本文整理汇总了Python中PhyloBuddy.make_copy方法的典型用法代码示例。如果您正苦于以下问题：Python PhyloBuddy.make_copy方法的具体用法？Python PhyloBuddy.make_copy怎么用？Python PhyloBuddy.make_copy使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类PhyloBuddy的用法示例。
在下文中一共展示了PhyloBuddy.make_copy方法的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_in_place_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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示例2: test_prune_taxa_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
def test_prune_taxa_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.prune_taxa = [["fir"]]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "99635c6dbf708f94cf4dfdca87113c44"
test_in_args.prune_taxa = [["fir", "ovi"]]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[1]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "2a385fa95024323fea412fd2b3c3e91f"示例3: test_root_ui_midpoint
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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"
test_in_args.root = [[True]]
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4: get
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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示例5: test_root_ui_mrca
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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6: test_rename_ids_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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7: test_root_ui_leaf
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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8: test_print_trees_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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9: test_distance_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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"示例10: test_screw_formats_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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11: test_consensus_tree_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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"示例12: test_print_trees_internal_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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"示例13: test_list_ids_ui
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
def test_list_ids_ui(capsys):
test_in_args = deepcopy(in_args)
test_in_args.list_ids = [True]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "4f0857e0211ff0cd058d0cf7cbaf64d5"
test_in_args.list_ids = [4]
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
out, err = capsys.readouterr()
assert string2hash(out) == "bf2fbfe1bd52e9b27ae21f5c06e7763a"
test_in_args.list_ids = [4]
Pb.command_line_ui(test_in_args, Pb.PhyloBuddy("(, );"), skip_exit=True)
out, err = capsys.readouterr()
assert out == "#### tree_1 ####\nNone\n\n"示例14: test_show_unique
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
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15: test_screw_formats_fail
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import make_copy [as 别名]
def test_screw_formats_fail(capsys):
test_in_args = deepcopy(in_args)
test_in_args.screw_formats = "foo"
Pb.command_line_ui(test_in_args, Pb.make_copy(pb_objects[0]), skip_exit=True)
foo_out, foo_err = capsys.readouterr()
assert foo_err == "Error: unknown format 'foo'\n"