INNER CODE UNIT · Python

get_min_taxon_coverage

wwood/singlem · singlem/main.py:346

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

def parse_genome_fasta_files(args):
    genomes = []
    if getattr(args, 'genome_fasta_files', None):
        genomes.extend(args.genome_fasta_files)
    if getattr(args, 'genome_fasta_directory', None):
        extension = getattr(args, 'genome_fasta_extension', 'fna')
        for fn in sorted(os.listdir(args.genome_fasta_directory)):
            if fn.endswith('.' + extension):
                genomes.append(os.path.join(args.genome_fasta_directory, fn))
    if getattr(args, 'genome_fasta_list', None):

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