Exemple #1
0
        dataSet.filters.addFilter(**filters)
        log.info("{i} other filters added".format(i=len(filters)))
    rlen = sanitize_read_length(read_length)
    if rlen:
        dataSet.filters.addRequirement(length=[('>=', rlen)])
    if rlen or other_filters:
        dataSet.updateCounts()
    dataSet.write(out_file)
    return 0


@registry("filterdataset",
          "0.1.0",
          FileTypes.DS_SUBREADS,
          subreads_file_type,
          is_distributed=True,
          nproc=1,
          options={
              "read_length": rl_opt,
              "other_filters": filters_opt
          })
def run_filterDataSet(rtc):
    return run_filter_dataset(
        rtc.task.input_files[0], rtc.task.output_files[0],
        rtc.task.options["pbcoretools.task_options.read_length"],
        rtc.task.options["pbcoretools.task_options.other_filters"])


if __name__ == '__main__':
    sys.exit(registry_runner(registry, sys.argv[1:]))
    # This is just for test purposes
    log.info("Running example main with {i} {o} kw:{k}".format(i=input_file,
                                                               o=output_file,
                                                               k=kwargs))

    # write mock output files, otherwise the End-to-End test will fail when
    # run within testkit
    with open(output_file, 'w') as f:
        f.write("MOCK TEST DATA")
    return 0


@registry("dev_mk_example_txt", "0.2.2", (FileTypes.TXT, ), (FileTypes.TXT, ), nproc=1, options=dict(alpha=1234))
def run_rtc(rtc):
    """Example Task for testing. Takes a txt file as input and writes a txt file with mock data"""
    # The above docstring will be used as the Task/ToolContract Description

    log.info("Got RTC task options {t}".format(t=rtc.task.options))
    log.info("Got nproc {n}".format(n=rtc.task.nproc))

    # The Task options are now accessible via global identifier
    alpha = rtc.task.options['pbsmrtpipe_examples.task_options.alpha']
    return _example_main(rtc.task.input_files[0], rtc.task.output_files[0], nproc=rtc.task.nproc, alpha=alpha)


if __name__ == '__main__':
    sys.exit(registry_runner(registry, sys.argv[1:]))


DRIVER_BASE = 'python -m pbinternal2.analysis_tools '

registry = registry_builder(TOOL_NAMESPACE, DRIVER_BASE)


@registry("hello_world_analysis", "0.1.0", FileTypes.FASTA, FileTypes.REPORT, is_distributed=True, nproc=1)
def run_rtc(rtc):
    return run_hello_world(rtc.task.input_files[0], rtc.task.output_files[0])


@registry("cond_to_report", "0.2.0", FileTypes.COND_RESEQ, FileTypes.REPORT, nproc=1, is_distributed=False)
def run_rtc(rtc):
    return run_cond_to_report(rtc.task.input_files[0], rtc.task.output_files[0])


@registry("cond_to_alignmentsets_report", "0.2.0", FileTypes.COND_RESEQ, FileTypes.REPORT, nproc=1, is_distributed=True)
def run_rtc(rtc):
    return run_cond_alignmentsets_to_report(rtc.task.input_files[0], rtc.task.output_files[0])


if __name__ == '__main__':
    default_log_level = logging.DEBUG
    sys.exit(registry_runner(registry,
                             sys.argv[1:],
                             default_log_level=default_log_level))


if __name__ == '__main__':
    sys.exit(registry_runner(registry, sys.argv[1:]))
    label = "label_" + file_type.file_type_id
    desc = "File {f}".format(f=file_type)
    return OutputFileType(file_type.file_type_id, label, repr(file_type), desc,
                          default_name)


def _to_outputs(file_types):
    return [_to_output(i, ft) for i, ft in enumerate(file_types)]


@registry("dev_txt_custom_outs",
          "0.1.0",
          FileTypes.TXT,
          _to_outputs((FileTypes.TXT, FileTypes.TXT)),
          name="Custom Txt Task")
def run_rtc(rtc):
    """Test for using OutputFileTypes as outputs

    Output types can be specified as FileType, or OutputFileType instances
    """
    return _example_main(rtc.task.input_files, rtc.task.output_files)


if __name__ == '__main__':
    default_log_level = logging.DEBUG
    sys.exit(
        registry_runner(registry,
                        sys.argv[1:],
                        default_log_level=default_log_level,
                        version=__version__))
Exemple #5
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    DRIVER_BASE = "python -m pbinternal2.tasks.loading "

    LOADING_DIST_ID = "loading_dist"
    LOADING_DIST = 20


def _get_id(base_opt):
    return "{n}.task_options.{o}".format(n=TOOL_NAMESPACE,
                                         o=base_opt)

registry = registry_builder(TOOL_NAMESPACE, Constants.DRIVER_BASE)


@registry("loading_vs_poisson_report", "0.1.0",
          FileTypes.STS_H5,
          FileTypes.REPORT,
          is_distributed=True,
          nproc=1,
          options={Constants.LOADING_DIST_ID: Constants.LOADING_DIST})
def task_loading_vs_poisson_report(rtc):
    return loading_vs_poisson(
        rtc.task.input_files[0],
        rtc.task.output_files[0],
        rtc.task.nproc,
        rtc.task.options[_get_id(Constants.LOADING_DIST_ID)])

if __name__ == '__main__':
    sys.exit(registry_runner(registry, sys.argv[1:],
                             default_log_level=logging.INFO))

@registry("dev_txt_hello", "0.1.0", FileTypes.TXT, (FileTypes.TXT, FileTypes.TXT), nproc=3, is_distributed=False)
def run_rtc(rtc):
    return _example_main(rtc.task.input_files, rtc.task.output_files)


def _to_output(i, file_type):
    default_name = "_".join([file_type.file_type_id, file_type.base_name + "_" + str(i)])
    label = "label_" + file_type.file_type_id
    desc = "File {f}".format(f=file_type)
    return OutputFileType(file_type.file_type_id, label, repr(file_type), desc, default_name)


def _to_outputs(file_types):
    return [_to_output(i, ft) for i, ft in enumerate(file_types)]


@registry(
    "dev_txt_custom_outs", "0.1.0", FileTypes.TXT, _to_outputs((FileTypes.TXT, FileTypes.TXT)), name="Custom Txt Task"
)
def run_rtc(rtc):
    """Test for using OutputFileTypes as outputs

    Output types can be specified as FileType, or OutputFileType instances
    """
    return _example_main(rtc.task.input_files, rtc.task.output_files)


if __name__ == "__main__":
    default_log_level = logging.DEBUG
    sys.exit(registry_runner(registry, sys.argv[1:], default_log_level=default_log_level, version=__version__))
Exemple #7
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@registry("dev_txt_hello", "0.1.0", FileTypes.TXT, (FileTypes.TXT, FileTypes.TXT), nproc=3, is_distributed=False)
def run_rtc(rtc):
    return _example_main(rtc.task.input_files, rtc.task.output_files)


def _to_output(i, file_type):
    default_name = "_".join([file_type.file_type_id, file_type.base_name + "_" + str(i)])
    label = "label_" + file_type.file_type_id
    desc = "File {f}".format(f=file_type)
    return OutputFileType(file_type.file_type_id, label, repr(file_type), desc, default_name)


def _to_outputs(file_types):
    return [_to_output(i, ft) for i, ft in enumerate(file_types)]


@registry("dev_txt_custom_outs", "0.1.0", FileTypes.TXT, _to_outputs((FileTypes.TXT, FileTypes.TXT)), name="Custom Txt Task")
def run_rtc(rtc):
    """Test for using OutputFileTypes as outputs

    Output types can be specified as FileType, or OutputFileType instances
    """
    return _example_main(rtc.task.input_files, rtc.task.output_files)


if __name__ == '__main__':
    default_log_level = logging.DEBUG
    sys.exit(registry_runner(registry,
                             sys.argv[1:],
                             default_log_level=default_log_level))