def test_cli_config_set_default_genome(tmp_dir):
args = parser.parse_args(
["config", "--set-default-genome", "/path/to/genome/root"])
config_file = os.path.join(tmp_dir, "test_cli_config.motifscanrc")
run(args=args, config_file=config_file)
config = Config(config_file)
assert config.get_genome_dir() == "/path/to/genome/root"
def install_genome(args, config_file=None):
config = Config(config_file)
if config.has_genome_assembly(args.name):
logger.error(f"Genome assembly {args.name!r} already exists!")
sys.exit(1)
genome_dir = os.path.abspath(
args.output_dir or os.path.join(config.get_genome_dir(), args.name))
logger.info(f"Installing genome assembly {args.name!r} into {genome_dir}")
if not os.path.isdir(genome_dir):
os.makedirs(genome_dir)
if os.listdir(genome_dir):
logger.error("Directory not empty! Please specify another directory "
"or delete files under it.")
sys.exit(1)
fasta_path = fasta_path_fmt.format(genome_dir, args.name)
bg_freq_path = bg_freq_path_fmt.format(genome_dir, args.name)
gene_path = gene_path_fmt.format(genome_dir, args.name)
if args.remote:
download_dir = os.path.join(genome_dir, 'downloads')
try:
db = UcscDatabase()
dst_fasta = db.download_sequence(args.remote, download_dir)
logger.debug(f"Extracting the sequence file to {fasta_path}")
merge_extracted_files(dst_fasta, fasta_path)
dst_gene = db.download_gene(args.remote, download_dir)
logger.debug(f"Extracting the gene annotation file to {gene_path}")
merge_extracted_files(dst_gene, gene_path)
if args.clean:
logger.debug(f"Removing the download directory {download_dir}")
shutil.rmtree(download_dir)
except RemoteGenomeNotFoundError as e:
logger.error(e)
sys.exit(1)
else:
logger.info("Copying the sequence file(s)")
merge_files(args.fasta_files, fasta_path)
logger.info("Copying the gene annotation file")
copy_file(args.gene_file, gene_path)
logger.info("Calculating nucleotide frequencies of the genome background")
bg_freq = cal_bg_freq(fasta_path)
logger.info("Writing nucleotide frequencies")
write_bg_freq(bg_freq_path, bg_freq)
logger.info("Updating the config file")
config.set_genome_path(args.name, genome_dir)
config.write()
logger.info("Successfully installed!")