darr = DistanceMatrix(data)
with self.assertRaises(KeyError):
tree = quick_tree.quick_tree(darr)
# when distance_matrix is None after dropping invalid
with self.assertRaises(ValueError):
quick_tree = tree_app.quick_tree(drop_invalid=True)
tree = quick_tree.quick_tree(darr)
data = {
("DogFaced", "FlyingFox"): 0.05,
("DogFaced", "FreeTaile"): 0.14,
("DogFaced", "LittleBro"): 0.16,
("DogFaced", "TombBat"): 0.15,
("FlyingFox", "DogFaced"): 0.05,
("FlyingFox", "FreeTaile"): 0.12,
("FlyingFox", "LittleBro"): 0.13,
("FlyingFox", "TombBat"): 0.14,
("FreeTaile", "DogFaced"): 0.14,
("FreeTaile", "FlyingFox"): 0.12,
("FreeTaile", "LittleBro"): 0.09,
("FreeTaile", "TombBat"): 0.1,
("LittleBro", "DogFaced"): 0.16,
("LittleBro", "FlyingFox"): 0.13,
("LittleBro", "FreeTaile"): 0.09,
("LittleBro", "TombBat"): 0.12,
("TombBat", "DogFaced"): 0.15,
("TombBat", "FlyingFox"): 0.14,
("TombBat", "FreeTaile"): 0.1,
("TombBat", "LittleBro"): 0.12,
}
darr = DistanceMatrix(data)
tree = quick_tree.quick_tree(darr)
self.assertIsInstance(tree, PhyloNode)
self.assertIsNotNone(tree.children)
self.assertEqual(set(tree.get_tip_names()),
set.union(*(set(tup) for tup in data.keys())))
