Python AtomicCmdBuilder.add_value方法代码示例

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [as 别名]
    def customize(cls, reference, infile, outfile, regions = None, dependencies = ()):
        assert outfile.lower().endswith(".vcf.bgz")

        pileup = AtomicCmdBuilder(["samtools", "mpileup"],
                              IN_REFERENCE = reference,
                              IN_BAMFILE   = infile,
                              IN_REGIONS   = regions,
                              OUT_STDOUT   = AtomicCmd.PIPE,
                              CHECK_SAM    = SAMTOOLS_VERSION)
        pileup.set_option("-u") # Uncompressed output
        pileup.set_option("-f", "%(IN_REFERENCE)s")
        pileup.add_value("%(IN_BAMFILE)s")

        if regions:
            pileup.set_option("-l", "%(IN_REGIONS)s")

        genotype = AtomicCmdBuilder(["bcftools", "view"],
                                IN_STDIN     = pileup,
                                OUT_STDOUT   = AtomicCmd.PIPE)
        genotype.add_value("-")

        bgzip    = AtomicCmdBuilder(["bgzip"],
                                IN_STDIN     = genotype,
                                OUT_STDOUT   = outfile)

        return {"commands" : {"pileup"   : pileup,
                              "genotype" : genotype,
                              "bgzip"    : bgzip}}

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [as 别名]
    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}

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [as 别名]
    def customize(cls, reference, in_bam, in_vcf, outfile, dependencies = ()):
        unicat = AtomicCmdBuilder(["unicat", "%(IN_VCF)s"],
                                  IN_VCF     = in_vcf,
                                  OUT_STDOUT = AtomicCmd.PIPE)

        vcfpileup = AtomicCmdBuilder(["vcf_create_pileup", "%(OUT_PILEUP)s"],
                                     IN_REF       = reference,
                                     IN_BAM       = in_bam,
                                     IN_STDIN     = unicat,
                                     OUT_PILEUP   = outfile,
                                     OUT_TBI      = outfile + ".tbi")
        vcfpileup.add_value("%(IN_BAM)s")
        vcfpileup.set_option("-f", "%(IN_REF)s")

        return {"commands" : {"unicat" : unicat,
                              "pileup" : vcfpileup}}

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [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("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

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [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 pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [as 别名]
def _process_output(stdin, output_file, reference, run_fixmate = False):
    convert = AtomicCmdBuilder("safeSAM2BAM")
    convert.set_option("--flag-as-sorted")
    convert.set_option("-F", "0x4", sep = "", fixed = False) # Remove misses
    convert.set_kwargs(IN_STDIN    = stdin,
                      OUT_STDOUT  = AtomicCmd.PIPE,
                      CHECK_PYSAM = PYSAM_VERSION,
                      CHECK_SAMTOOLS = SAMTOOLS_VERSION)

    fixmate = None
    if run_fixmate:
        fixmate = AtomicCmdBuilder(("samtools", "fixmate", "-", "-"),
                               IN_STDIN   = convert,
                               OUT_STDOUT = AtomicCmd.PIPE,
                               CHECK_SAMTOOLS = SAMTOOLS_VERSION)

    sort = AtomicCmdBuilder(("samtools", "sort"))
    sort.set_option("-o") # Output to STDOUT on completion
    sort.add_value("-")
    sort.add_value("%(TEMP_OUT_BAM)s")
    sort.set_kwargs(IN_STDIN     = fixmate or convert,
                   OUT_STDOUT   = AtomicCmd.PIPE,
                   TEMP_OUT_BAM = "sorted",
                   CHECK_SAM = SAMTOOLS_VERSION)

    calmd = AtomicCmdBuilder(("samtools", "calmd"))
    calmd.add_value("-")
    calmd.add_value("%(IN_REF)s")
    calmd.set_option("-b") # Output BAM
    calmd.set_kwargs(IN_REF   = reference,
                    IN_STDIN = sort,
                    OUT_STDOUT = output_file,
                    CHECK_SAM = SAMTOOLS_VERSION)

    order = ["convert", "sort", "calmd"]
    commands = {"convert" : convert,
                "sort"    : sort,
                "calmd"   : calmd}

    if run_fixmate:
        order.insert(1, "fixmate")
        commands["fixmate"] = fixmate

    return order, commands

# 需要导入模块: from pypeline.atomiccmd.builder import AtomicCmdBuilder [as 别名]
# 或者: from pypeline.atomiccmd.builder.AtomicCmdBuilder import add_value [as 别名]
def test_builder__add_value__two_values():
    builder = AtomicCmdBuilder("ls")
    builder.add_value("%(IN_FILE)s")
    builder.add_value("%(OUT_FILE)s")
    assert_equal(builder.call, ["ls", "%(IN_FILE)s", "%(OUT_FILE)s"])