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

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

ModelLocation

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

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

MetaDefLoc

class macsypy.registries.MetaDefLoc

DefinitionLocation

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

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 subdefintions if it exists

__eq__(other)

Return self==value.

__gt__(other)

Return self>value.

__hash__()

Return hash(self).

__init__(name=None, fqn=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.

all()

Returns:the defintion and all recursivelly all subdefintions

family_name

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

classmethod root_name(fqn)

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

classmethod split_fqn(fqn)

Parameters:fqn (str) – the fully qualified name of a defintion Returns:each member of the fully qn in list.

split_def_name

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

join_def_path

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

scan_models_dir

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, …]