hit¶

This module implements class relative to hit and some functions to do some computation on hit objects.

`macsypy.hit.CoreHit`	Modelize a hmm hit on the replicon. There is only one Corehit for a CoreGene.
`macsypy.hit.ModelHit`	Modelize a hit and its relation to the Model.
`macsypy.hit.AbstractCounterpartHit`	Parent class of Loner, MultiSystem. It’s inherits from ModelHit.
`macsypy.hit.Loner`	Modelize “true” Loner.
`macsypy.hit.MultiSystem`	Modelize hit which can be used in several Systems (same model)
`macsypy.hit.LonerMultiSystem`	Modelize a hit representing a gene Loner and MultiSystem at same time.
`macsypy.hit.HitWeight`	The weights apply to the hit to compute score
`macsypy.hit.get_best_hit_4_func()`	Return the best hit for a given function
`macsypy.hit.sort_model_hits()`	Sort hits
`macsypy.hit.compute_best_MSHit()`	Choose among svereal multisystem hits the best one
`macsypy.hit.get_best_hits()`	If several profile hit the same gene return the best hit

A Hit is created when hmmsearch find similarities between a profile and protein of the input dataset

Below the ingheritance diagram of Hits

And a diagram showing the interaction between CoreGene, ModelGene, Model, Hit, Loner, … interactions

The diagram above represents the models, genes and hit generated from the definitions below.¶

<model name="A" inter_gene_max_space="2">
    <gene name="abc" presence="mandatory"/>
    <gene name="def" presence="accessory"/>
</model>

<model name="B" inter_gene_max_space="5">
    <gene name="def" presence="mandatory"/>
        <exchangeables>
            <gene name="abc"/>
        </exchangeables>
    <gene name="ghj" presence="accessory"
</model>

hit¶

hit API reference¶

CoreHit¶

ModelHit¶

AbstractCounterpartHit¶

Loner¶

MultiSystem¶

LonerMultiSystem¶

HitWeight¶

get_best_hit_4_func¶

sort_model_hits¶

compute_best_MSHit¶

get_best_hits¶