Example #1
0
def get_parser():
    p = get_pbparser(tool_id=Constants.TOOL_ID,
                     version=__version__,
                     name="Coverage",
                     description=__doc__,
                     driver_exe=Constants.DRIVER_EXE,
                     is_distributed=True)
    ap = p.arg_parser.parser
    p.add_input_file_type(FileTypes.DS_REF,
                          "reference",
                          name="Reference DataSet",
                          description="Reference DataSet XML or FASTA file")
    p.add_input_file_type(FileTypes.GFF,
                          "gff",
                          name="Alignment Summary GFF",
                          description="Alignment Summary GFF")
    p.add_output_file_type(FileTypes.REPORT,
                           "report_json",
                           name=meta_rpt.title,
                           description="Path to write report JSON output",
                           default_name=meta_rpt.id)
    p.add_int(
        option_id=Constants.MAX_CONTIGS_ID,
        option_str="maxContigs",
        default=Constants.MAX_CONTIGS_DEFAULT,
        name="Maximum number of contigs to plot",
        description="Maximum number of contigs to plot in coverage report")
    return p
Example #2
0
def _get_parser():
    parser = get_pbparser(TOOL_ID, __version__, "CCS Mapping Statistics", __doc__, DRIVER_EXE)

    parser.add_input_file_type(FileTypes.DS_ALIGN_CCS, "alignment_file", "ConsensusAlignment XML DataSet", "BAM, SAM or ConsensusAlignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json", "PacBio Json Report", "Output report JSON file.", "mapping_stats_report.json")

    return parser
Example #3
0
def get_contract_parser():
    """
    Central point of programmatically defining a Parser.
    :rtype: PbParser
    :return: PbParser
    """
    # Commandline exe to call "{exe}" /path/to/resolved-tool-contract.json

    driver_exe = "python -m pbcommand.cli.example.dev_app --resolved-tool-contract "
    desc = "Dev app for Testing that supports emitting tool contracts"
    subcomponents = [("my_subcomponent", "1.2.3")]

    resource_types = (ResourceTypes.TMP_FILE, ResourceTypes.TMP_FILE, ResourceTypes.TMP_DIR)

    p = get_pbparser(
        TOOL_ID,
        __version__,
        "Example Dev App",
        desc,
        driver_exe,
        is_distributed=False,
        resource_types=resource_types,
        subcomponents=subcomponents,
    )

    add_args_and_options(p)
    return p
Example #4
0
    def test_misc_parser_types(self):
        p = get_pbparser("pbcommand.tasks.test_parsers", "0.1.0", "Tool Name",
                         "Tool Descripion", "pbcommand-driver-exe ")

        p.add_int("pbcommand.task_options.n",
                  "n",
                  default=0,
                  name="N",
                  description="Integer option")

        p.add_float("pbcommand.task_options.f",
                    "f",
                    default=0,
                    name="F",
                    description="Float option")

        # XXX note that the 'default' value is not actually what the option is
        # set to by default - it simply signals that action=store_true
        p.add_boolean("pbcommand.task_options.loud",
                      "loud",
                      default=False,
                      name="Verbose",
                      description="Boolean option")

        pa = p.arg_parser.parser.parse_args

        opts = pa(["--n", "250", "--f", "1.2345", "--loud"])
        self.assertEqual(opts.n, 250)
        self.assertEqual(opts.f, 1.2345)
        self.assertTrue(opts.loud)

        opts2 = pa([])
        self.assertFalse(opts2.loud)
Example #5
0
def get_parser():
    driver_exe = "python -m pbcommand.cli.examples.dev_app --resolved-tool-contract "
    desc = "Dev app for Testing that supports emitting tool contracts"
    # Can specify libs or other dependencies that
    subcomponents = [("pbcommand", VERSION), ("my_component", "0.1.0"), ("my_component_id", "1.2.3")]
    # ResourceTypes.*
    resource_types = (ResourceTypes.TMP_FILE, ResourceTypes.TMP_FILE, ResourceTypes.TMP_DIR)

    # Create an instance of a Pacbio Parser
    p = get_pbparser(
        TOOL_ID,
        VERSION,
        "Txt App",
        desc,
        driver_exe,
        is_distributed=False,
        resource_types=resource_types,
        subcomponents=subcomponents,
    )

    # Add Input Files types
    p.add_input_file_type(FileTypes.TXT, "txt_in", "Txt file", "Generic Text File")
    # Add output files types
    p.add_output_file_type(FileTypes.TXT, "txt_out", "Txt outfile", "Generic Output Txt file", "output.txt")
    p.add_int("pbcommand.task_options.dev_max_nlines", "max_nlines", 10, "Max Lines", "Max Number of lines to Copy")
    return p
Example #6
0
def _get_parser():
    driver_exe = ("python -m "
                  "pbreports.report.polished_assembly "
                  "--resolved-tool-contract ")
    p = get_pbparser(Constants.TOOL_ID, __version__, spec.title, __doc__,
                     driver_exe)
    return _add_options_to_parser(p)
    def test_misc_parser_types(self):
        p = get_pbparser(
            "pbcommand.tasks.test_parsers",
            "0.1.0",
            "Tool Name",
            "Tool Descripion",
            "pbcommand-driver-exe ")

        p.add_int("pbcommand.task_options.n", "n", default=0, name="N",
            description="Integer option")

        p.add_float("pbcommand.task_options.f", "f", default=0, name="F",
            description="Float option")

        # XXX note that the 'default' value is not actually what the option is
        # set to by default - it simply signals that action=store_true
        p.add_boolean("pbcommand.task_options.loud", "loud", default=False,
                      name="Verbose", description="Boolean option")

        pa = p.arg_parser.parser.parse_args

        opts = pa(["--n", "250", "--f", "1.2345", "--loud"])
        self.assertEqual(opts.n, 250)
        self.assertEqual(opts.f, 1.2345)
        self.assertTrue(opts.loud)

        opts2 = pa([])
        self.assertFalse(opts2.loud)
Example #8
0
def get_parser():
    p = get_pbparser(tool_id=Constants.TOOL_ID,
                     version=__version__,
                     name=Constants.TOOL_NAME,
                     description=__doc__,
                     driver_exe=Constants.DRIVER_EXE)
    p.add_input_file_type(FileTypes.DS_SUBREADS,
                          "subreads",
                          name="BarcodedSubreadSet",
                          description="Barcoded Subread DataSet XML")
    p.add_input_file_type(FileTypes.DS_BARCODE,
                          "barcodes",
                          name="BarcodeSet",
                          description="Barcode DataSet XML")
    p.add_output_file_type(FileTypes.REPORT,
                           "report_json",
                           name="Barcode Report",
                           description="Summary of barcoding results",
                           default_name="barcode_report")
    # TODO(nechols)(2016-03-15) not yet supported in SA 3.x
    # this is necessary for BasH5Reader to handle the differences between the
    # .ccs.h5 files and .bas.h5 files.
    ap = p.arg_parser.parser
    ap.add_argument('--ccs',
                    action='store_true',
                    help='Use consensus reads instead of subreads.')
    return p
Example #9
0
def get_contract_parser():
    """
    Central point of programmatically defining a Parser.
    :rtype: PbParser
    :return: PbParser
    """
    # Commandline exe to call "{exe}" /path/to/resolved-tool-contract.json

    driver_exe = "python -m pbcommand.cli.example.dev_app --resolved-tool-contract "
    desc = "Dev app for Testing that supports emitting tool contracts"
    subcomponents = [("my_subcomponent", "1.2.3")]

    resource_types = (ResourceTypes.TMP_FILE,
                      ResourceTypes.TMP_FILE,
                      ResourceTypes.TMP_DIR)

    p = get_pbparser(TOOL_ID,
                     __version__,
                     "Example Dev App",
                     desc,
                     driver_exe,
                     is_distributed=False,
                     resource_types=resource_types,
                     subcomponents=subcomponents)

    add_args_and_options(p)
    return p
Example #10
0
def get_parser():
    p = get_pbparser(
        tool_id=Constants.TOOL_ID,
        version=__version__,
        name=Constants.TOOL_NAME,
        description=__doc__,
        driver_exe=Constants.DRIVER_EXE,
    )
    p.add_input_file_type(
        FileTypes.DS_SUBREADS, "subreads", name="BarcodedSubreadSet", description="Barcoded Subread DataSet XML"
    )
    p.add_input_file_type(FileTypes.DS_BARCODE, "barcodes", name="BarcodeSet", description="Barcode DataSet XML")
    p.add_output_file_type(
        FileTypes.REPORT,
        "report_json",
        name="Barcode report",
        description="Path to write Report json output.",
        default_name="barcode_report",
    )
    # TODO(nechols)(2016-03-15) not yet supported in SA 3.x
    # this is necessary for BasH5Reader to handle the differences between the
    # .ccs.h5 files and .bas.h5 files.
    ap = p.arg_parser.parser
    ap.add_argument("--ccs", action="store_true", help="Use consensus reads instead of subreads.")
    return p
Example #11
0
def get_contract_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        spec.title,
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    add_base_options_pbcommand(p, "Top Variants Report")
    p.add_input_file_type(FileTypes.GFF,
                          file_id="gff",
                          name="GFF file",
                          description="variants.gff (can be gzip'ed)")
    p.add_input_file_type(FileTypes.DS_REF,
                          file_id="reference",
                          name="Reference dataset",
                          description="ReferenceSet or FASTA")
    # p.add_output_file_type(FileTypes.REPORT, "report",
    #                       "JSON report", "JSON report", "report.json")
    p.add_int(Constants.HOW_MANY_ID, "how_many",
              default=Constants.HOW_MANY_DEFAULT,
              name="Number of variants",
              description="number of top variants to show (default=100)")
    p.add_int(Constants.BATCH_SORT_SIZE_ID, "batch_sort_size",
              default=Constants.BATCH_SORT_SIZE_DEFAULT,
              name="Batch sort size",
              description="Intermediate sort size parameter (default=10000)")
    # XXX do we need a flag for minor variants?
    return p
Example #12
0
def get_parser():
    p = get_pbparser(tool_id=Constants.TOOL_ID,
                     version=__version__,
                     name=Constants.TOOL_NAME,
                     description=__doc__,
                     driver_exe=Constants.DRIVER_EXE)
    p.add_input_file_type(
        FileTypes.DATASTORE,
        "ds_bc",
        name="JSON Datastore or SubreadSet or ConsensusReadSet",
        description="Datastore of barcoded SubreadSet/ConsensusReadSet files")
    p.add_input_file_type(FileTypes.DS_SUBREADS,
                          "subreads_in",
                          name="Input SubreadSet",
                          description="Input SubreadSet (without barcodes)")
    p.add_input_file_type(FileTypes.DS_BARCODE,
                          "barcodes",
                          name="BarcodeSet",
                          description="Barcode DataSet XML")
    p.add_output_file_type(FileTypes.REPORT,
                           "report_json",
                           name="Barcode Report",
                           description="Summary of barcoding results",
                           default_name="barcode_report")
    p.tool_contract_parser.add_output_file_type(
        FileTypes.CSV,
        "report_csv",
        name="Barcode Report Details",
        description="Barcode Details Table as CSV",
        default_name="barcodes_report")
    p.add_boolean(Constants.ISOSEQ_MODE, "isoseq_mode", False, "Iso-Seq mode",
                  "Iso-Seq mode")
    return p
Example #13
0
def get_parser():
    """
    Construct a hybrid PbParser with most tool contract parameters defined
    separately from argparser parameters.
    """
    p = get_pbparser(
        tool_id=Constants.TOOL_ID,
        version=__VERSION__,
        name="variantCaller",
        description="Compute genomic consensus and call variants relative to the reference.",
        driver_exe=Constants.DRIVER_EXE,
        nproc=SymbolTypes.MAX_NPROC,
        resource_types=(),
        default_level="WARN")
    tcp = p.tool_contract_parser
    tcp.add_input_file_type(FileTypes.DS_ALIGN, "infile",
        "Alignment DataSet", "BAM or Alignment DataSet")
    tcp.add_input_file_type(FileTypes.DS_REF, "reference",
        "Reference DataSet", "Fasta or Reference DataSet")
    tcp.add_output_file_type(FileTypes.GFF, "variants",
        name="Consensus GFF",
        description="Consensus GFF",
        default_name="variants")
    tcp.add_output_file_type(FileTypes.DS_CONTIG, "consensus",
        name="Consensus ContigSet",
        description="Consensus sequence in Fasta format",
        default_name="consensus")
    tcp.add_output_file_type(FileTypes.FASTQ, "consensus_fastq",
        name="Consensus fastq",
        description="Consensus fastq",
        default_name="consensus")
    tcp.add_str(
        option_id=Constants.ALGORITHM_ID,
        option_str="algorithm",
        default=Constants.DEFAULT_ALGORITHM,
        name="Algorithm",
        description="Variant calling algorithm")
    tcp.add_int(
        option_id=Constants.MIN_CONFIDENCE_ID,
        option_str="minConfidence",
        default=Constants.DEFAULT_MIN_CONFIDENCE,
        name="Minimum confidence",
        description="The minimum confidence for a variant call to be output "+\
                    "to variants.gff")
    tcp.add_int(
        option_id=Constants.MIN_COVERAGE_ID,
        option_str="minCoverage",
        default=Constants.DEFAULT_MIN_COVERAGE,
        name="Minimum coverage",
        description="The minimum site coverage that must be achieved for " +\
                    "variant calls and consensus to be calculated for a site.")

    tcp.add_boolean(
        option_id=Constants.DIPLOID_MODE_ID,
        option_str="diploid",
        default=False,
        name="Diploid mode (experimental)",
        description="Enable detection of heterozygous variants (experimental)")
    add_options_to_argument_parser(p.arg_parser.parser)
    return p
def get_parser():
    p = get_pbparser(Constants.TOOL_ID,
                     Constants.VERSION,
                     "AlignmentSet consolidate",
                     __doc__,
                     Constants.DRIVER,
                     is_distributed=True,
                     resource_types=(ResourceTypes.TMP_DIR,))

    p.add_input_file_type(FileTypes.DS_ALIGN, "align_in", "Input AlignmentSet",
                          "Gathered AlignmentSet to consolidate")
    p.add_output_file_type(FileTypes.DS_ALIGN,
                           "ds_out",
                           "Alignments",
                           description="Alignment results dataset",
                           default_name="combined")
    p.add_boolean(Constants.CONSOLIDATE_ID, "consolidate",
        default=False,
        name="Consolidate .bam",
        description="Merge chunked/gathered .bam files")
    p.add_int(Constants.N_FILES_ID, "consolidate_n_files",
        default=1,
        name="Number of .bam files",
        description="Number of .bam files to create in consolidate mode")
    return p
Example #15
0
def get_parser():
    p = get_pbparser(
        tool_id=Constants.TOOL_ID,
        version=__version__,
        name="Coverage",
        description=__doc__,
        driver_exe=Constants.DRIVER_EXE,
        is_distributed=True)
    ap = p.arg_parser.parser
    p.add_input_file_type(FileTypes.DS_REF, "reference",
                          name="Reference DataSet",
                          description="Reference DataSet XML or FASTA file")
    p.add_input_file_type(FileTypes.GFF, "gff",
                          name="Alignment Summary GFF",
                          description="Alignment Summary GFF")
    p.add_output_file_type(FileTypes.REPORT, "report_json",
                           name="JSON report",
                           description="Path to write report JSON output",
                           default_name="coverage_report")
    p.add_int(
        option_id=Constants.MAX_CONTIGS_ID,
        option_str="maxContigs",
        default=Constants.MAX_CONTIGS_DEFAULT,
        name="Maximum number of contigs to plot",
        description="Maximum number of contigs to plot in coverage report")
    return p
Example #16
0
def get_parser():
    driver_exe = "python -m pbcommand.cli.examples.dev_app --resolved-tool-contract "
    desc = "Dev app for Testing that supports emitting tool contracts"
    # Can specify libs or other dependencies that
    subcomponents = [("pbcommand", VERSION), ("my_component", "0.1.0"),
                     ("my_component_id", "1.2.3")]
    # ResourceTypes.*
    resource_types = (ResourceTypes.TMP_FILE, ResourceTypes.TMP_FILE,
                      ResourceTypes.TMP_DIR)

    # Create an instance of a Pacbio Parser
    p = get_pbparser(TOOL_ID,
                     VERSION,
                     "Txt App",
                     desc,
                     driver_exe,
                     is_distributed=False,
                     resource_types=resource_types,
                     subcomponents=subcomponents)

    # Add Input Files types
    p.add_input_file_type(FileTypes.TXT, "txt_in", "Txt file",
                          "Generic Text File")
    # Add output files types
    p.add_output_file_type(FileTypes.TXT, "txt_out", "Txt outfile",
                           "Generic Output Txt file", "output")
    p.add_int("pbcommand.task_options.dev_max_nlines", "max_nlines", 10,
              "Max Lines", "Max Number of lines to Copy")
    return p
Example #17
0
def get_contract_parser():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     meta_rpt.title,
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    add_base_options_pbcommand(p, "Top Variants Report")
    p.add_input_file_type(FileTypes.GFF,
                          file_id="gff",
                          name="GFF file",
                          description="variants.gff (can be gzip'ed)")
    p.add_input_file_type(FileTypes.DS_REF,
                          file_id="reference",
                          name="Reference dataset",
                          description="ReferenceSet or FASTA")
    # p.add_output_file_type(FileTypes.REPORT, "report",
    #                       "JSON report", "JSON report", "report.json")
    p.add_int(Constants.HOW_MANY_ID,
              "how_many",
              default=Constants.HOW_MANY_DEFAULT,
              name="Number of variants",
              description="number of top variants to show (default=100)")
    p.add_int(Constants.BATCH_SORT_SIZE_ID,
              "batch_sort_size",
              default=Constants.BATCH_SORT_SIZE_DEFAULT,
              name="Batch sort size",
              description="Intermediate sort size parameter (default=10000)")
    # XXX do we need a flag for minor variants?
    return p
Example #18
0
def get_contract_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Iso-Seq Cluster Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)

    p.add_input_file_type(FileTypes.DS_CONTIG, "inReadsFN", "Fasta reads",
                          description="Reads in FASTA format, usually are consensus, " +
                          "isoforms produced by Iso-Seq Cluster.")

    p.add_input_file_type(FileTypes.DS_CONTIG, "hq_isoforms_fq", "HQ isoforms in Fastq",
                          description="HQ isoforms in FASTQ format produced by Iso-Seq Cluster.")

    p.add_input_file_type(FileTypes.DS_CONTIG, "lq_isoforms_fq", "LQ isoforms in Fastq",
                          description="LQ isoforms in FASTQ format produced by Iso-Seq Cluster.")

    p.add_input_file_type(FileTypes.JSON, "inSummaryFN", "Summary text",
                          description="A summary produced by Iso-Seq Cluster, e.g. " +
                          "cluster_summary.txt")
    p.add_output_file_type(FileTypes.REPORT, "outJson", "Transcript Clustering Report",
                           description="Summary of results from pbtranscript",
                           default_name="isoseq_cluster_report")
    return p
Example #19
0
def _get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Iso-Seq Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    p.add_input_file_type(
        FileTypes.DS_TRANSCRIPT,
        "hq_transcripts",
        "Clustered high-quality transcripts",
        description="Clustered transcripts from 'sierra' in BAM dataset format")
    p.add_input_file_type(
        FileTypes.DS_TRANSCRIPT,
        "lq_transcripts",
        "Clustered low-quality transcripts",
        description="Clustered transcripts from 'sierra' in BAM dataset format")
    p.add_output_file_type(
        FileTypes.REPORT,
        "outJson",
        "Transcript Clustering Report",
        description="Summary of results from pbtranscript",
        default_name="isoseq3_report")
    return p
Example #20
0
def get_parser():
    """
    Construct a hybrid PbParser with most tool contract parameters defined
    separately from argparser parameters.
    """
    p = get_pbparser(
        tool_id=Constants.TOOL_ID,
        version=__VERSION__,
        name="variantCaller",
        description="Compute genomic consensus and call variants relative to the reference.",
        driver_exe=Constants.DRIVER_EXE,
        nproc=SymbolTypes.MAX_NPROC,
        resource_types=(),
        default_level="WARN")
    tcp = p.tool_contract_parser
    tcp.add_input_file_type(FileTypes.DS_ALIGN, "infile",
        "Alignment DataSet", "BAM or Alignment DataSet")
    tcp.add_input_file_type(FileTypes.DS_REF, "reference",
        "Reference DataSet", "Fasta or Reference DataSet")
    tcp.add_output_file_type(FileTypes.GFF, "variants",
        name="Variant Calls",
        description="List of variants from the reference",
        default_name="variants")
    tcp.add_output_file_type(FileTypes.DS_CONTIG, "consensus",
        name="Consensus Contigs",
        description="Consensus contigs dataset",
        default_name="consensus")
    tcp.add_output_file_type(FileTypes.FASTQ, "consensus_fastq",
        name="Consensus Contigs",
        description="Consensus contigs in FASTQ format",
        default_name="consensus")
    tcp.add_str(
        option_id=Constants.ALGORITHM_ID,
        option_str="algorithm",
        default=Constants.DEFAULT_ALGORITHM,
        name="Algorithm",
        description="Variant calling algorithm")
    tcp.add_int(
        option_id=Constants.MIN_CONFIDENCE_ID,
        option_str="minConfidence",
        default=Constants.DEFAULT_MIN_CONFIDENCE,
        name="Minimum confidence",
        description="The minimum confidence for a variant call to be output "+\
                    "to variants.gff")
    tcp.add_int(
        option_id=Constants.MIN_COVERAGE_ID,
        option_str="minCoverage",
        default=Constants.DEFAULT_MIN_COVERAGE,
        name="Minimum coverage",
        description="The minimum site coverage that must be achieved for " +\
                    "variant calls and consensus to be calculated for a site.")

    tcp.add_boolean(
        option_id=Constants.DIPLOID_MODE_ID,
        option_str="diploid",
        default=False,
        name="Diploid mode (experimental)",
        description="Enable detection of heterozygous variants (experimental)")
    add_options_to_argument_parser(p.arg_parser.parser)
    return p
Example #21
0
def _get_parser():
    driver_exe = ("python -m "
                  "pbreports.report.summarize_coverage.summarize_coverage "
                  "--resolved-tool-contract ")
    p = get_pbparser(Constants.TOOL_ID, __version__, "Summarize Coverage",
                     __doc__, driver_exe)
    return add_options_to_parser(p)
Example #22
0
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.amplicon_analysis_timing "
                  "--resolved-tool-contract ")
    p = get_pbparser(Constants.TOOL_ID, __version__, spec.title, __doc__,
                     driver_exe)
    return p
Example #23
0
def _get_parser():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     "Minor Variants Report",
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    return _add_options_to_parser(p)
Example #24
0
def _get_parser_core():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     meta_rpt.title,
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    return p
Example #25
0
def _get_parser():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     spec.title,
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    return _add_options_to_parser(p)
Example #26
0
def get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Summarize Coverage (CCS)",
        __doc__,
        Constants.DRIVER_EXE)
    return p
Example #27
0
def _get_parser_core():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     "Loading XML Report",
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    return p
Example #28
0
def _get_parser_core():
    p = get_pbparser(Constants.TOOL_ID,
                     __version__,
                     "Raw Dataset Statistics XML Report",
                     __doc__,
                     Constants.DRIVER_EXE,
                     is_distributed=True)
    return p
Example #29
0
def get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Summarize Coverage (CCS)",
        __doc__,
        Constants.DRIVER_EXE)
    return p
Example #30
0
def _get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Amplicon Analysis Input",
        __doc__,
        Constants.DRIVER_EXE)
    return _add_options_to_parser(p)
def _get_parser_core():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Amplicon Analysis Input",
        __doc__,
        Constants.DRIVER_EXE)
    return p
Example #32
0
def _get_parser_core():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Loading XML Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    return p
Example #33
0
def _get_parser_core():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        spec.title,
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    return p
Example #34
0
def _get_parser_core():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Raw Dataset Statistics XML Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    return p
Example #35
0
def _get_parser():
    desc = "Create a Mapping Report from a Aligned BAM or Alignment DataSet"
    driver_exe = "python -m pbreports.report.mapping_stats --resolved-tool-contract "
    parser = get_pbparser(TOOL_ID, __version__, "Mapping Statistics", desc, driver_exe)

    parser.add_input_file_type(FileTypes.DS_ALIGN, "alignment_file", "Alignment XML DataSet", "BAM, SAM or Alignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json", "PacBio Json Report", "Output report JSON file.", "mapping_stats_report.json")

    return parser
Example #36
0
 def test_catch_output_file_extension(self):
     p = get_pbparser("pbcommand.tasks.test_parsers", "0.1.0", "Tool Name",
                      "Tool Descripion", "pbcommand-driver-exe ")
     p.add_output_file_type(file_type=FileTypes.GFF,
                            file_id="gff",
                            name="GFF file",
                            description="GFF file description",
                            default_name="annotations.gff")
     tc = p.to_contract()
     self.assertRaises(ValueError, tc.to_dict)
Example #37
0
def get_base_contract_parser(Constants=BaseConstants, default_level="WARN"):
    p = get_pbparser(tool_id=Constants.TOOL_ID,
                     version=get_version(),
                     name=Constants.TOOL_ID,
                     description=Constants.PARSER_DESC,
                     driver_exe=Constants.DRIVER_EXE,
                     nproc=SymbolTypes.MAX_NPROC,
                     resource_types=(ResourceTypes.TMP_DIR, ),
                     default_level=default_level)
    return p
Example #38
0
def _get_parser_core():
    driver_exe = "python -m pbreports.report.sat --resolved-tool-contract "
    p = get_pbparser(
        TOOL_ID,
        __version__,
        "SAT Report",
        __doc__,
        driver_exe,
        is_distributed=True)
    return p
    def test_input_output_files(self):
        p = get_pbparser(
            "pbcommand.tasks.test_parsers",
            "0.1",
            "Display Name",
            "Tool Description ",
            "pbcommand-driver-cmd",
            is_distributed=False,
            nproc=1,
            resource_types=())

        p.add_input_file_type(
            file_type=FileTypes.FASTA,
            file_id="fasta",
            name="Fasta file",
            description="Fasta file description")

        p.add_input_file_type(FileTypes.JSON,
            "json",
            "JSON file",
            "JSON file description")

        p.add_output_file_type(
            file_type=FileTypes.GFF,
            file_id="gff",
            name="GFF file",
            description="GFF file description",
            default_name="annotations")
        tc_contract = p.to_contract()
        d = tc_contract.to_dict()
        inputs = d['tool_contract']['input_types']
        self.assertEqual(inputs, [
            {
                'description': 'Fasta file description',
                'title': 'Fasta file',
                'id': 'fasta',
                'file_type_id': 'PacBio.FileTypes.Fasta'
            },
            {
                'description': 'JSON file description',
                'title': 'JSON file',
                'id': 'json',
                'file_type_id': 'PacBio.FileTypes.json'
            }
        ])
        outputs = d['tool_contract']['output_types']
        self.assertEqual(outputs, [
            {
                'title': 'GFF file',
                'description': 'GFF file description',
                'default_name': 'annotations',
                'id': 'gff',
                'file_type_id': 'PacBio.FileTypes.gff'
            }
        ])
Example #40
0
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.preassembly "
                  "--resolved-tool-contract ")
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Preassembly",
        __doc__,
        driver_exe)
    return p
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.amplicon_analysis_timing "
                  "--resolved-tool-contract ")
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Amplicon Analysis Timing",
        __doc__,
        driver_exe)
    return p
Example #42
0
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.polished_assembly "
                  "--resolved-tool-contract ")
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        meta_rpt.title,
        __doc__,
        driver_exe)
    return p
Example #43
0
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.summarize_coverage.summarize_coverage "
                  "--resolved-tool-contract ")
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Summarize Coverage",
        __doc__,
        driver_exe)
    return p
def _get_parser_core():
    driver_exe = ("python -m "
                  "pbreports.report.amplicon_analysis_consensus "
                  "--resolved-tool-contract ")
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        spec.title,
        __doc__,
        driver_exe)
    return p
def get_base_contract_parser(Constants=BaseConstants, default_level="WARN"):
    p = get_pbparser(
        tool_id=Constants.TOOL_ID,
        version=get_version(),
        name=Constants.TOOL_ID,
        description=Constants.PARSER_DESC,
        driver_exe=Constants.DRIVER_EXE,
        nproc=SymbolTypes.MAX_NPROC,
        resource_types=(ResourceTypes.TMP_DIR,),
        default_level=default_level)
    return p
Example #46
0
def _get_parser():
    parser = get_pbparser(Constants.TOOL_ID, __version__,
                          ccs_spec.title, __doc__,
                          Constants.DRIVER_EXE)
    parser.add_input_file_type(FileTypes.DS_ALIGN_CCS, "alignment_file",
                               "ConsensusAlignment XML DataSet",
                               "BAM, SAM or ConsensusAlignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json",
                                "Mapping Statistics Report",
                                "Summary of alignment results",
                                default_name=Constants.R_ID)
    return parser
def _get_parser():
    parser = get_pbparser(Constants.TOOL_ID, __version__,
                          spec.title, __doc__,
                          Constants.DRIVER_EXE)
    parser.add_input_file_type(FileTypes.DS_ALIGN_CCS, "alignment_file",
                               "ConsensusAlignment XML DataSet",
                               "BAM, SAM or ConsensusAlignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json",
                                "Mapping Statistics Report",
                                "Summary of alignment results",
                                default_name=Constants.R_ID)
    return parser
Example #48
0
def _get_parser():
    parser = get_pbparser(Constants.TOOL_ID, __version__,
                          meta_rpt.title, __doc__,
                          Constants.DRIVER_EXE)
    parser.add_input_file_type(FileTypes.DS_ALIGN_CCS, "alignment_file",
                               "ConsensusAlignment XML DataSet",
                               "BAM, SAM or ConsensusAlignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json",
                                "CCS Mapping Statistics Report",
                                "Output report JSON file.",
                                default_name=meta_rpt.id)
    return parser
Example #49
0
def get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Modifications Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    p.add_input_file_type(FileTypes.H5, "basemods_h5", "HDF5 file",
                          "HDF5 file of base modifications from ipdSummary")
    add_base_options_pbcommand(p, "Basemods report")
    return p
Example #50
0
def _get_parser():
    desc = "Create a Mapping Report from a Aligned BAM or Alignment DataSet"
    driver_exe = "python -m pbreports.report.mapping_stats --resolved-tool-contract "
    parser = get_pbparser(Constants.TOOL_ID, __version__,
                          "Mapping Statistics", desc, driver_exe,
                          nproc=1)

    parser.add_input_file_type(FileTypes.DS_ALIGN, "alignment_file",
                               "Alignment XML DataSet", "BAM, SAM or Alignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json", "Mapping Statistics Report",
                                "Output report JSON file.", meta_rpt.id)

    return parser
def _get_parser():
    desc = "Create a Mapping Report from a Aligned BAM or Alignment DataSet"
    driver_exe = "python -m pbreports.report.mapping_stats --resolved-tool-contract "
    parser = get_pbparser(Constants.TOOL_ID, __version__,
                          "Mapping Statistics", desc, driver_exe,
                          nproc=1)

    parser.add_input_file_type(FileTypes.DS_ALIGN, "alignment_file",
                               "Alignment XML DataSet", "BAM, SAM or Alignment DataSet")
    parser.add_output_file_type(FileTypes.REPORT, "report_json",
                                "Mapping Statistics Report",
                                "Summary of alignment results", Constants.R_ID)

    return parser
Example #52
0
def get_parser():
    p = get_pbparser(Constants.TOOL_ID, __version__, meta_rpt.title, __doc__,
                     Constants.DRIVER_EXE)

    p.add_input_file_type(FileTypes.GFF, 'gff_file', "GFF file",
                          "Path to motifs.gff.gz")
    p.add_input_file_type(FileTypes.CSV, 'motif_summary_csv', "CSV file",
                          'Path to Motif summary CSV')
    p.add_output_file_type(FileTypes.REPORT,
                           'report_json',
                           name="Motifs report",
                           description="Path of output JSON report",
                           default_name="motifs_report")
    return p
Example #53
0
def get_subreads_report_parser(tool_id, version, title, desc, driver_exe):
    p = get_pbparser(tool_id, version, title, desc, driver_exe,
                     is_distributed=True)
    p.add_input_file_type(
        FileTypes.DS_SUBREADS,
        file_id="subread_set",
        name="SubreadSet",
        description="SubreadSet")
    p.add_output_file_type(FileTypes.REPORT, "report", title,
                           description=("Filename of JSON output report. "
                                        "Should be name only, and will be "
                                        "written to output dir"),
                           default_name="report")
    return p
def get_parser():
    p = get_pbparser(
        Constants.TOOL_ID,
        __version__,
        "Modifications Report",
        __doc__,
        Constants.DRIVER_EXE,
        is_distributed=True)
    p.add_input_file_type(FileTypes.H5, "basemods_h5", "HDF5 file",
                          "HDF5 file of base modifications from ipdSummary")
    p.add_output_file_type(FileTypes.REPORT, "report", "Basemods report",
                           description="Summary of basemod results",
                           default_name="report")
    return p
Example #55
0
def _get_contract_parser():
    """
    Central point of programmatically defining a Parser.
    :rtype: PbParser
    :return: PbParser
    """
    # Number of processors to use
    nproc = 2
    # Commandline exe to call "{exe}" /path/to/resolved-tool-contract.json
    driver_exe = "python -m pbcommand.cli.example.dev_app --resolved-tool-contract "
    desc = "Dev app for Testing that supports emitting tool contracts"
    p = get_pbparser(TOOL_ID, __version__, "DevApp", desc, driver_exe,
                     is_distributed=False, nproc=nproc)
    return p
 def test_catch_output_file_extension(self):
     p = get_pbparser(
         "pbcommand.tasks.test_parsers",
         "0.1.0",
         "Tool Name",
         "Tool Descripion",
         "pbcommand-driver-exe ")
     p.add_output_file_type(
         file_type=FileTypes.GFF,
         file_id="gff",
         name="GFF file",
         description="GFF file description",
         default_name="annotations.gff")
     tc = p.to_contract()
     self.assertRaises(ValueError, tc.to_dict)
def _get_parser():
    parser = get_pbparser(Constants.TOOL_ID, __version__, spec.title, __doc__,
                          Constants.DRIVER_EXE)
    parser.add_input_file_type(FileTypes.DS_ALIGN, "alignment_file",
                               "Alignment XML DataSet",
                               "BAM, SAM or Alignment DataSet")
    parser.add_input_file_type(FileTypes.DS_SUBREADS, "subreads_file",
                               "Subreads XML DataSet",
                               "Unmapped BAM or Subreads DataSet")
    parser.add_output_file_type(FileTypes.REPORT,
                                "report_json",
                                "Mapping Statistics Report",
                                "Summary of alignment results",
                                default_name=Constants.R_ID)
    return parser