def evaluation(args):
FLAGS = args
FLAGS.input_dir = FLAGS.input
FLAGS.output_dir = FLAGS.output
extract(FLAGS)
FLAGS.input = FLAGS.output + '/raw/'
chiron_eval.run(args)
def evaluation(args):
if args.preset is None:
default_p = {'start':0,'batch_size':400,'segment_len':500,'jump':490,'threads':0,'beam':30}
elif args.preset == 'dna-pre':
default_p = {'start':0,'batch_size':400,'segment_len':400,'jump':390,'threads':0,'beam':30}
if args.mode=='rna':
raise ValueError('Try to use the DNA preset parameter setting in RNA mode.')
elif args.preset == 'rna-pre':
default_p = {'start':0,'batch_size':300,'segment_len':2000,'jump':1900,'threads':0,'beam':30}
if args.mode=='dna':
raise ValueError('Attempt to use the RNA preset parameter setting in DNA mode, enable RNA basecalling by --mode rna')
else:
raise ValueError('Unknown presetting %s undifiend'%(args.preset))
args = set_paras(args,default_p)
FLAGS = args
FLAGS.input_dir = FLAGS.input
FLAGS.output_dir = FLAGS.output
FLAGS.unit = False
FLAGS.recursive = True
FLAGS.polya = None
if args.mode=='rna':
args.reverse_fast5 = True
else:
args.reverse_fast5 = False
extract(FLAGS)
FLAGS.input = FLAGS.output + '/raw/'
chiron_eval.run(args)
def evaluation(args: argparse.Namespace):
FLAGS = args
FLAGS.input_dir = FLAGS.input
FLAGS.output_dir = FLAGS.output
FLAGS.recursive = True
extract(FLAGS)
FLAGS.input = FLAGS.output + '/raw/'
chiron_eval.run(args)