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¶
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
