def test_root_ui_mrca(capsys):
test_in_args = deepcopy(in_args)
test_in_args.root = [["firSA25a", "penSH31b"]]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "757489907bd5c82882d084ffcb22cfba"
def test_root_ui_leaf(capsys):
test_in_args = deepcopy(in_args)
test_in_args.root = [["firSA25a"]]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "f32bdc34bfe127bb0453a80cf7b01302"
def test_screw_formats_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "nexus"
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "543d2fc90ca1f391312d6b8fe896c59c"
def test_screw_formats_inplace_ui(capsys):
temp_file = MyFuncs.TempFile()
with open(resource("compare_trees.newick"), "r") as ifile:
temp_file.write(ifile.read())
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "nexus"
test_in_args.in_place = True
test_in_args.trees[0] = temp_file.path
tester = Pb.PhyloBuddy(temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File over-written at:" in err
check_file = os.path.isfile("%s.nex" % temp_file.path)
assert check_file
test_in_args.trees[0] = "%s.nex" % temp_file.path
test_in_args.screw_formats = "newick"
tester = Pb.PhyloBuddy("%s.nex" % temp_file.path)
Pb.command_line_ui(test_in_args, tester, skip_exit=True)
out, err = capsys.readouterr()
assert "File over-written at:" in err
check_file = os.path.isfile("%s.nwk" % temp_file.path)
assert check_file
def test_screw_formats_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "nexus"
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "543d2fc90ca1f391312d6b8fe896c59c"
def test_root_ui_midpoint(capsys):
test_in_args = deepcopy(in_args)
test_in_args.root = [[]]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "25ea14c2e89530a0fb48163c0ef2a102"
def test_rename_ids_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.rename_ids = ['Mle', 'Phylo']
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "6843a620b725a3a0e0940d4352f2036f"
def test_unroot_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.unroot = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(resource("figtree.nexus")), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "10e9024301b3178cdaed0b57ba33f615"
def test_num_tips_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.num_tips = True
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "f43920f4df66e76fbacae4af178eeebb"
def test_print_trees_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.print_trees = True
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "fe340117cb8f573100c00fc897e6c8ce"
def test_stdout(capsys):
Pb._stdout("Hello std_out", quiet=False)
out, err = capsys.readouterr()
assert out == "Hello std_out"
Pb._stdout("Hello std_out", quiet=True)
out, err = capsys.readouterr()
assert out == ""
def test_stderr(capsys):
Pb._stderr("Hello std_err", quiet=False)
out, err = capsys.readouterr()
assert err == "Hello std_err"
Pb._stderr("Hello std_err", quiet=True)
out, err = capsys.readouterr()
assert err == ""
def test_show_unique():
tester = Pb.PhyloBuddy(resource("compare_trees.newick"))
Pb.show_unique(tester)
assert phylo_to_hash(tester) == "ea5b0d1fcd7f39cb556c0f5df96281cf"
with pytest.raises(AssertionError): # If only a single tree is present
tester = Pb.PhyloBuddy(Pb.make_copy(pb_objects[0]))
Pb.show_unique(tester)
def test_print_trees_internal_ui(capsys):
# Most of this function is covered repeatedly below, so just test the -t flag
test_in_args = deepcopy(in_args)
test_in_args.test = True
test_in_args.unroot = True
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert err == "*** Test passed ***\n"
def test_generate_tree_ui2():
test_in_args = deepcopy(in_args)
test_in_args.in_format, test_in_args.out_format = "nexus", "newick"
test_in_args.trees = [resource("Mnemiopsis_cds.nex")]
test_in_args.generate_tree = [["fasttree", "-s 12345"]] # Command doesn't exist in fasttree
with pytest.raises(SystemExit):
Pb.command_line_ui(test_in_args, [])
def test_generate_tree_ui3():
test_in_args = deepcopy(in_args)
test_in_args.in_format, test_in_args.out_format = "nexus", "newick"
test_in_args.trees = [resource("Mnemiopsis_cds.nex")]
test_in_args.generate_tree = [["foo"]]
with pytest.raises(SystemExit):
Pb.command_line_ui(test_in_args, [])
def test_phyml_inputs():
# Nucleotide
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'phyml', '-m GTR --r_seed 12345')
assert phylo_to_hash(tester) == 'd3a4e7601998885f333ddd714ca764db'
# Peptide
tester = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(tester, 'phyml', '-m Blosum62 --r_seed 12345')
assert phylo_to_hash(tester) == '52c7d028341b250bcc867d57a68c794c'
def test_split_polytomies():
tester = Pb.PhyloBuddy('(A,(B,C,D));')
Pb.split_polytomies(tester)
assert str(tester) in ['(A:1.0,(B:1.0,(C:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(B:1.0,(D:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(B:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(D:1.0,B:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(B:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(C:1.0,B:1.0):1e-06):1.0):1.0;\n']
def test_in_place_ui(capsys):
# Some of this function is covered below, so just test an edge
test_in_args = deepcopy(in_args)
test_in_args.in_place = True
test_in_args.trees = [Pb.make_copy(pb_objects[0])]
test_in_args.screw_formats = "nexus"
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert "Warning: The -i flag was passed in, but the positional" in err
def test_generate_tree_ui1(capsys):
test_in_args = deepcopy(in_args)
test_in_args.in_format, test_in_args.out_format = "nexus", "newick"
test_in_args.trees = [resource("Mnemiopsis_cds.nex")]
test_in_args.generate_tree = [["fasttree", "-seed 12345"]]
Pb.command_line_ui(test_in_args, [], skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "d7f505182dd1a1744b45cc326096f70c"
def test_raxml_inputs():
# Nucleotide
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'raxml')
assert phylo_to_hash(tester) == '706ba436f8657ef3aee7875217dd07c0'
# Peptide
tester = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(tester, 'raxml')
assert phylo_to_hash(tester) == 'fc35569091eeba49ac4dcec7fc6890bf'
def test_argparse_init(capsys):
sys.argv = ['PhyloBuddy.py', resource("compare_trees.newick")]
temp_in_args, phylobuddy = Pb.argparse_init()
assert string2hash(str(phylobuddy)) == "d8e14a2bfc8e9c0ac3c524f5fb478c67"
sys.argv += ["-f", "foo"]
with pytest.raises(SystemExit):
Pb.argparse_init()
out, err = capsys.readouterr()
assert "Error: The format 'foo' passed in with the -f flag is not recognized." in err
def test_fasttree_inputs():
temp_dir = MyFuncs.TempDir()
# Nucleotide
alignbuddy = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(alignbuddy, 'fasttree', '-seed 12345')
assert phylo_to_hash(tester) == 'd7f505182dd1a1744b45cc326096f70c'
alignbuddy = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(alignbuddy, 'fasttree', '-seed 12345', keep_temp="%s/new_dir" % temp_dir.path)
assert phylo_to_hash(tester) == '57eace9bdd2074297cbd2692c1f4cd38'
def test_split_polytomies_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.split_polytomies = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(Pb.PhyloBuddy('(A,(B,C,D));')), skip_exit=True)
out, err = capsys.readouterr()
assert out in ['(A:1.0,(B:1.0,(C:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(B:1.0,(D:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(B:1.0,D:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(C:1.0,(D:1.0,B:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(B:1.0,C:1.0):1e-06):1.0):1.0;\n',
'(A:1.0,(D:1.0,(C:1.0,B:1.0):1e-06):1.0):1.0;\n']
def test_show_unique_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.show_unique = True
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy(resource("compare_trees.newick")), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "ea5b0d1fcd7f39cb556c0f5df96281cf"
with pytest.raises(SystemExit):
Pb.command_line_ui(test_in_args, pb_resources.get_one("m k"))
out, err = capsys.readouterr()
assert err == "AssertionError: PhyloBuddy object should have exactly 2 trees.\n"
def test_display_trees_ui(capsys, monkeypatch):
test_in_args = deepcopy(in_args)
test_in_args.display_trees = True
show = mock.Mock(return_value=True)
monkeypatch.setattr(ete3.TreeNode, "show", show)
Pb.command_line_ui(test_in_args, pb_resources.get_one("o k"), skip_exit=True)
# noinspection PyUnresolvedReferences
with mock.patch.dict('os.environ'):
del os.environ['DISPLAY']
Pb.command_line_ui(test_in_args, pb_resources.get_one("o k"), skip_exit=True)
out, err = capsys.readouterr()
assert "Error: Your system is non-graphical, so display_trees can not work." in err
def get(self, code="", mode="objs"):
"""
Returns copies of PhyloBuddy objects, the
:param code:
:param mode: {"objs", "paths"}
:return: OrderedDict {key: resource}
"""
files = self._parse_code(code)
output = OrderedDict()
key = ["", ""]
for num_aligns in files["num_trees"]:
key[0] = num_aligns
n = self.code_dict["num_trees"][num_aligns]
for _format in files["format"]:
key[1] = _format
f = self.code_dict["format"][_format]
try:
assert not " ".join(key) in output
if mode == "objs":
output[" ".join(key)] = Pb.make_copy(self.pb_objs[n][f])
elif mode == "paths":
output[" ".join(key)] = self.res_paths[n][f]
else:
raise ValueError("The 'mode' parameter only accepts 'objs' or 'paths' as input.")
except KeyError:
pass
return output
def test_generate_trees_edge_cases():
temp_file = MyFuncs.TempFile()
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
with pytest.raises(FileExistsError):
Pb.generate_tree(tester, "raxml", keep_temp=temp_file.path)
with pytest.raises(AttributeError):
Pb.generate_tree(tester, "foo")
with pytest.raises(FileNotFoundError):
Pb.generate_tree(tester, "raxml", "-m BINCATLG")
with pytest.raises(RuntimeError):
Pb.generate_tree(tester, "fasttree", "-s 12345")
# noinspection PyUnresolvedReferences
with mock.patch.dict(os.environ, {"PATH": ""}):
with pytest.raises(ProcessLookupError):
Pb.generate_tree(tester, "raxml")
def test_distance_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.distance = [False]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "7a9f9902ef30ca3d7ac97b63cfdd0b2e"
test_in_args.distance = ["uwrf"]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "6e520f6911aabdf91dfd075d1545bc1e"
test_in_args.distance = ["ed"]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "f0acdd9c751bce77fe14355cc77b69cc"
def test_consensus_tree_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.consensus_tree = [False]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "f20cbd5aae5971cce8efbda15e4e0b7e"
test_in_args.consensus_tree = [0.9]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "447862ed1ed6e98f2fb535ecce70218b"
test_in_args.consensus_tree = [1.5]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "f20cbd5aae5971cce8efbda15e4e0b7e"
def test_root_leaf(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
tester = Pb.root(tester, "firSA25a")
assert hf.buddy2hash(tester) == next_hash
def test_consensus_tree(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
tester = Pb.consensus_tree(tester)
assert hf.buddy2hash(tester) == next_hash, tester.write("error_files%s%s" % (next_hash, os.path.sep))
def test_distance_ed(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
output = str(Pb.distance(tester, method='ed'))
assert hf.string2hash(output) == next_hash, print(output)
def test_raxml(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
root, dirs, files = next(os.walk("%smock_resources%stest_raxml_inputs" % (RES_PATH, os.path.sep)))
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file), "%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml')
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-w path{0}to{0}nowhere".format(os.path.sep), quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("o p n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml-HPC', tmp_dir.path, quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# bootstraps
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-b 1234 -N 4", quiet=True)
assert hf.buddy2hash(tester) == "b8a3b6068aa06bd8a70fcc9bda0efad9", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester, 'raxml', keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(kept_output) == "7f2fdfe55dbe805bd994f3f56c79bb1b"
else:
assert hf.string2hash(kept_output) == "393353fb47861460aecaefa69a6ec55c"
# multi-run
os.remove("%s%sRAxML_bestTree.result" % (mock_tmp_dir.path, os.path.sep))
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-N 3", quiet=True)
assert hf.buddy2hash(tester) == "e8ce19bba744f0188df2ebb4ffced4d8", tester.write("temp.del")
# bipartitions
shutil.copy("{0}mock_resources{1}test_raxml_inputs{1}bipartitions{1}RAxML_bipartitions.result".format(RES_PATH,
os.path.sep),
"%s%s" % (mock_tmp_dir.path, os.path.sep))
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-f b -z {0}{1}RAxML_bootstrap.result "
"-t {0}{1}RAxML_bestTree.result".format(tmp_dir.path, os.path.sep))
assert hf.buddy2hash(tester) == "457533ada8e987fd0c50a41aabe1700b"
def test_hash_ids(pb_resources, hf):
for phylobuddy in pb_resources.get_list("m o k n l"):
orig_hash = hf.buddy2hash(phylobuddy)
Pb.hash_ids(phylobuddy)
assert hf.buddy2hash(phylobuddy) != orig_hash
def test_list_ids(key, next_hash, pb_resources, hf):
tester = str(Pb.list_ids(pb_resources.get_one(key)))
assert hf.string2hash(tester) == next_hash
def test_prune_taxa(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
Pb.prune_taxa(tester, 'fir')
assert hf.buddy2hash(tester) == next_hash
def test_rename_ids(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
tester = Pb.rename(tester, 'Mle', 'Phylo')
assert hf.buddy2hash(tester) == next_hash
def test_rename_nodes(pb_odd_resources, hf):
tester = Pb.PhyloBuddy(pb_odd_resources["node_lables"])
Pb.rename(tester, "Equus|Ruminantiamorpha|Canis", "Family")
assert hf.buddy2hash(tester) == "46ba6ce0f3a1859b4c7326a6f5e69263"
def test_root_middle(key, next_hashes, pb_resources, hf):
tester = pb_resources.get_one(key)
tester = Pb.root(tester)
assert hf.buddy2hash(tester) in next_hashes
def test_root_mrca1(key, next_hash, pb_resources, hf):
tester = pb_resources.get_one(key)
tester = Pb.root(tester, "ovi47[ab]", "penIT11b")
assert hf.buddy2hash(tester) == next_hash
