def list_models(args):
"""
:param args: The command line argument once parsed
:type args: :class:`argparse.Namespace` object
:return: a string representation of all models and submodels installed.
:rtype: str
"""
config = Config(MacsyDefaults(), args)
registry = ModelRegistry()
models_loc_available = scan_models_dir(
config.models_dir(),
profile_suffix=config.profile_suffix(),
relative_path=config.relative_path())
for model_loc in models_loc_available:
registry.add(model_loc)
return str(registry)
def _find_all_installed_packages(models_dir=None) -> ModelRegistry:
"""
:return: all models installed
"""
defaults = MacsyDefaults()
args = argparse.Namespace()
if models_dir is not None:
args.models_dir = models_dir
config = Config(defaults, args)
model_dirs = config.models_dir()
registry = ModelRegistry()
for model_dir in model_dirs:
try:
for model_loc in scan_models_dir(
model_dir, profile_suffix=config.profile_suffix()):
registry.add(model_loc)
except PermissionError as err:
_log.warning(f"{model_dir} is not readable: {err} : skip it.")
return registry
def main(args=None, log_level=None) -> None:
"""
main entry point to macsyprofile
:param args: the arguments passed on the command line without the program name
:type args: List of string
:param log_level: the output verbosity
:type log_level: a positive int or a string among 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
"""
global _log
args = sys.argv[1:] if args is None else args
parsed_args = parse_args(args)
if log_level is None:
log_level = verbosity_to_log_level(parsed_args.verbosity)
_log = init_logger(log_level, out=(not parsed_args.mute))
if not os.path.exists(parsed_args.previous_run):
_log.critical(f"{parsed_args.previous_run}: No such directory.")
sys.tracebacklimit = 0
raise FileNotFoundError() from None
elif not os.path.isdir(parsed_args.previous_run):
_log.critical(f"{parsed_args.previous_run} is not a directory.")
sys.tracebacklimit = 0
raise ValueError() from None
defaults = MacsyDefaults(i_evalue_sel=1.0e9, coverage_profile=-1.0)
cfg = Config(defaults, parsed_args)
msf_run_path = cfg.previous_run()
hmmer_results = os.path.join(msf_run_path, cfg.hmmer_dir())
hmm_suffix = cfg.res_search_suffix()
profile_suffix = cfg.profile_suffix()
if parsed_args.out:
profile_report_path = os.path.normpath(parsed_args.out)
dirname = os.path.normpath(os.path.dirname(parsed_args.out))
if not os.path.exists(dirname):
_log.critical(f"The {dirname} directory is not writable")
sys.tracebacklimit = 0
raise ValueError() from None
else:
profile_report_path = os.path.join(cfg.previous_run(),
'hmm_coverage.tsv')
if os.path.exists(profile_report_path) and not parsed_args.force:
_log.critical(
f"The file {profile_report_path} already exists. "
f"Remove it or specify a new output name --out or use --force option"
)
sys.tracebacklimit = 0
raise ValueError() from None
hmmer_files = sorted(
glob.glob(
os.path.join(hmmer_results, f"{parsed_args.pattern}{hmm_suffix}")))
try:
model_familly_name = cfg.models()[0]
model_dir = [
p for p in
[os.path.join(p, model_familly_name) for p in cfg.models_dir()]
if os.path.exists(p)
][-1]
profiles_dir = os.path.join(model_dir, 'profiles')
except IndexError:
_log.critical(
f"Cannot find models in conf file {msf_run_path}. "
f"May be these results have been generated with an old version of macsyfinder."
)
sys.tracebacklimit = 0
raise ValueError() from None
_log.debug(f"hmmer_files: {hmmer_files}")
all_hits = []
with open(profile_report_path, 'w') as prof_out:
print(header(args), file=prof_out)
for hmmer_out_path in hmmer_files:
_log.info(f"parsing {hmmer_out_path}")
gene_name = get_gene_name(hmmer_out_path, hmm_suffix)
profile_path = os.path.join(profiles_dir,
f"{gene_name}{profile_suffix}")
gene_profile_len = get_profile_len(profile_path)
hmm = HmmProfile(gene_name, gene_profile_len, hmmer_out_path, cfg)
hits = hmm.parse()
all_hits += hits
if len(all_hits) > 0:
if parsed_args.best_hits:
# It's important to keep this sorting to have in last all_hits version
# the hits with the same replicon_name and position sorted by score
# the best score in first
hits_by_replicon = {}
for hit in all_hits:
if hit.replicon_name in hits_by_replicon:
hits_by_replicon[hit.replicon_name].append(hit)
else:
hits_by_replicon[hit.replicon_name] = [hit]
all_hits = []
for rep_name in hits_by_replicon:
hits_by_replicon[rep_name] = get_best_hits(
hits_by_replicon[rep_name], key=parsed_args.best_hits)
all_hits += sorted(hits_by_replicon[rep_name],
key=lambda h: h.position)
all_hits = sorted(
all_hits,
key=lambda h:
(h.gene_name, h.replicon_name, h.position, h.score))
_log.info(f"found {len(all_hits)} hits")
for hit in all_hits:
print(hit, file=prof_out)
_log.info(f"result is in '{profile_report_path}'")
else:
_log.info("No hit found")
