system

This module classes and functions which a given set of hits and a model compute if this set satisfy the model or not

The object which check the compliance of hits to a model is MatchMaker which have 2 sub-classes for ordered and unordered replicons

MatchMaker.match method link hit to a model (macsypy.hit.ValidHit) and then check if these valid hit satisfy the quorum constraints defined in the model. According this it instanciate a macsypy.system.System or macsypy.system.RejectedCandidate for ordered replicons or macsypy.system.LikelySystem or macsypy.system.UnlikelySystem for unordered replicons

below the inheritance diagram:

Warning

The abstract class macsypy.system.AbstractSetOfHits is controlled by the metaclass macsypy.system.MetaSetOfHits which inject on the fly several private attributes and public properties (see more in macsypy.system.MetaSetOfHits documentation)

system reference api

MatchMaker

class macsypy.system.MatchMaker(model)

Is an abstract class for (Odered/Unordered)MatchMaker the match class method must be implemented in concrete classes

__init__(model)

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

__weakref__

list of weak references to the object (if defined)

_create_exchangeable_map(genes)

create a map between an exchangeable (formly homolog or analog) gene name and it’s gene reference

Parameters:genes (list of macsypy.gene.ModelGene objects) – The genes to get the exchangeable genes Return type:a dict with keys are the exchangeable gene_name and the value the reference gene

present_genes()

Returns:the lists of genes name in model which are present in the replicon (included exchangeable) Return type:tuple of 4 lists for mandatory, accessory, neutral and forbidden ([str gene_name, ..], [str gene_name], [str gene_name], [str gene_name])

sort_hits_by_status(hits)

sort macsypy.hit.ModelHit according the the status of the gene the hit code for.

Parameters:hits – list of macsypy.hit.ModelHit object Returns:the valid hits according their status Return type:a tuple of 4 lists

• macsypy.hit.ModelHit for MANDATORY genes
• macsypy.hit.ModelHit for ACCESSORY genes
• macsypy.hit.ModelHit for NEUTRAL genes
• macsypy.hit.ModelHit for FORBIDDEN genes

OrderedMatchMaker

class macsypy.system.OrderedMatchMaker(model, redundancy_penalty)

check if a set of hits match the quorum for ordered replicons (ordered_replicon or gembase)

__init__(model, redundancy_penalty)

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

match(clusters)

Check a set of clusters fill model constraints. If yes create a macsypy.system.System otherwise create a macsypy.cluster.RejectedCandidate.

Parameters:clusters (list of macsypy.cluster.Cluster objects) – The list of cluster to check if fit the model Returns:either a System or a RejectedCandidates Return type:macsypy.system.System or macsypy.system.RejectedCandidate object

UnorderedMatchMaker

class macsypy.system.UnorderedMatchMaker(model)

match(hits)

Parameters:hits – Returns:

HitSystemTracker

class macsypy.system.HitSystemTracker(systems)

track in which system is implied each hit

__init__(systems)

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

__weakref__

list of weak references to the object (if defined)

MetaSetOfHits

class macsypy.system.MetaSetOfHits

This metaclass control the AbstractSetOfHits class creation. In this metaclass we inject on the fly several attributes and properties two private attributes and one public property corresponding to each value of _supported_status class attribute defined in the concrete classes. for instance for System class

• the attributes

  • self._mandatory
  • self._mandatory_occ
  • self._accessory
  • self._accessory_occ
  • self._neutral
  • self._neutral_occ

• and the properties

  • mandatory
  • accessory
  • neutral

are automatically injected

The value for attributes _<status>_occ are filled by the count method which is defined in AbstractSetOfHits

__call__(*args, **kwargs)

Call self as a function.

getter_maker()

Create a property which allow to access to the gene corresponding of the cat of the model

Parameters:cat (str) – the type of gene category to which we create the getter Returns:unbound method

AbstractSetOfHits

class macsypy.system.AbstractSetOfHits(model)

Is the mother class of System, RejectedCandidates, LikelySystems UnlikelySystem, …

__init__(model)

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

__weakref__

list of weak references to the object (if defined)

count()

fill structures one for supported status mandatory, accessory, … each structure count how many hit for each gene of the model mandatory_occ = { gene_name : [ModelHit, …] :return: None

position

Returns:The position of the first and last hit, excluded the hit coding for loners. If the system is composed only by loners, used loners to compute position Return type:tuple (start: int, end:int)

replicon_name

Returns:The name of the replicon Return type:str

wholeness

Returns:a score indicating the genes ratio of the model which have at least one hit by default full system is mandatory + accessory (‘neutral’ genes do not count) but for special corner case it can be sepcified in model definition (xml) or on the command line Return type:float

AbstractClusterizedHits

class macsypy.system.AbstractClusterizedHits(model, clusters)

__init__(model, clusters)

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

fulfilled_function(*genes)

Parameters:gene – The genes which must be tested. Returns:the common functions between genes and this system. Return type:set of string

System

class macsypy.system.System(model, clusters, redundancy_penalty=1.5)

Modelize as system. a system is an occurrence of a given model on a replicon.

__init__(model, clusters, redundancy_penalty=1.5)

Parameters:

• model (macsypy.model.Model object) – The model which has ben used to build this system
• clusters (list of macsypy.cluster.Cluster objects) – The list of cluster that form this system

__str__()

Return str(self).

get_hits_encoding_multisystem()

Returns:The hits codding for a gene taged as multi system Return type:set of macsypy.hit.ModelHit object

get_loners()

Returns:The True Loners (Loner which not colocalize with an other hit) belonging to the systems Return type:set of macsypy.hit.Loner object

get_multisystems()

Returns:The MultiSystem hit (comming from out system (other cluster or loner) and tag as multisystem) Return type:set of macsypy.hit.MultiSystem | macsypy.hit.LonerMultiSystem object

hits

Returns:The list of all hits that compose this system Return type:[macsypy.hit.ValidHits , … ]

is_compatible(other)

Parameters:other (macsypy.system.System object) – the other systems to test compatibility Returns:True if other system is compatible with this one. False otherwise. Two systems are compatible if they do not share macsypy.hit.CoreHit except hit corresponding to a multi_system gene in the model.

Note

This method is used to compute the best combination of systems.

loci_nb

Returns:The number of loci of this system (loners are not considered) Return type:int >= 0

loci_num

Returns:the number of the corresponding locus for each cluster the cluster made of only one Loner are not considered as a loci so these clusters have a negative locus_num Return type:list of int

multi_loci

Returns:True if the systems is encoded in multiple loci. False otherwise Return type:bool

occurrence()

sometimes several systems collocates so they form only one cluster so macsyfinder build only one system the occurrence is an indicator of how many systems are it’s based on the number of occurrence of each mandatory genes The multi_system genes are not take in account.

Returns:a predict number of biologic systems

score

Returns:a score take in account * if a hit match for the gene or it is an exchangeable gene * if a hit is duplicated and already present in the system or the cluster * if a hit match for mandatory/accessory gene of the model Return type:float

RejectedCandidate

class macsypy.system.RejectedCandidate(model, clusters, reasons)

Handle a set of clusters which has been rejected during the macsypy.system.match() step This clusters (can be one) does not fill the requirements or contains forbidden genes.

__init__(model, clusters, reasons)

Parameters:

• model (macsypy.model.Model object) –
• clusters (list of macsypy.cluster.Cluster objects) – list of clusters. These Clusters should be created with macsypy.cluster.Cluster of macsypy.hit.ModelHit objects
• reasons (list of string) – the reason why these clusters have been rejected

__str__()

Returns:a string representation of this RejectedCandidates

hits

Returns:The list of all hits that compose this system Return type:[macsypy.hit.ModelHit , … ]

AbstractUnordered

class macsypy.system.AbstractUnordered(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits)

Technical abstract class to factorize code share between LikelySystem and UnlikelySystem

__init__(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits)

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

accessory_hits

Returns:The list of accesory hits Return type:list of macsypy.hit.ModelHit objects

allowed_hits

Returns:The list of allowed (mandatory, accessory, neutral) hits Return type:list of macsypy.hit.ModelHit objects

forbidden_hits

Returns:The list of forbidden hits Return type:list of macsypy.hit.ModelHit objects

hits

Returns:The list of all hits sorted by their position Return type:list of macsypy.hit.ModelHit objects

mandatory_hits

Returns:The list of mandatory hits Return type:list of macsypy.hit.ModelHit objects

neutral_hits

Returns:The list of neutral hits Return type:list of macsypy.hit.ModelHit objects

LikelySystem

class macsypy.system.LikelySystem(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits)

” Handle components that fill the quorum requirements defined in model. with no idea about genetic organization (gene cluster) so we cannot take in account forbidden genes

__str__()

Returns:a string representation of this LikelySystem

UnlikelySystem

class macsypy.system.UnlikelySystem(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits, reasons)

Handle components that not fill the quorum requirements defined in model.

__init__(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits, reasons)

Parameters:

• model (macsypy.model.Model object) – The model which has ben used to build this system
• mandatory_hits (list of macsypy.hit.ModelHit objects) – The list of mandatory hits (encode for a gene tagged as mandatory)
• accessory_hits (list of macsypy.hit.ModelHit objects) – The list of accessory hits (encode for a gene tagged as accessory)
• neutral_hits (list of macsypy.hit.ModelHit objects) – The list of neutral hits (encode for a gene tagged as neutral)
• forbidden_hits (list of macsypy.hit.ModelHit objects) – The list of hits that are forbidden
• reasons (List of str) – the reasons why this set of hits has been rejected

__str__()

Returns:a string representation of this UnlikelySystem

reasons

Returns:The reasons why it probably not a system Return type:list of string