Python AtomicCmdBuilder.set_option方法代码示例

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
    def customize(cls, input_alignment, input_partition, output_alignment, output_partition, dependencies = ()):
        command = AtomicCmdBuilder("raxmlHPC")

        # Read and (in the case of empty columns) reduce input
        command.set_option("-f", "c")
        # Output files are saved with a .Pypeline postfix, and subsequently renamed
        command.set_option("-n", "Pypeline")
        # Model required, but not used
        command.set_option("-m", "GTRGAMMA")
        # Ensures that output is saved to the temporary directory
        command.set_option("-w", "%(TEMP_DIR)s")

        # Symlink to sequence and partitions, to prevent the creation of *.reduced files outside temp folder
        # In addition, it may be nessesary to remove the .reduced files if created
        command.set_option("-s", "%(TEMP_IN_ALIGNMENT)s")
        command.set_option("-q", "%(TEMP_IN_PARTITION)s")

        command.set_kwargs(IN_ALIGNMENT      = input_alignment,
                          IN_PARTITION      = input_partition,

                          TEMP_IN_ALIGNMENT = "RAxML_alignment",
                          TEMP_IN_PARTITION = "RAxML_partitions",
                          TEMP_OUT_INFO     = "RAxML_info.Pypeline",

                          OUT_ALIGNMENT     = output_alignment,
                          OUT_PARTITION     = output_partition,
                          CHECK_VERSION     = RAXML_VERSION)

        return {"command" : command}

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
    def customize(cls, input_alignment, input_partition, output_file, dependencies = ()):
        """
        Arguments:
        input_alignment  -- An alignment file in a format readable by RAxML.
        input_partition  -- A set of partitions in a format readable by RAxML.
        output_filename  -- Filename for the output binary sequence."""

        command = AtomicCmdBuilder("parse-examl", set_cwd = True)

        command.set_option("-s", "%(TEMP_OUT_ALN)s")
        command.set_option("-q", "%(TEMP_OUT_PART)s")
        # Output file will be named output.binary, and placed in the CWD
        command.set_option("-n", "output")

        # Substitution model
        command.set_option("-m", "DNA", fixed = False)


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

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

                          # Final output file, are not created directly
                          OUT_BINARY      = output_file,

                          CHECK_EXAML     = PARSER_VERSION)

        return {"command" : command}

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [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)

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
    def __init__(self, config, reference, input_bam, output_bam, tags,
                 min_mapq=0, filter_unmapped=False, dependencies=()):
        flt_params = AtomicCmdBuilder(("samtools", "view", "-bu"),
                                      IN_BAM=input_bam,
                                      OUT_STDOUT=AtomicCmd.PIPE)

        if min_mapq:
            flt_params.set_option("-q", min_mapq, sep="")
        if filter_unmapped:
            flt_params.set_option("-F", "0x4", sep="")

        flt_params.add_value("%(IN_BAM)s")

        jar_params = picard.picard_command(config, "AddOrReplaceReadGroups")
        jar_params.set_option("INPUT", "/dev/stdin", sep="=")
        # Output is written to a named pipe, since the JVM may, in some cases,
        # emit warning messages to stdout, resulting in a malformed BAM.
        jar_params.set_option("OUTPUT", "%(TEMP_OUT_BAM)s", sep="=")
        jar_params.set_option("COMPRESSION_LEVEL", "0", sep="=")
        # Ensure that the BAM is sorted; this is required by the pipeline, and
        # needs to be done before calling calmd (avoiding pathologic runtimes).
        jar_params.set_option("SORT_ORDER", "coordinate", sep="=")

        # All tags are overwritten; ID is set since the default (e.g. '1')
        # causes problems with pysam due to type inference (is read as a length
        # 1 string, but written as a character).
        for tag in ("ID", "SM", "LB", "PU", "PL"):
            jar_params.set_option(tag, tags[tag], sep="=")

        jar_params.set_kwargs(IN_STDIN=flt_params,
                              TEMP_OUT_BAM="bam.pipe")

        calmd = AtomicCmdBuilder(["samtools", "calmd", "-b",
                                 "%(TEMP_IN_BAM)s", "%(IN_REF)s"],
                                 IN_REF=reference,
                                 TEMP_IN_BAM="bam.pipe",
                                 OUT_STDOUT=output_bam)

        commands = [cmd.finalize() for cmd in (flt_params, jar_params, calmd)]
        description = "<Cleanup BAM: %s -> '%s'>" \
            % (input_bam, output_bam)
        PicardNode.__init__(self,
                            command=ParallelCmds(commands),
                            description=description,
                            dependencies=dependencies)

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
def test_builder__set_option__overwrite_fixed():
    builder = AtomicCmdBuilder("find")
    builder.set_option("-name", "*.txt")
    assert_raises(AtomicCmdBuilderError, builder.set_option, "-name", "*.bat")

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
def test_builder__set_option__overwrite():
    builder = AtomicCmdBuilder("find")
    builder.set_option("-name", "*.txt", fixed=False)
    builder.set_option("-name", "*.bat")
    assert_equal(builder.call, ["find", "-name", "*.bat"])

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
def test_builder__set_option():
    builder = AtomicCmdBuilder("find")
    builder.set_option("-name", "*.txt")
    assert_equal(builder.call, ["find", "-name", "*.txt"])

# 需要导入模块: from paleomix.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from paleomix.atomiccmd.builder.AtomicCmdBuilder import set_option [as 别名]
def test_builder__pop_option__missing_key():
    builder = AtomicCmdBuilder("find")
    builder.set_option("-size", 0)
    assert_raises(KeyError, builder.pop_option, "-isize")