ORFsClustering.py 文件源码

def get_args():
    parser = argparse.ArgumentParser(description='Clustering ORFs by position in the graph')
    parser.add_argument('sequences', type=str, help='Path to ORFs sequences file')
    parser.add_argument('paths', type=str, help='Path to ORFs paths file from ORFFinderInGraph.py')
    parser.add_argument('graph', type=str, help='Path to graph in GFA format')
    parser.add_argument('threshold', type=int, help='Max level of dissimilarity of ORFs in one cluster(between 0 and 1)')
    parser.add_argument('-o', '--output', type=str, default='', help='Output folder')
    parser.add_argument('-sd', '--savedistances', default='False', action='store_true',
                        help='Save pairwise distances matrix (in .npy format)')
    parser.set_defaults(savedistances=False)
    return parser.parse_args()