model

The model is a formal representation of system. The model is describe in terms of components. There are 4 component classes:

  • genes which are mandatory

  • genes which are accessory

  • genes which are neutral

  • genes which are forbiden

Each genes can have Exchangeable. An exchangeable is another gene which can paly the same role in the system. Usualy an analog or homolog. The models describe also distance constraints between genes:

  • inter_gene_max_space

  • loner

  • multi_loci

and quorum constraints

  • min_mandatory_genes_required

  • min_genes_required

and if a gene can be shared by several systems (several occurrences of the same model)

  • multisystem

model API reference

ModelBank

class macsypy.model.ModelBank[source]

Store all Models objects.

__contains__(model)[source]

Implement the membership test operator

Parameters

model (macsypy.model.Model object) – the model to test

Returns

True if the model is in the Model factory, False otherwise

Return type

boolean

__getitem__(fqn)[source]
Parameters

fqn (string) – the fully qualified name of the model

Returns

the model corresponding to the fqn.

Return type

macsypy.model.Model object

Raises

KeyError – if the model corresponding to the name does not exists

__init__()[source]

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

__iter__()[source]

Return an iterator object on the models contained in the bank

__len__()[source]
Returns

the number of models stored in the bank

Return type

integer

__weakref__

list of weak references to the object (if defined)

add_model(model)[source]
Parameters

model (macsypy.model.Model object) – the model to add

Raise

KeyError if a model with the same name is already registered.

Model

class macsypy.model.Model(*args, **kwargs)[source]

Handles a macromolecular model.

Contains all its pre-defined characteristics expected to be fulfilled to predict a complete model:
  • component list (genes that are mandatory, accessory, neutral, forbidden)

  • quorum (number of genes)

  • genetic architecture

__eq__(other)[source]
Parameters

other – the other model to compare

Returns

True if this fully qualified name is equal to other fully qualified name. False otherwise.

Return type

boolean

__gt__(other)[source]
Parameters

other – the other model to compare

Returns

True if this fully qualified name is greater than to other fully qualified name. False otherwise.

Return type

boolean

__hash__()[source]
Returns

__init__(fqn, inter_gene_max_space, min_mandatory_genes_required=None, min_genes_required=None, max_nb_genes=None, multi_loci=False)[source]
Parameters
  • fqn (string) – the fully qualified name of the model CRISPR-Cas/sub-typing/CAS-TypeIE

  • 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 model

  • min_genes_required (integer) – the quorum of genes to define this model

  • max_nb_genes (integer) – The number of gene to be considered as full system Used to compute the wholeness. If None the mx_nb_genes = mandatory + accessory

  • multi_loci (boolean) –

Raises

ModelInconsistencyError – if an error is found in model logic. For instance genes_required > min_mandatory_genes_required

__lt__(other)[source]
Parameters

other – the other model to compare

Returns

True if this fully qualified name is lesser than to other fully qualified name. False otherwise.

Return type

boolean

__str__()[source]

Return str(self).

__weakref__

list of weak references to the object (if defined)

property family_name
Returns

the family name of the model for instance ‘CRISPRCas’ or ‘TXSS’

Return type

str

filter(hits)[source]

filter out the hits according to this model. The filtering is based on the name of CoreGene associated to hit and the name of ModelGene of the model (the name of the ModelGene is the name of the CoreGene embed in the ModelGene) only the hits related to genes implied in the model are kept.

Parameters

hits (list of macsypy.report.CoreHit object) – list of hits to filter

Returns

list of hits

Return type

list of macsypy.report.Model object

genes(exchangeable=False)[source]
Parameters

exchangeable (bool) – include exchageables if True

Returns

all the genes described in the model. with exchangeables if exchageable is True. otherwise only “first level” genes.

Return type

set of macsypy.gene.ModelGene 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.ModelGene object.

Raise

KeyError the model does not contain any gene with name gene_name.

property inter_gene_max_space
Returns

set the maximum distance allowed between 2 genes for this model

Return type

integer

property max_nb_genes
Returns

the maximum number of genes to assess the model presence.

Return type

int (or None)

property min_genes_required
Returns

get the minimum number of genes to assess for the model presence.

Return type

integer

property min_mandatory_genes_required
Returns

get the quorum of mandatory genes required for this model

Return type

integer

property multi_loci
Returns

True if the model is authorized to be inferred from multiple loci, False otherwise

Return type

boolean

property name
Returns

the short name of this model