本文整理汇总了Python中paleomix.atomiccmd.builder.AtomicCmdBuilder.finalize方法的典型用法代码示例。如果您正苦于以下问题：Python AtomicCmdBuilder.finalize方法的具体用法？Python AtomicCmdBuilder.finalize怎么用？Python AtomicCmdBuilder.finalize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paleomix.atomiccmd.builder.AtomicCmdBuilder的用法示例。
在下文中一共展示了AtomicCmdBuilder.finalize方法的5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_builder__set_kwargs__after_finalize
# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import finalize [as 别名]
def test_builder__set_kwargs__after_finalize():
expected = {"IN_PATH": "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH="/a/b/")
builder.finalize()
assert_raises(AtomicCmdBuilderError, builder.set_kwargs, OUT_PATH="/dst/file")
assert_equal(builder.kwargs, expected)示例2: test_builder__finalize__calls_atomiccmd
# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import finalize [as 别名]
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args, (["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"],))
assert_equal(kwargs, {"IN_FILE": "/in/file",
"OUT_FILE": "/out/file",
"set_cwd": True})
was_called.append(True)
with Monkeypatch("paleomix.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd=True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE="/out/file",
IN_FILE="/in/file")
builder.finalize()
assert was_called示例3: __init__
# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import finalize [as 别名]
def __init__(self, input_file, k_groups, output_root,
samples=None, dependencies=()):
self._samples = samples
self._input_file = input_file
self._k_groups = k_groups
group_key = "Group(%i)" % (self._k_groups,)
self._supervised = samples and any((row[group_key] != '-')
for row in samples.itervalues())
assert k_groups in (2, 3), k_groups
prefix = os.path.splitext(os.path.basename(input_file))[0]
output_prefix = os.path.join(output_root,
"%s.%i" % (prefix, k_groups))
cmd = AtomicCmdBuilder("admixture",
IN_FILE_BED=input_file,
IN_FILE_BIM=fileutils.swap_ext(input_file,
".bim"),
IN_FILE_FAM=fileutils.swap_ext(input_file,
".fam"),
TEMP_OUT_FILE_BED=prefix + ".bed",
TEMP_OUT_FILE_BIM=prefix + ".bim",
TEMP_OUT_FILE_FAM=prefix + ".fam",
TEMP_OUT_FILE_POP=prefix + ".pop",
OUT_P=output_prefix + ".P",
OUT_Q=output_prefix + ".Q",
OUT_STDOUT=output_prefix + ".log",
CHECK_VERSION=ADMIXTURE_VERSION,
set_cwd=True)
cmd.set_option("-s", random.randint(0, 2 ** 16 - 1))
if self._supervised:
cmd.set_option("--supervised")
cmd.add_value("%(TEMP_OUT_FILE_BED)s")
cmd.add_value(int(k_groups))
CommandNode.__init__(self,
description="<Admixture -> '%s.*''>"
% (output_prefix,),
command=cmd.finalize(),
dependencies=dependencies)示例4: test_builder__finalize__returns_singleton
# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import finalize [as 别名]
def test_builder__finalize__returns_singleton():
builder = AtomicCmdBuilder("echo")
assert builder.finalize() is builder.finalize()示例5: _do_test_builder__add_or_set_option__after_finalize
# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import finalize [as 别名]
def _do_test_builder__add_or_set_option__after_finalize(setter):
builder = AtomicCmdBuilder("find")
builder.finalize()
assert_raises(AtomicCmdBuilderError, setter, builder, "-size", "1")