INNER CODE UNIT · Python
n_pass
BigDataBiology/SemiBin · SemiBin/main.py:1589
n_pass = sum(len(c) >= binned_length for c in contig_dict.values())
if n_pass == 0:
logger.error(f'Input file {args.contig_fasta} contains {len(contig_dict)} contigs, but all are shorter than {binned_length} basepairs.')
sys.exit(1)
elif n_pass < 4:
logger.error(f'There are {len(contig_dict)} contigs in input file {args.contig_fasta}, but only {n_pass} contain(s) at least {binned_length} basepairs.')
sys.exit(1)
if args.cmd in ['generate_cannot_links', 'generate_sequence_features_single', 'generate_sequence_features_multi', 'single_easy_bin', 'multi_easy_bin']:
if args.ml_threshold is not None:
must_link_threshold = args.ml_threshold
if args.cmd in ['generate_sequence_features_single', 'single_easy_bin']:
longest = max(len(c) for c in contig_dict.values())
if longest < must_link_threshold:
logger.error(f'There are {len(contig_dict)} contigs in input file {args.contig_fasta}, but none contain at least {must_link_threshold} basepairs (the longest is {longest}), so no must-link pairs can be generated.')
sys.exit(1)