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)[source]¶ Is an abstract class for (Odered/Unordered)MatchMaker the match class method must be implemented in concrete classes
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__weakref__
¶ list of weak references to the object (if defined)
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_create_exchangeable_map
(genes)[source]¶ 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 genesReturn type: a dict with keys are the exchangeable gene_name and the value the reference gene
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present_genes
()[source]¶ 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])
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sort_hits_by_status
(hits)[source]¶ sort
macsypy.hit.ModelHit
according the the status of the gene the hit code for.Parameters: hits – list of macsypy.hit.ModelHit
objectReturns: the valid hits according their status Return type: a tuple of 4 lists macsypy.hit.ModelHit
for MANDATORY genesmacsypy.hit.ModelHit
for ACCESSORY genesmacsypy.hit.ModelHit
for NEUTRAL genesmacsypy.hit.ModelHit
for FORBIDDEN genes
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OrderedMatchMaker¶
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class
macsypy.system.
OrderedMatchMaker
(model, redundancy_penalty)[source]¶ check if a set of hits match the quorum for ordered replicons (ordered_replicon or gembase)
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__init__
(model, redundancy_penalty)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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match
(clusters)[source]¶ Check a set of clusters fill model constraints. If yes create a
macsypy.system.System
otherwise create amacsypy.cluster.RejectedCandidate
.Parameters: clusters (list of macsypy.cluster.Cluster
objects) – The list of cluster to check if fit the modelReturns: either a System or a RejectedCandidates Return type: macsypy.system.System
ormacsypy.system.RejectedCandidate
object
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UnorderedMatchMaker¶
HitSystemTracker¶
MetaSetOfHits¶
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class
macsypy.system.
MetaSetOfHits
[source]¶ 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
AbstractSetOfHits¶
-
class
macsypy.system.
AbstractSetOfHits
(model)[source]¶ Is the mother class of System, RejectedCandidates, LikelySystems UnlikelySystem, …
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__weakref__
¶ list of weak references to the object (if defined)
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count
()[source]¶ 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
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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)
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replicon_name
¶ Returns: The name of the replicon Return type: str
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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
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System¶
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class
macsypy.system.
System
(model, clusters, redundancy_penalty=1.5)[source]¶ Modelize as system. a system is an occurrence of a given model on a replicon.
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__init__
(model, clusters, redundancy_penalty=1.5)[source]¶ 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
- model (
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get_hits_encoding_multisystem
()[source]¶ Returns: The hits codding for a gene taged as multi system Return type: set of macsypy.hit.ModelHit
object
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get_loners
()[source]¶ Returns: The True Loners (Loner which not colocalize with an other hit) belonging to the systems Return type: set of macsypy.hit.Loner
object
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get_multisystems
()[source]¶ 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
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hits
¶ Returns: The list of all hits that compose this system Return type: [ macsypy.hit.ValidHits
, … ]
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is_compatible
(other)[source]¶ Parameters: other ( macsypy.system.System
object) – the other systems to test compatibilityReturns: 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.
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loci_nb
¶ Returns: The number of loci of this system (loners are not considered) Return type: int >= 0
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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
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multi_loci
¶ Returns: True if the systems is encoded in multiple loci. False otherwise Return type: bool
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occurrence
()[source]¶ 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
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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
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RejectedCandidate¶
-
class
macsypy.system.
RejectedCandidate
(model, clusters, reasons)[source]¶ 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)[source]¶ Parameters: - model (
macsypy.model.Model
object) – - clusters (list of
macsypy.cluster.Cluster
objects) – list of clusters. These Clusters should be created withmacsypy.cluster.Cluster
ofmacsypy.hit.ModelHit
objects - reasons (list of string) – the reason why these clusters have been rejected
- model (
-
hits
¶ Returns: The list of all hits that compose this system Return type: [ macsypy.hit.ModelHit
, … ]
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AbstractUnordered¶
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class
macsypy.system.
AbstractUnordered
(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits)[source]¶ Technical abstract class to factorize code share between LikelySystem and UnlikelySystem
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__init__
(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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accessory_hits
¶ Returns: The list of accesory hits Return type: list of macsypy.hit.ModelHit
objects
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allowed_hits
¶ Returns: The list of allowed (mandatory, accessory, neutral) hits Return type: list of macsypy.hit.ModelHit
objects
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forbidden_hits
¶ Returns: The list of forbidden hits Return type: list of macsypy.hit.ModelHit
objects
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hits
¶ Returns: The list of all hits sorted by their position Return type: list of macsypy.hit.ModelHit
objects
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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
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LikelySystem¶
UnlikelySystem¶
-
class
macsypy.system.
UnlikelySystem
(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits, reasons)[source]¶ Handle components that not fill the quorum requirements defined in model.
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__init__
(model, mandatory_hits, accessory_hits, neutral_hits, forbidden_hits, reasons)[source]¶ 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
- model (
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reasons
¶ Returns: The reasons why it probably not a system Return type: list of string
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