csfrag.py 文件源码

def command_line(self):

        cmd = csb.apps.ArgHandler(self.program, __doc__)
        cpu = multiprocessing.cpu_count()

        cmd.add_scalar_option('database', 'd', str, 'PDBS25 database directory (containing PDBS25cs.scs)', required=True)
        cmd.add_scalar_option('shifts', 's', str, 'assigned chemical shifts table (NMR STAR file fragment)', required=True)    

        cmd.add_scalar_option('window', 'w', int, 'sliding window size', default=8)
        cmd.add_scalar_option('top', 't', int, 'maximum number per starting position', default=25)                
        cmd.add_scalar_option('cpu', 'c', int, 'maximum degree of parallelism', default=cpu)

        cmd.add_scalar_option('verbosity', 'v', int, 'verbosity level', default=1)        
        cmd.add_scalar_option('output', 'o', str, 'output directory', default='.')        
        cmd.add_boolean_option('filtered-map', 'f', 'make an additional filtered fragment map of centroids', default=False)

        cmd.add_positional_argument('QUERY', str, 'query sequence  (FASTA file)')

        return cmd