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
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
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
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_)
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_)
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)
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)