System API
It represents a macromolecular system to detect. See The System object for an overview of its implementation.
SystemBank API reference
-
class macsypy.system.SystemBank[source]
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)[source]
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)[source]
| 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__()[source]
Return an iterator object on the systems contained in the bank
-
__len__()[source]
| 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)[source]
| 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)[source]
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)[source]
| 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[source]
| Returns: | the list of genes that are allowed in this secretion system |
|---|
| Return type: | list of macsypy.gene.Gene objects |
|---|
-
add_accessory_gene(gene)[source]
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)[source]
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)[source]
Add a gene to the list of mandatory genes
-
forbidden_genes[source]
| Returns: | the list of genes that are forbidden in this secretion system |
|---|
| Return type: | list of macsypy.gene.Gene objects |
|---|
-
get_gene(gene_name)[source]
| 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)[source]
| 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[source]
| Returns: | set the maximum distance allowed between 2 genes for this system |
|---|
| Return type: | integer |
|---|
-
mandatory_genes[source]
| Returns: | the list of genes that are mandatory in this secretion system |
|---|
| Return type: | list of macsypy.gene.Gene objects |
|---|
-
max_nb_genes[source]
| Returns: | the maximum number of genes to assess the system presence. |
|---|
| Return type: | int (or None) |
|---|
-
min_genes_required[source]
| Returns: | get the minimum number of genes to assess for the system presence. |
|---|
| Return type: | integer |
|---|
-
min_mandatory_genes_required[source]
| Returns: | get the quorum of mandatory genes required for this system |
|---|
| Return type: | integer |
|---|
-
multi_loci[source]
| Returns: | True if the system is authorized to be inferred from multiple loci, False otherwise |
|---|
| Return type: | boolean |
|---|