Ejemplos de get_run_directory_and_file en Python

Ejemplo n.º 1

Archivo: phenotype_prediction.py Proyecto: nahilsobh/Phenotype_Prediction_Pipeline

def main():
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters['method']](run_parameters)

Ejemplo n.º 2

Archivo: samples_clustering_main.py Proyecto: candicegjing/KnowEnG_NBS_Base

def main():
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    
    run_directory, run_file, num_of_process, num_of_boostraps = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters["method"]](run_parameters, num_of_process, num_of_boostraps)

Ejemplo n.º 3

def data_cleanup():
    try:
        logger.init()
        run_directory, run_file = get_run_directory_and_file(sys.argv)
        run_parameters = get_run_parameters(run_directory, run_file)
        run_pipelines(run_parameters, SELECT[run_parameters['pipeline_type']])
    except Exception as err:
        logger.logging.append("ERROR: {}".format(str(err)))
        raise RuntimeError(str(err))

Ejemplo n.º 4

def main():
    """
    This is the main function to perform general clustering
    """
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters["method"]](run_parameters)

Ejemplo n.º 5

Archivo: data_checker.py Proyecto: nahilsobh/Data_Cleanup_Pipeline

def checker():
    try:
        logger.init()
        run_directory, run_file = get_run_directory_and_file(sys.argv)
        run_parameters = get_run_parameters(run_directory, run_file)
        obj = Checker(run_parameters)
        obj.condition_check()

    except Exception as err:
        logger.logging.append("ERROR: {}".format(str(err)))
        raise RuntimeError(str(err))

Ejemplo n.º 6

Archivo: clustering_eval.py Proyecto: KnowEnG/Clustering_Evaluation

def main():
    """
    This is the main function to perform clustering evaluation.
    """
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    clustering_evaluation(run_parameters)

Ejemplo n.º 7

def main():
    """
    This is the main function to perform feature prioritization.
    """
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters["method"]](run_parameters)

Ejemplo n.º 8

Archivo: geneset_characterization.py Proyecto: KnowEnG/GeneSet_Characterization_Pipeline

def main():
    """
    This the main function to characterize gene
    set from three methods: fisher, DRaWR, net path.
    """
    import sys
    from knpackage.toolbox import get_run_directory_and_file
    from knpackage.toolbox import get_run_parameters

    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters["method"]](run_parameters)

Ejemplo n.º 9

Archivo: network_prep.py Proyecto: KnowEnG/Network_Prepper

def network_prepper():
    try:
        logger.init()
        run_directory, run_file = get_run_directory_and_file(sys.argv)
        run_parameters = get_run_parameters(run_directory, run_file)
        run_pipelines(run_parameters, "network_prepper_pipeline")
    except Exception as err:
        logger.logging.append("ERROR: {}".format(str(err)))
        # try to write the log
        logger.generate_logging(
            False, logger.logging, run_parameters["results_directory"] +
            "/log_" + "network_prepper_pipeline" + ".yml")
        raise RuntimeError(str(err))

Ejemplo n.º 10

def data_cleanup():
    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    SELECT[run_parameters['pipeline_type']](run_parameters)

Ejemplo n.º 11

def main():
    run_directory, run_file = get_run_directory_and_file(sys.argv)
    run_parameters = get_run_parameters(run_directory, run_file)
    pasted_gene_cleanup(run_parameters)