utils

Here some useful functions in the rest of macsyfinder code

utils API reference

get_def_to_detect

macsypy.utils.get_def_to_detect(models: list[tuple[str, tuple[str]]], model_registry: ModelRegistry) → tuple[list[DefinitionLocation], str, str]

Parameters:

• models (list of tuple with the following structure: [('model_fqn', ('def1, def2, ...)), ('model_2', ('def1', ...)), ...]) – the list of models to detect as returned by config.models.

• model_registry – the models registry for this run.

Returns:

the definitions to parse

Raises:

ValueError – if a model name provided in models is not in model_registry.

get_replicon_names

macsypy.utils.get_replicon_names(genome_path, db_type) → list[str]

threads_available

macsypy.utils.threads_available() → int

Returns:

The maximal number of threads available. It’s nice with cluster scheduler or linux. On Mac it uses the number of physical cores

parse_time

macsypy.utils.parse_time(user_time: int | str) → int

parse user-friendly time and return it in seconds user time supports units as s h m d for sec min hour day or a combination of them 1h10m50s means 1 hour 10 minutes 50 seconds all terms will be converted in seconds and added

Parameters:

user_time –

Returns:

seconds

Raise:

ValueError if user_time is not parseable