本文整理汇总了Python中PhyloBuddy类的典型用法代码示例。如果您正苦于以下问题：Python PhyloBuddy类的具体用法？Python PhyloBuddy怎么用？Python PhyloBuddy使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了PhyloBuddy类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_screw_formats_inplace_ui
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示例2: test_unroot_ui
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"示例3: test_show_unique
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)示例4: test_split_polytomies
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']示例5: test_screw_formats_ui
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"示例6: test_root_ui_mrca
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"示例7: test_num_tips_ui
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"示例8: test_rename_ids_ui
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"示例9: test_root_ui_leaf
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"示例10: test_root_ui_midpoint
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"示例11: test_screw_formats_ui
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"示例12: test_print_trees_ui
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"示例13: test_generate_tree_ui3
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, [])示例14: test_generate_tree_ui2
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, [])示例15: test_print_trees_internal_ui
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"