def test_cli_config_set_default_motif(tmp_dir):
args = parser.parse_args(
["config", "--set-default-motif", "/path/to/motif/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_motif_dir() == "/path/to/motif/root"
def install_motif(args, config_file=None):
config = Config(config_file)
if config.has_motif_set(args.name):
logger.error(f"Motif set {args.name!r} already exists!")
sys.exit(1)
motif_dir = os.path.abspath(
args.output_dir or os.path.join(config.get_motif_dir(), args.name))
logger.info(f"Installing motif set {args.name!r} into {motif_dir}")
if not os.path.isdir(motif_dir):
os.makedirs(motif_dir)
if os.listdir(motif_dir):
logger.error("Directory not empty! Please specify another directory "
"or delete files under it.")
sys.exit(1)
pfms_path = pfms_path_fmt.format(motif_dir, args.name)
if args.remote:
try:
db = JasparDatabase()
if args.database == 'jaspar_core':
dst_pfms = db.download_core(args.remote, motif_dir)
else:
dst_pfms = db.download_other_collections(
args.remote, motif_dir)
logger.debug(
f"Renaming downloaded file to {os.path.basename(pfms_path)}")
shutil.move(dst_pfms, pfms_path)
except RemoteMotifPFMsNotFoundError as e:
logger.error(e)
sys.exit(1)
else:
logger.info("Copying the PFMs file(s)")
merge_files(args.pfm_files, pfms_path)
logger.info("Updating the config file")
config.set_motif_path(args.name, motif_dir)
config.write()
logger.info("Successfully installed!")
if args.genome:
build_motif(args, config_file)