cluster

A cluster is an ordered set of hits related to a model which satisfy the model distance constraints.

cluster API reference

cluster

class macsypy.cluster.Cluster(hits, model, hit_weights)[source]

Handle hits relative to a model which collocates

__contains__(v_hit)[source]
Parameters:v_hit (macsypy.hit.ModelHit object) – The hit to test
Returns:True if the hit is in the cluster hits, False otherwise
__init__(hits, model, hit_weights)[source]
Parameters:
__str__()[source]
Returns:a string representation of this cluster
__weakref__

list of weak references to the object (if defined)

_check_replicon_consistency()[source]
Raise:MacsypyError if all hits of a cluster are NOT related to the same replicon
fulfilled_function(*genes)[source]
Parameters:gene – The genes which must be tested.
Returns:the common functions between genes and this cluster.
Return type:set of string
hit_weights
Returns:the different weight for the hits used to compute the score
Return type:macsypy.hit.HitWeight
loner
Returns:True if this cluster is made of only one hit representing a loner gene False otherwise: - contains several hits - contains one hit but gene is not tag as loner (max_gene_required = 1)
merge(cluster, before=False)[source]

merge the cluster in this one. (do it in place)

Parameters:
  • cluster (macsypy.cluster.Cluster object) –
  • before (bool) – If False the hits of the cluster will be add at the end of this one, Otherwise the cluster hits will be inserted before the hits of this one.
Returns:

None

Raises:

MacsypyError – if the two clusters have not the same model

multi_system
Returns:True if this cluster is made of only one hit representing a multi_system gene False otherwise: - contains several hits - contains one hit but gene is not tag as loner (max_gene_required = 1)
replace(old, new)[source]

replace hit old in this cluster by new one. (work in place)

Parameters:
Returns:

None

replicon_name
Returns:The name of the replicon where this cluster is located
Return type:str
score
Returns:The score for this cluster
Return type:float

build_clusters

macsypy.cluster.build_clusters(hits, rep_info, model, hit_weights)[source]

From a list of filtered hits, and replicon information (topology, length), build all lists of hits that satisfied the constraints:

  • max_gene_inter_space
  • loner
  • multi_system

If Yes create a cluster A cluster contains at least two hits separated by less or equal than max_gene_inter_space Except for loner genes which are allowed to be alone in a cluster

Parameters:
  • hits (list of macsypy.hit.ModelHit objects) – list of filtered hits
  • rep_info (macsypy.Indexes.RepliconInfo object) – the replicon to analyse
  • model (macsypy.model.Model object) – the model to study
Returns:

list of regular clusters, the special clusters (loners not in cluster and multi systems)

Return type:

tuple with 2 elements

  • true_clusters which is list of Cluster objects
  • true_loners: a dict { str function: :class:macsypy.hit.Loner | :class:macsypy.hit.LonerMultiSystem object}