gene

The Gene object represents genes encoding the protein components of a Model. There is 2 kind of gene The CoreGene (macsypy.gene.CoreGene) which must be unique given a name. A CoreGene must have a corresponding HMM protein profile. A ModelGene encapsulate a CoreGene and is linked to a Model.

Warning

To optimize computation and to avoid concurrency problems when we search several models, each gene must be instantiated only once, and stored in gene_bank. gene_bank is a macsypy.gene.GeneBank object. The gene_bank and model_bank (macsypy.model.ModelBank object) are instantiated in macsypy.scripts.macsyfinder.main() function and filled by a definition_parser (macsypy.defintion_parser.DefinitionParser)

Example to get a CoreGene object:

# get a model object
model_a = model_bank("TXSS/model_a")
model_b = model_bank("TXSS/model_b")

# get of a <CoreGene> object
t2ss =  gene_bank[("TXSS", "T2SS")]
pilO = gene_bank[("TXSS", "pilO")]

to create a ModelGene

modelA_t2ss(t2ss, model_A)
modelA_pilO(pilO, model_a, loner=True, inter_gene_max_space=12)
modelB_pilO(pilO, model_b, inter_gene_max_space=5)

There is only one instance of CoreGene with a given name (model family name, gene name) in one MSF run. But several instance of a ModelGene with the same name may exists. Above, there is 2 <ModelGene> representing pilO one in model_a the second in model_b with different properties.

Exchangeable inherits from ModelGene. Then a gene in some model is seen as a Gene, in some other models as an Exchangeable. But there only one instance of the corresponding CoreGene.:

core_sctn = gene_bank(("TXSS", "sctN"))
core_sctn_flg = gene_bank(("TXSS", "sctN_FLG"))
model_sctn = ModelGene(core_sctn, model_a)
ex_sctn_flg = Exchangeable(core_stn_flg, model_sctn)
model_sctn.add_exchangeable(ex_sctn_flg)

model_sctn_flg = ModelGene(core_sctn_flg, model_b)

which means that in model_a the gene sctn can be functionally replaced by sctn_flg. In Model_a it appear as an alternative to sctn but in model_B it appear as sctn_flg itself. In one MacSyFinder run several instances of ModelGene and/or Exchangeable with the same name may coexists . But in A whole macsyfinder run there is only one instance core_sctn_flg and core_sctn.

gene API reference

GeneBank

class macsypy.gene.GeneBank[source]

Store all Gene objects. Ensure that genes are instanciated only once.

__contains__(gene)[source]

Implement the membership test operator

Parameters:

gene (macsypy.gene.CoreGene object) – the gene to test

Returns:

True if the gene is in, False otherwise

Return type:

boolean

__getitem__(key)[source]

Parameters:

key (tuple (string, string)) – The key to retrieve a gene. The key is composed of the name of models family and the gene name. for instance CRISPR-Cas/cas9_TypeIIB (‘CRISPR-Cas’ , ‘cas9_TypeIIB’) or TXSS/T6SS_tssH (‘TXSS’, ‘T6SS_tssH’)

Returns:

return the Gene corresponding to the key.

Return type:

macsypy.gene.CoreGene object

Raises:

KeyError – if the key does not exist in GeneBank.

__init__()[source]

__iter__()[source]

Return an iterator object on the genes contained in the bank

__weakref__

list of weak references to the object (if defined)

add_new_gene(model_location, name, profile_factory)[source]

Create a gene and store it in the bank. If the same gene (same name) is add twice, it is created only the first time.

Parameters:

model_location (macsypy.registry.ModelLocation object) – the location where the model family can be found.

name (str) – the name of the gene to add

profile_factory (profile.ProfileFactory object.) – The Profile factory

genes_fqn()[source]

Returns:

the fully qualified name for all genes in the bank

Return type:

str

Gene

There is two classes to modelize a gene: macsypy.gene.CoreGene and macsypy.gene.ModelGene. The CoreGene are created using the macsypy.gene.GeneBank factory and there is only one instance of a CoreGene with a given name. Whereas several ModelGene with the same name can appear in different model and can have differents properties, loner in one model and not in an other, have different inter_gene_max_space … The ModelGene is attached to the model and is composed of a CoreGene.

Note

The macsypy.hit.Hit object are link to a CoreGene, whereas the macsypy.hit.ValidHit ref_gene attribute reference a macsypy.gene.ModelGene

CoreGene

class macsypy.gene.CoreGene(model_location, name, profile_factory)[source]

Modelize gene attach to a profile. It can be only one instance with the the same name (familly name, gene name)

__hash__()[source]: Return hash(self).

__init__(model_location, name, profile_factory)[source]

__weakref__: list of weak references to the object (if defined)

property model_family_name: The name of the model family for instance ‘CRISPRCas’ or ‘TXSS’

property name: The name of the gene a hmm profile with the same name must exists.

property profile: The HMM protein Profile corresponding to this gene macsypy.profile.Profile object

ModelGene

class macsypy.gene.ModelGene(gene, model, loner=False, multi_system=False, inter_gene_max_space=None, multi_model=False)[source]

Handle Gene describe in a Model

__hash__()[source]: Return hash(self).

__init__(gene, model, loner=False, multi_system=False, inter_gene_max_space=None, multi_model=False)[source]

Handle gene described in a Model

Parameters:

gene (a macsypy.gene.CoreGene object.) – a gene link to a profile
model (macsypy.model.Model object.) – the model that owns this Gene
loner (bool) – True if the Gene can be isolated on the genome (with no contiguous genes), False otherwise.
multi_system (bool) – True if this Gene can belong to different occurrences of this System.
inter_gene_max_space (int) – the maximum space between this Gene and another gene of the System.
multi_model (bool) – True if this Gene is allowing to appear in several system occurence from diferent model.

__str__()[source]: Print the name of the gene and of its exchangeable genes.

__weakref__: list of weak references to the object (if defined)

add_exchangeable(exchangeable)[source]

Add a exchangeable gene to this Gene

Parameters:: exchangeable (macsypy.gene.Exchangeable object) – the exchangeable to add

alternate_of()[source]

Returns:: the gene to which this one is an exchangeable to (reference gene), or itself if it is a first level gene.
Return type:: macsypy.gene.ModelGene object

property core_gene

Returns:: The CoreGene associated to this ModelGene
Return type:: macsypy.gene.CoreGene object

property exchangeables

Returns:: the list of genes which can replace this one without any effect on the model
Return type:: list of macsypy.gene.ModelGene objects

property inter_gene_max_space

Returns:: The maximum distance allowed between this gene and another gene for them to be considered co-localized. If the value is not set at the Gene level, return None.
Return type:: integer. or None

is_accessory(model)[source]

Returns:: True if the gene is within the accessory genes of the model, False otherwise.
Parameters:: model (macsypy.model.Model object.) – the query of the test
Return type:: boolean.

property is_exchangeable

Returns:: True if this gene is describe in the model as an exchangeable. False if ot is describe as first level gene.

is_forbidden(model)[source]

Returns:: True if the gene is within the forbidden genes of the model, False otherwise.
Parameters:: model (macsypy.model.Model object.) – the query of the test
Return type:: boolean.

is_mandatory(model)[source]

Returns:: True if the gene is within the mandatory genes of the model, False otherwise.
Parameters:: model (macsypy.model.Model object.) – the query of the test
Return type:: boolean.

property loner

Returns:: True if the gene can be isolated on the genome, False otherwise
Return type:: boolean

property model

Returns:: the Model that owns this Gene
Return type:: macsypy.model.Model object

property multi_model

Returns:: True if this Gene can belong to different occurrences of systems from different model macsypy.model.Model (and can be used for multiple System assessments), False otherwise.
Return type:: boolean.

property multi_system

Returns:: True if this Gene can belong to different occurrences of the model (and can be used for multiple System assessments), False otherwise.
Return type:: boolean.

set_status(status)[source]

Set the status for this gene

Parameters:: status (macsypy.gene.GeneStatus object) – the status of this gene

property status

Returns:: The status of this gene
Return type:: macsypy.gene.GeneStatus object

Exchangeable

class macsypy.gene.Exchangeable(c_gene, gene_ref, loner=None, multi_system=None, multi_model=None, inter_gene_max_space=None)[source]

Handle Exchangeables. Exchangeable are ModelGene which can replaced functionally an other ModelGene. Biologically it can be Homolog or Analog

__init__(c_gene, gene_ref, loner=None, multi_system=None, multi_model=None, inter_gene_max_space=None)[source]

Parameters:

c_gene (macsypy.gene.CoreGene object.) – the gene
gene_ref (macsypy.gene.ModelGene object.) – the gene to which the current can replace it.

add_exchangeable(exchangeable)[source]

This method should never be called, it’s a security to avoid to add exchangeable to an exchangeable.

Parameters:: exchangeable (macsypy.gene.Exchangeable) –
Raises:: MacsypyError –

alternate_of()[source]

Returns:: the gene to which this one is an exchangeable to (reference gene)
Return type:: macsypy.gene.ModelGene object

property is_exchangeable

Returns:: True

property status

Returns:: The status of this gene. if the status is not define for this gene itself, return the status of the reference gene.
Return type:: macsypy.gene.GeneStatus object

GeneStatus

class macsypy.gene.GeneStatus(value, names=None, *values, module=None, qualname=None, type=None, start=1, boundary=None)[source]

Handle status of Gene GeneStatus can take 4 value:

MANDATORY
ACCESSORY
FORBIDDEN
NEUTRAL