registries

The registry manage the different location where macsyfinder can find models definitions and their associated profiles.

registries API reference

ModelRegistry

class macsypy.registries.ModelRegistry[source]

scan canonical directories to register the different models available in global macsyfinder share data location (depending on installation /usr/share/data/models) or can be overloaded with the location specify in the macsyfinder configuration (either in config file or command line)

__getitem__(name: str) → ModelLocation[source]

Parameters:: name –
Returns:: the model corresponding to name.
Raises:: KeyError – if name does not match any ModelLocation registered.

__init__() → None[source]

__str__() → str[source]: Return str(self).

__weakref__: list of weak references to the object (if defined)

add(model_loc: ModelLocation) → None[source]

Parameters:: model_loc – the model location to add to the registry

models() → list[ModelLocation][source]

Returns:: the list of models

ModelLocation

class macsypy.registries.ModelLocation(path: str | None = None, profile_suffix: str = '.hmm', relative_path: bool = False)[source]

Handle where are store Models. Models are organized in families and subfamilies. each family match to a ModelLocation. a ModelLocation contains the path toward the definitions and the paths to corresponding to the profiles.

__eq__(other: ModelLocation) → bool[source]: Return self==value.

__gt__(other: ModelLocation) → bool[source]: Return self>value.

__hash__ = None

__init__(path: str | None = None, profile_suffix: str = '.hmm', relative_path: bool = False) → None[source]

Parameters:

path – if it’s an installed model, path is the absolute path to a model family.
profile_suffix – the suffix of hmm files
relative_path – True if you want to work with relative path, False to work with absolute path.

__lt__(other: ModelLocation) → bool[source]: Return self<value.

__str__() → str[source]: Return str(self).

__weakref__: list of weak references to the object (if defined)

_scan_definitions(parent_def: DefinitionLocation | None = None, def_path: str | None = None) → DefinitionLocation[source]

Scan recursively the definitions tree on the file model and store them.

Parameters:

parent_def – the current model definition to add new submodel location
def_path – the absolute path to analyse

Returns:

a definition location

_scan_profiles(path: str, profile_suffix: str = '.hmm', relative_path: bool = False) → dict[slice(<class 'str'>, <class 'str'>, None)][source]

Store all hmm profiles associated to the model

Parameters:

path – the path to a directory containing hmm profiles
profile_suffix – the extension of hmm profile file
relative_path – True if the path is relative, False otherwise.

Returns:

all profiles found in the path

get_all_definitions(root_def_name: str | None = None) → list[DefinitionLocation][source]

Name root_def_name:: The name of the root definition to get sub definitions. If root_def is None, return all definitions for this set of models
Returns:: the list of definitions or subdefinitions if root_def is specified for this model.
Raises:: ValueError – if root_def_name does not match with any definitions

get_definition(fqn: str) → DefinitionLocation[source]

Parameters:: fqn – the fully qualified name of the definition to retrieve. it’s complete path without extension. for instance for a file with path like this: models/TXSS/defintions/T3SS.xml the name is: TXSS/T3SS for models/CRISPR-Cas/definitions/typing/CAS.xml: the name is CRISPR-Cas/typing/CAS
Returns:: the definition corresponding to the given name.
Raise:: valueError if fqn does not match with any model definition.

get_definitions() → list[DefinitionLocation][source]

Returns:: the list of the definitions of this modelLocation. It returns the 1rst level only (not recursive). For recursive explorations see macsypy.registries.ModelLocation.get_all_definitions()

get_profile(name: str) → str[source]

Parameters:: name – the name of the profile to retrieve (without extension).
Returns:: the absolute path of the hmm profile.
Raise:: KeyError if name does not match with any profiles.

get_profiles_names() → list[str][source]

Returns:: The list of profiles name (without extension) for this model location

property version: str

Returns:: The version of the models

MetaDefLoc

class macsypy.registries.MetaDefLoc[source]

DefinitionLocation

class macsypy.registries.DefinitionLocation(name: str | None = None, fqn: str | None = None, subdefinitions: DefinitionLocation | None = None, path: str | None = None)[source]

Manage where definitions are stored. a Model is a xml definition and associated profiles. It has 3 attributes

name: the fully qualified definitions name like TXSS/T3SS or CRISPR-cas/Typing/Cas path: the absolute path to the definitions or set of definitions subdefinitions: the subdefinitions if it exists

__eq__(other: DefinitionLocation) → bool[source]: Return self==value.

__gt__(other: DefinitionLocation) → bool[source]: Return self>value.

__hash__() → int[source]: Return hash(self).

__init__(name: str | None = None, fqn: str | None = None, subdefinitions: DefinitionLocation | None = None, path: str | None = None) → None[source]

__lt__(other: DefinitionLocation) → bool[source]: Return self<value.

__str__() → str[source]: Return str(self).

__weakref__: list of weak references to the object (if defined)

add_subdefinition(subdefinition: DefinitionLocation) → None[source]

add new sub category of definitions to this definition

Parameters:: subdefinition – the new definition to add as subdefinition.

all() → list[DefinitionLocation][source]

Returns:: the definition and all recursively all subdefinitions

property family_name: str

Returns:: the models family name which is the name of the package

classmethod root_name(fqn: str) → str[source]

Parameters:: fqn (str) – the fully qualified name of a definition
Returns:: the root name of this definition (family name)

classmethod split_fqn(fqn: str) → list[str][source]

Parameters:: fqn – the fully qualified name of a definition
Returns:: each member of the fully qn in list.

split_def_name

macsypy.registries.split_def_name(fqn: str) → list[str][source]

Parameters:: fqn – the fully qualified de name of a DefinitionLocation object the follow the schema model_name/<def_name>*/def_name for instance CRISPR-Cas/typing/cas
Returns:: the list of components of the def path [‘CRISPR-Cas’, ‘typing’, ‘cas’]

join_def_path

macsypy.registries.join_def_path(*args: str) → str[source]: join different elements of the definition path :param str args: the elements of the definition path, each element must be a string :return: The return value is the concatenation of different elements of args with one separator

scan_models_dir

macsypy.registries.scan_models_dir(models_dir: str, profile_suffix: str = '.hmm', relative_path: bool = False) → list[ModelLocation][source]

Parameters:

models_dir (str) – The path to the directory where are stored the models
profile_suffix – the suffix of the hmm profiles
relative_path – True if models_dir is relative false otherwise

Returns:

the list of models in models_dir

Return type:

[macsypy.registries.ModelLocation, …]