registries

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

registries API reference

class macsypy.registries.DefinitionLocation(name=None, subdefinitions=None, path=None)

Manage were 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 subdefintions if it exists

__eq__(other)

Return self==value.

__gt__(other)

Return self>value.

__hash__()

Return hash(self).

__init__(name=None, subdefinitions=None, path=None)

Initialize self. See help(type(self)) for accurate signature.

__lt__(other)

Return self<value.

__str__()

Return str(self).

__weakref__

list of weak references to the object (if defined)

add_subdefinition(subdefinition)

add new sub category of definitions to this definition

Parameters:subdefinition (DefinitionLocation object) – the new definition to add as subdefinition.

class macsypy.registries.ModelLocation(path=None, profile_dir=None, def_dir=None, profile_suffix='.hmm', relative_path=False)

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

__eq__(other)

Return self==value.

__gt__(other)

Return self>value.

__init__(path=None, profile_dir=None, def_dir=None, profile_suffix='.hmm', relative_path=False)

Parameters:

• path (str) – if it’s an installed model, path is the absolute path to a model family. otherwise path is None, and profile_dir and def_dir must be specified.
• profile_dir (str) – the absolute path to the directory which contains the hmm profiles files.
• def_dir (str) – The absolute path to the directory which contains the models definitions (xml files) or submodels.
• profile_suffix (str) – the suffix of hmm files
• relative_path (bool) – True if you want to work with relative path, False to work with absolute path.

Raise:

MacsypyError if path is set and profile_dir or def_dir is set

Raise:

MacsypyError if profile_dir is set but not def_dir and vice versa

__lt__(other)

Return self<value.

__str__()

Return str(self).

__weakref__

list of weak references to the object (if defined)

_scan_definitions(model_def=None, def_path=None)

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

Parameters:

• model_def (DefinitionLocation) – the current model definition to add new submodel location
• def_path (string) – the absolute path to analyse

Returns:

a definition location

Return type:

DefinitionLocation object

_scan_profiles(path, profile_suffix='.hmm', relative_path=False)

Store all hmm profiles associated to the model

get_all_definitions(root_def_name=None)

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 Parameters:root_def_name – string Returns:the list of definitions or subdefinitions if root_def is specified for this model. Return type:list of :class: DefinitionLocation` object Raises:ValueError – if root_def_name does not match with any definitions

get_definition(fqn)

Parameters:fqn (string.) – 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. Return type:a DefinitionLocation object. Raise:valueError if fqn does not match with any model definition.

get_definitions()

Returns:

get_profile(name)

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

get_profiles_names()

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

class macsypy.registries.ModelRegistry

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

__getitem__(name)

Parameters:name (string) – Returns:the model corresponding to name. Return type:ModelLocation object. Raises:KeyError – if name does not match any ModelLocation registered.

__init__()

Initialize self. See help(type(self)) for accurate signature.

__str__()

Return str(self).

__weakref__

list of weak references to the object (if defined)

add(model_loc)

Parameters:model_loc (ModelLocation object) – the model location to add to the registry

models()

Returns:the list of models Return type:list of ModelLocation object

macsypy.registries.join_def_path(*args)

join different elements of the definition path :param str args: the elements of the definition path, each elements must be a string :return: The return value is the concatenation of different elements of args with one separator :rtype: string

macsypy.registries.scan_models_dir(models_dir, profile_suffix='.hmm', relative_path=False)

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, …]

macsypy.registries.split_def_name(fqn)

Parameters:fqn (string) – 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’] Return type:list of string