INNER CODE UNIT · Python
single_easy_binning
BigDataBiology/SemiBin · SemiBin/main.py:1241
def single_easy_binning(logger, args, binned_length,
must_link_threshold,
contig_dict, device):
"""
contain `generate_cannot_links`, `generate_sequence_features_single`, `train`, `bin` in one command for single-sample and co-assembly binning
"""
if args.environment is None:
logger.info('Generating training data...')
else:
logger.info('Generating features for pretrained model...')
if args.depth_metabat2 is None and args.bams is None and args.abundances is None:
logger.error(
"You need to input BAM files if you want to calculate coverage features.")
sys.exit(1)
if (args.bams is not None or args.abundances is not None) and args.depth_metabat2 is not None:
logger.info('We will use abundance information from Metabat2.')