INNER CODE UNIT · Python

parse_genome_fasta_files

wwood/singlem · singlem/main.py:354

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):
        with open(args.genome_fasta_list) as f:
            genomes.extend([line.strip() for line in f if line.strip()])
    args.genome_fasta_files = genomes if genomes else None
    return args

def main():
    bird_argparser = BirdArgparser(
        program='SingleM',

View source record →