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Python builder.AtomicCmdBuilder类代码示例

本文整理汇总了Python中pypeline.atomiccmd.builder.AtomicCmdBuilder的典型用法代码示例。如果您正苦于以下问题:Python AtomicCmdBuilder类的具体用法?Python AtomicCmdBuilder怎么用?Python AtomicCmdBuilder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AtomicCmdBuilder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_builder__set_kwargs__after_finalize

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)
开发者ID:CarlesV,项目名称:paleomix,代码行数:7,代码来源:builder_test.py

示例2: _bowtie2_template

def _bowtie2_template(call, prefix, iotype = "IN", **kwargs):
    params = AtomicCmdBuilder(call, **kwargs)
    for postfix in ("1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"):
        key = "%s_PREFIX_%s" % (iotype, postfix.upper())
        params.set_kwargs(**{key : (prefix + "." + postfix)})

    return params
开发者ID:CarlesV,项目名称:paleomix,代码行数:7,代码来源:bowtie2.py

示例3: _do_test_builder__pop_option

 def _do_test_builder__pop_option(setter):
     builder = AtomicCmdBuilder("find")
     setter(builder, "-empty", fixed = False)
     setter(builder, "-size", "1", fixed = False)
     setter(builder, "-name", "*.txt", fixed = False)
     builder.pop_option("-size")
     assert_equal(builder.call, ["find", "-empty", "-name", "*.txt"])
开发者ID:CarlesV,项目名称:paleomix,代码行数:7,代码来源:builder_test.py

示例4: _get_common_parameters

def _get_common_parameters(version):
    global _DEPRECATION_WARNING_PRINTED

    if version == VERSION_14:
        version_check = _VERSION_14_CHECK
    elif version == VERSION_15:
        version_check = _VERSION_15_CHECK
    else:
        raise CmdError("Unknown version: %s" % version)

    cmd = AtomicCmdBuilder("AdapterRemoval",
                           CHECK_VERSION=version_check)

    # Trim Ns at read ends
    cmd.set_option("--trimns", fixed=False)
    # Trim low quality scores
    cmd.set_option("--trimqualities", fixed=False)

    try:
        if not _DEPRECATION_WARNING_PRINTED and version_check.version < (2, 0):
            import pypeline.ui as ui
            ui.print_warn("\nWARNING: AdapterRemoval v1.5.x is deprecated;")
            ui.print_warn("         Upgrading to 2.1.x is strongly adviced!\n")
            ui.print_warn("         Download the newest version of AdapterRemoval at ")
            ui.print_warn("         https://github.com/MikkelSchubert/adapterremoval\n")

            _DEPRECATION_WARNING_PRINTED = True
    except versions.VersionRequirementError:
        pass

    return cmd
开发者ID:UMNPonyClub,项目名称:paleomix,代码行数:31,代码来源:adapterremoval.py

示例5: customize

    def customize(cls, input_file, output_file, algorithm = "auto", dependencies = ()):
        command = AtomicCmdBuilder(_PRESETS[algorithm.lower()])
        command.add_value("%(IN_FASTA)s")
        command.set_kwargs(IN_FASTA   = input_file,
                           OUT_STDOUT = output_file,
                           CHECK_VERSION = MAFFT_VERSION)

        return {"command"      : command,
                "dependencies" : dependencies}
开发者ID:CarlesV,项目名称:paleomix,代码行数:9,代码来源:mafft.py

示例6: customize

    def customize(cls, infile, intervals, outfile, dependencies = ()):
        params = AtomicCmdBuilder(["bam_sample_regions"],
                                  IN_PILEUP    = infile,
                                  IN_INTERVALS = intervals,
                                  OUT_STDOUT   = outfile)
        params.set_option("--genotype", "%(IN_PILEUP)s")
        params.set_option("--intervals", "%(IN_INTERVALS)s")

        return {"command" : params}
开发者ID:schae234,项目名称:pypeline,代码行数:9,代码来源:genotype.py

示例7: test_builder__add_multiple_values

def test_builder__add_multiple_values():
    values = ("file_a", "file_b")
    expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}

    builder = AtomicCmdBuilder("ls")
    kwargs = builder.add_multiple_values(values)

    assert_equal(kwargs, expected)
    assert_equal(builder.kwargs, expected)
    assert_equal(builder.call, ["ls", "%(IN_FILE_01)s", "%(IN_FILE_02)s"])
开发者ID:CarlesV,项目名称:paleomix,代码行数:10,代码来源:builder_test.py

示例8: test_builder__add_multiple_values_with_template

def test_builder__add_multiple_values_with_template():
    values = ("file_a", "file_b")
    expected = {"OUT_BAM_1": "file_a", "OUT_BAM_2": "file_b"}

    builder = AtomicCmdBuilder("ls")
    kwargs = builder.add_multiple_values(values, template="OUT_BAM_%i")

    assert_equal(kwargs, expected)
    assert_equal(builder.kwargs, expected)
    assert_equal(builder.call, ["ls", "%(OUT_BAM_1)s", "%(OUT_BAM_2)s"])
开发者ID:CarlesV,项目名称:paleomix,代码行数:10,代码来源:builder_test.py

示例9: test_builder__add_multiple_options_with_sep

def test_builder__add_multiple_options_with_sep():
    values = ("file_a", "file_b")
    expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}

    builder = AtomicCmdBuilder("ls")
    kwargs = builder.add_multiple_options("-i", values, sep="=")

    assert_equal(kwargs, expected)
    assert_equal(builder.kwargs, expected)
    assert_equal(builder.call, ["ls", "-i=%(IN_FILE_01)s", "-i=%(IN_FILE_02)s"])
开发者ID:UMNPonyClub,项目名称:paleomix,代码行数:10,代码来源:builder_test.py

示例10: test_builder__add_multiple_options_with_template_fixed

def test_builder__add_multiple_options_with_template_fixed():
    values = ("file_a", "file_b")
    expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}

    builder = AtomicCmdBuilder("ls")
    kwargs = builder.add_multiple_options("-i", values)

    assert_equal(kwargs, expected)
    assert_equal(builder.kwargs, expected)
    assert_raises(AtomicCmdBuilderError,
                  builder.add_multiple_options, "-i", values)
开发者ID:health1987,项目名称:paleomix,代码行数:11,代码来源:builder_test.py

示例11: test_builder__add_multiple_options_multiple_times

def test_builder__add_multiple_options_multiple_times():
    expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}

    builder = AtomicCmdBuilder("ls")
    kwargs = builder.add_multiple_options("-i", ("file_a",))
    assert_equal(kwargs, {"IN_FILE_01": "file_a"})
    kwargs = builder.add_multiple_options("-i", ("file_b",))
    assert_equal(kwargs, {"IN_FILE_02": "file_b"})

    assert_equal(builder.kwargs, expected)
    assert_equal(builder.call, ["ls", "-i", "%(IN_FILE_01)s", "-i", "%(IN_FILE_02)s"])
开发者ID:UMNPonyClub,项目名称:paleomix,代码行数:11,代码来源:builder_test.py

示例12: _get_bwa_template

def _get_bwa_template(call, prefix, iotype = "IN", **kwargs):
    extensions = ["amb", "ann", "bwt", "pac", "sa"]
    try:
        if BWA_VERSION.version < (0, 6, 0):
            extensions.extend(("rbwt", "rpac", "rsa"))
    except versions.VersionRequirementError:
        pass # Ignored here, handled elsewhere

    params = AtomicCmdBuilder(call, **kwargs)
    for postfix in extensions:
        key = "%s_PREFIX_%s" % (iotype, postfix.upper())
        params.set_kwargs(**{key : (prefix + "." + postfix)})

    return params
开发者ID:schae234,项目名称:pypeline,代码行数:14,代码来源:bwa.py

示例13: _get_common_parameters

def _get_common_parameters(version):
    if version == VERSION_14:
        version_check = _VERSION_14_CHECK
    elif version == VERSION_15:
        version_check = _VERSION_15_CHECK
    else:
        raise CmdError("Unknown version: %s" % version)

    cmd = AtomicCmdBuilder("AdapterRemoval",
                           CHECK_VERSION=version_check)

    # Trim Ns at read ends
    cmd.set_option("--trimns", fixed=False)
    # Trim low quality scores
    cmd.set_option("--trimqualities", fixed=False)

    return cmd
开发者ID:CarlesV,项目名称:paleomix,代码行数:17,代码来源:adapterremoval.py

示例14: test_builder__finalize__calls_atomiccmd

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("pypeline.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
开发者ID:CarlesV,项目名称:paleomix,代码行数:17,代码来源:builder_test.py

示例15: customize

    def customize(cls, input_alignment, output_tree, dependencies = ()):
        """
        Arguments:
        input_alignment  -- An alignment file in a format readable by RAxML.
        output_tree      -- Filename for the output newick tree."""

        command = AtomicCmdBuilder("parsimonator", set_cwd = True)

        command.set_option("-s", "%(TEMP_OUT_ALN)s")
        command.set_option("-n", "output")
        # Random seed for the stepwise addition process
        command.set_option("-p", int(random.random() * 2**31 - 1), fixed = False)

        command.set_kwargs(# Auto-delete: Symlinks
                          TEMP_OUT_ALN   = os.path.basename(input_alignment),

                          # Input files, are not used directly (see below)
                          IN_ALIGNMENT    = input_alignment,

                          # Final output file, are not created directly
                          OUT_TREE       = output_tree)

        return {"command"         : command}
开发者ID:health1987,项目名称:paleomix,代码行数:23,代码来源:examl.py


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