INNER CODE UNIT · Python

get_min_orf_length

wwood/singlem · singlem/main.py:336

def get_min_orf_length(args, subparser='pipe'):
    if args.min_orf_length:
        return args.min_orf_length
    elif subparser == 'pipe' and args.genome_fasta_files:
        return SearchPipe.DEFAULT_GENOME_MIN_ORF_LENGTH
    elif subparser in ('pipe', 'renew'):
        return SearchPipe.DEFAULT_MIN_ORF_LENGTH
    else:
        raise Exception("Programming error")

def get_min_taxon_coverage(args, subparser='pipe'):
    if args.min_taxon_coverage:
        return args.min_taxon_coverage
    elif subparser == 'pipe' and args.genome_fasta_files:
        return CONDENSE_DEFAULT_GENOME_MIN_TAXON_COVERAGE
    else:
        return CONDENSE_DEFAULT_MIN_TAXON_COVERAGE

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