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:	hits ([ `macsypy.hit.CoreHit` \| `macsypy.hit.ModelHit`, … ]) – the hits constituting this cluster model (`macsypy.model.Model`) – the model associated to this cluster

__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 some hits representing the same gene and this gene is tag as loner False otherwise: - contains several hits coding for different genes - 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:	old (`macsypy.hit.ModelHit` object.) – the hit to replace new (`macsypy.hit.ModelHit` object.) – the new hit
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}