Python get_parserの例

コード例 #1

ファイル: main.py プロジェクト: lpp1985/lpp_Script

def resolved_tool_contract_runner(resolved_contract):
    rc = resolved_contract
    alignment_path = rc.task.input_files[0]
    reference_path = rc.task.input_files[1]
    gff_path = rc.task.output_files[0]
    dataset_path = rc.task.output_files[1]
    fasta_path = re.sub(".contigset.xml", ".fasta", dataset_path)
    fastq_path = rc.task.output_files[2]
    args = [
        alignment_path,
        "--verbose",
        "--reference", reference_path,
        "--outputFilename", gff_path,
        "--outputFilename", fasta_path,
        "--outputFilename", fastq_path,
        "--numWorkers", str(rc.task.nproc),
        "--minCoverage", str(rc.task.options[Constants.MIN_COVERAGE_ID]),
        "--minConfidence", str(rc.task.options[Constants.MIN_CONFIDENCE_ID]),
        "--algorithm", rc.task.options[Constants.ALGORITHM_ID],
        "--alignmentSetRefWindows",
    ]
    if rc.task.options[Constants.DIPLOID_MODE_ID]:
        args.append("--diploid")
    args_ = get_parser().arg_parser.parser.parse_args(args)
    rc = args_runner(args_)
    if rc == 0:
        pysam.faidx(fasta_path)
        ds = ContigSet(fasta_path, strict=True)
        ds.write(dataset_path)
    return rc

コード例 #2

def resolved_tool_contract_runner(resolved_contract):
    rc = resolved_contract
    alignment_path = rc.task.input_files[0]
    reference_path = rc.task.input_files[1]
    gff_path = rc.task.output_files[0]
    vcf_path = rc.task.output_files[1]
    dataset_path = rc.task.output_files[2]
    fasta_path = re.sub(".contigset.xml", ".fasta", dataset_path)
    fastq_path = rc.task.output_files[3]
    args = [
        alignment_path,
        "--verbose",
        "--reference", reference_path,
        "--outputFilename", gff_path,
        "--outputFilename", fasta_path,
        "--outputFilename", fastq_path,
        "--outputFilename", vcf_path,
        "--numWorkers", str(rc.task.nproc),
        "--minCoverage", str(rc.task.options[Constants.MIN_COVERAGE_ID]),
        "--minConfidence", str(rc.task.options[Constants.MIN_CONFIDENCE_ID]),
        "--maskRadius", str(Constants.DEFAULT_MASK_RADIUS) if \
                        bool(rc.task.options[Constants.MASKING_ID]) else "0",
        "--algorithm", rc.task.options[Constants.ALGORITHM_ID],
        "--alignmentSetRefWindows",
    ]
    args_ = get_parser().arg_parser.parser.parse_args(args)
    rc = args_runner(args_)
    if rc == 0:
        pysam.faidx(fasta_path)
        ds = ContigSet(fasta_path, strict=True)
        ds.write(dataset_path)
    return rc

コード例 #3

ファイル: main.py プロジェクト: PacificBiosciences/GenomicConsensus

def resolved_tool_contract_runner(resolved_contract):
    rc = resolved_contract
    alignment_path = rc.task.input_files[0]
    reference_path = rc.task.input_files[1]
    gff_path = rc.task.output_files[0]
    vcf_path = rc.task.output_files[1]
    dataset_path = rc.task.output_files[2]
    fasta_path = re.sub(".contigset.xml", ".fasta", dataset_path)
    fastq_path = rc.task.output_files[3]
    args = [
        alignment_path,
        "--verbose",
        "--reference", reference_path,
        "--outputFilename", gff_path,
        "--outputFilename", fasta_path,
        "--outputFilename", fastq_path,
        "--outputFilename", vcf_path,
        "--numWorkers", str(rc.task.nproc),
        "--minCoverage", str(rc.task.options[Constants.MIN_COVERAGE_ID]),
        "--minConfidence", str(rc.task.options[Constants.MIN_CONFIDENCE_ID]),
        "--maskRadius", str(Constants.DEFAULT_MASK_RADIUS) if \
                        bool(rc.task.options[Constants.MASKING_ID]) else "0",
        "--algorithm", rc.task.options[Constants.ALGORITHM_ID],
        "--alignmentSetRefWindows",
    ]
    args_ = get_parser().arg_parser.parser.parse_args(args)
    rc = args_runner(args_)
    if rc == 0:
        pysam.faidx(fasta_path)
        ds = ContigSet(fasta_path, strict=True)
        ds.write(dataset_path)
    return rc

コード例 #4

def main(argv=sys.argv):
    setup_log_ = functools.partial(setup_log,
                                   str_formatter=LogFormats.LOG_FMT_LVL)
    return pbparser_runner(argv=argv[1:],
                           parser=get_parser(),
                           args_runner_func=args_runner,
                           contract_runner_func=resolved_tool_contract_runner,
                           alog=logging.getLogger(),
                           setup_log_func=setup_log_)

コード例 #5

ファイル: main.py プロジェクト: lpp1985/lpp_Script

def main(argv=sys.argv):
    setup_log_ = functools.partial(setup_log,
        str_formatter=LogFormats.LOG_FMT_LVL)
    return pbparser_runner(
        argv=argv[1:],
        parser=get_parser(),
        args_runner_func=args_runner,
        contract_runner_func=resolved_tool_contract_runner,
        alog=logging.getLogger(),
        setup_log_func=setup_log_)

コード例 #6

ファイル: main.py プロジェクト: crschvarcz/GenomicConsensus

def main(argv=sys.argv):
    logFormat = '[%(levelname)s] %(message)s'
    logging.basicConfig(level=logging.WARN, format=logFormat)
    log = logging.getLogger()
    def dummy_setup(*args, **kwargs):
        pass
    return pbparser_runner(
        argv=argv[1:],
        parser=get_parser(),
        args_runner_func=args_runner,
        contract_runner_func=resolved_tool_contract_runner,
        alog=log,
        setup_log_func=dummy_setup)

コード例 #7

ファイル: main.py プロジェクト: voutcn/GenomicConsensus

def main(argv=sys.argv):
    logFormat = '[%(levelname)s] %(message)s'
    logging.basicConfig(level=logging.WARN, format=logFormat)
    log = logging.getLogger()

    def dummy_setup(*args, **kwargs):
        pass

    return pbparser_runner(argv=argv[1:],
                           parser=get_parser(),
                           args_runner_func=args_runner,
                           contract_runner_func=resolved_tool_contract_runner,
                           alog=log,
                           setup_log_func=dummy_setup)