System API

It represents a macromolecular system to detect. See The System object for an overview of its implementation.

Note

a complete description of macromolecular systems modelling is available in the section Macromolecular systems definition

SystemBank API reference

class macsypy.system.SystemBank

Build and store all Systems objects. Systems must not be instanciated directly. This system factory must be used. It ensures there is a unique instance of a system for a given system name. To get a system, use the method __getitem__ via the “[]”. If the System is already cached in the SystemBank, it is returned. Otherwise a new system is built, stored and then returned.

__contains__(system)

Implement the membership test operator

Parameters:system (macsypy.system.System object) – the system to test Returns:True if the system is in the System factory, False otherwise Return type:boolean

__getitem__(name)

Parameters:name (string) – the name of the system Returns:the system corresponding to the name. If the system already exists, return it, otherwise build it and return it. Return type:macsypy.system.System object

__iter__()

Return an iterator object on the systems contained in the bank

__len__()

Returns:the number of systems stored in the bank Return type:integer

__weakref__

list of weak references to the object (if defined)

add_system(system)

Parameters:system (macsypy.system.System object) – the system to add Raise:KeyError if a system with the same name is already registered.

Note

Don’t instanciate your own SystemBank use the system_bank at the top level of the module.

from macsypy.system import system_bank

System API reference

class macsypy.system.System(cfg, name, inter_gene_max_space, min_mandatory_genes_required=None, min_genes_required=None, max_nb_genes=None, multi_loci=False)

Handle a secretion system.

__init__(cfg, name, inter_gene_max_space, min_mandatory_genes_required=None, min_genes_required=None, max_nb_genes=None, multi_loci=False)

Parameters:

• cfg (macsypy.config.Config object) – the configuration object
• name (string) – the name of the system
• inter_gene_max_space (integer) – the maximum distance between two genes (co-localization parameter)
• min_mandatory_genes_required (integer) – the quorum of mandatory genes to define this system
• min_genes_required (integer) – the quorum of genes to define this system
• max_nb_genes (integer) –
• multi_loci (boolean) –

__weakref__

list of weak references to the object (if defined)

accessory_genes

Returns:the list of genes that are allowed in this secretion system Return type:list of macsypy.gene.Gene objects

add_accessory_gene(gene)

Add a gene to the list of accessory genes

Parameters:gene (macsypy.gene.Gene object) – gene that is allowed to be present in this system

add_forbidden_gene(gene)

Add a gene to the list of forbidden genes

Parameters:gene (macsypy.genen.Gene object) – gene that must not be found in this system

add_mandatory_gene(gene)

Add a gene to the list of mandatory genes

Parameters:gene (macsypy.gene.Gene object) – gene that is mandatory for this system

forbidden_genes

Returns:the list of genes that are forbidden in this secretion system Return type:list of macsypy.gene.Gene objects

get_gene(gene_name)

Parameters:gene_name (string) – the name of the gene to get Returns:the gene corresponding to gene_name. Return type:a macsypy.gene.Gene object. Raise:KeyError the system does not contain any gene with name gene_name.

get_gene_ref(gene)

Parameters:gene (a macsypy.gene.Gene or macsypy.gene.Homolog` or macsypy.gene.Analog` object.) – the gene to get the gene reference. Returns:the gene reference of the gene if exists (if the gene is an Homolog or an Analog), otherwise return None. Return type:macsypy.gene.Gene object or None Raise:KeyError if gene is not in the system

inter_gene_max_space

Returns:set the maximum distance allowed between 2 genes for this system Return type:integer

mandatory_genes

Returns:the list of genes that are mandatory in this secretion system Return type:list of macsypy.gene.Gene objects

max_nb_genes

Returns:the maximum number of genes to assess the system presence. Return type:int (or None)

min_genes_required

Returns:get the minimum number of genes to assess for the system presence. Return type:integer

min_mandatory_genes_required

Returns:get the quorum of mandatory genes required for this system Return type:integer

multi_loci

Returns:True if the system is authorized to be inferred from multiple loci, False otherwise Return type:boolean