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

Inheritance diagram of macsypy.hit.CoreHit, macsypy.hit.ModelHit, macsypy.hit.AbstractCounterpartHit, macsypy.hit.Loner, macsypy.hit.MultiSystem, macsypy.hit.LonerMultiSystem

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.

hit API reference¶

CoreHit¶

class macsypy.hit.CoreHit(gene, hit_id, hit_seq_length, replicon_name, position_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match)[source]¶

Handle the hits filtered from the Hmmer search. The hits are instanciated by HMMReport.extract() method In one run of MacSyFinder, there exists only one CoreHit per gene These hits are independent of any macsypy.model.Model instance.

__eq__(other)[source]¶

Return True if two hits are totally equivalent, False otherwise.

Parameters:	other (`macsypy.report.CoreHit` object) – the hit to compare to the current object
Returns:	the result of the comparison
Return type:	boolean

__gt__(other)[source]¶

compare two Hits. If the sequence identifier is the same, do the comparison on the score. Otherwise, do it on alphabetical comparison of the sequence identifier.

Parameters:	other (`macsypy.report.CoreHit` object) – the hit to compare to the current object
Returns:	True if self is > other, False otherwise

__hash__()[source]¶: To be hashable, it’s needed to be put in a set or used as dict key

__init__(gene, hit_id, hit_seq_length, replicon_name, position_hit, i_eval, score, profile_coverage, sequence_coverage, begin_match, end_match)[source]¶

Parameters:

gene (macsypy.gene.CoreGene object) – the gene corresponding to this profile
hit_id (str) – the identifier of the hit
hit_seq_length (int) – the length of the hit sequence
replicon_name (str) – the name of the replicon
position_hit (int) – the rank of the sequence matched in the input dataset file
i_eval (float) – the best-domain evalue (i-evalue, “independent evalue”)
score (float) – the score of the hit
profile_coverage (float) – percentage of the profile that matches the hit sequence
sequence_coverage (float) – percentage of the hit sequence that matches the profile
begin_match (int) – where the hit with the profile starts in the sequence
end_match (int) – where the hit with the profile ends in the sequence

__lt__(other)[source]¶

Compare two Hits. If the sequence identifier is the same, do the comparison on the score. Otherwise, do it on alphabetical comparison of the sequence identifier.

Parameters:	other (`macsypy.report.CoreHit` object) – the hit to compare to the current object
Returns:	True if self is < other, False otherwise

__str__()[source]¶

Returns:	Useful information on the CoreHit: regarding Hmmer statistics, and sequence information
Return type:	str

__weakref__¶: list of weak references to the object (if defined)

get_position()[source]¶

Returns:	the position of the hit (rank in the input dataset file)
Return type:	integer

ModelHit¶

class macsypy.hit.ModelHit(hit, gene_ref, gene_status)[source]¶

Encapsulates a macsypy.report.CoreHit This class stores a CoreHit that has been attributed to a putative system. Thus, it also stores:

the system,
the status of the gene in this system, (‘mandatory’, ‘accessory’, …
the gene in the model for which it’s an occurrence

for one gene it can exist several ModelHit instance one for each Model containing this gene

__eq__(other)[source]¶: Return self==value.

__gt__(other)[source]¶: Return self>value.

__hash__()[source]¶: To be hashable, it’s needed to be put in a set or used as dict key

__init__(hit, gene_ref, gene_status)[source]¶

Parameters:

hit (macsypy.hit.CoreHit object) – a match between a hmm profile and a replicon
gene_ref (macsypy.gene.ModelGene object) –
The ModelGene link to this hit The ModeleGene have the same name than the CoreGene But one hit can be link to several ModelGene (several Model) To know for what gene this hit play role use the macsypy.gene.ModelGene.alternate_of()
```
hit.gene_ref.alternate_of()
```
gene_status (macsypy.gene.GeneStatus object) –

__lt__(other)[source]¶: Return self<value.

__str__()[source]¶: Return str(self).

__weakref__¶: list of weak references to the object (if defined)

hit¶

Returns:	The CoreHit below this ModelHit
Return type:	`macsypy.hit.CoreHit` oject

loner¶

Returns:

True if the hit represent a loner macsypy.Gene.ModelGene, False otherwise. A True Loner is a hit representing a gene with the attribute loner and which does not include in a cluster.

a hit representing a loner gene but include in a cluster is not a true loner
a hit which is not include with other gene in a cluster but does not represent a gene loner is not a True loner (This situation may append when min_genes_required = 1)

Return type: bool

multi_model¶

Returns:	True if the hit represent a multi_model `macsypy.Gene.ModelGene`, False otherwise.
Return type:	bool

multi_system¶

Returns:	True if the hit represent a multi_system `macsypy.Gene.ModelGene`, False otherwise.
Return type:	bool

AbstractCounterpartHit¶

class macsypy.hit.AbstractCounterpartHit(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

Abstract Class to handle ModelHit wit equivalent for instance Loner or MultiSystem hit

__init__(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

Parameters:

hit (macsypy.hit.CoreHit object) – a match between a hmm profile and a replicon
gene_ref (macsypy.gene.ModelGene object) –
The ModelGene link to this hit The ModeleGene have the same name than the CoreGene But one hit can be link to several ModelGene (several Model) To know for what gene this hit play role use the macsypy.gene.ModelGene.alternate_of()
```
hit.gene_ref.alternate_of()
```
gene_status (macsypy.gene.GeneStatus object) –

__str__()[source]¶: Return str(self).

counterpart¶

Returns:	The set of hits that can play the same role

loner¶

Returns:

True if the hit represent a loner macsypy.Gene.ModelGene, False otherwise. A True Loner is a hit representing a gene with the attribute loner and which does not include in a cluster.

a hit representing a loner gene but include in a cluster is not a true loner
a hit which is not include with other gene in a cluster but does not represent a gene loner is not a True loner (This situation may append when min_genes_required = 1)

Return type: bool

multi_system¶

Returns:	True if the hit represent a multi_system `macsypy.Gene.ModelGene`, False otherwise.
Return type:	bool

Loner¶

class macsypy.hit.Loner(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

Handle hit which encode for a gene tagged as loner and which not clustering with other hit.

__init__(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

hit that is outside a cluster, the gene_ref is a loner

Parameters:

hit (macsypy.hit.CoreHit object) – a match between a hmm profile and a replicon
gene_ref (macsypy.gene.ModelGene object) –
The ModelGene link to this hit The ModeleGene have the same name than the CoreGene But one hit can be link to several ModelGene (several Model) To know for what gene this hit play role use the macsypy.gene.ModelGene.alternate_of()
```
hit.gene_ref.alternate_of()
```
gene_status (macsypy.gene.GeneStatus object) –
counterpart (list of macsypy.hit.CoreHit) – the other occurence of the gene or exchangeable in the replicon

loner¶

Returns:

True if the hit represent a loner macsypy.Gene.ModelGene, False otherwise. A True Loner is a hit representing a gene with the attribute loner and which does not include in a cluster.

a hit representing a loner gene but include in a cluster is not a true loner
a hit which is not include with other gene in a cluster but does not represent a gene loner is not a True loner (This situation may append when min_genes_required = 1)

Return type: bool

MultiSystem¶

class macsypy.hit.MultiSystem(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

Handle hit which encode for a gene tagged as loner and which not clustering with other hit.

__init__(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

hit that is outside a cluster, the gene_ref is a loner

Parameters:

hit (macsypy.hit.CoreHit object) – a match between a hmm profile and a replicon
gene_ref (macsypy.gene.ModelGene object) –
The ModelGene link to this hit The ModeleGene have the same name than the CoreGene But one hit can be link to several ModelGene (several Model) To know for what gene this hit play role use the macsypy.gene.ModelGene.alternate_of()
```
hit.gene_ref.alternate_of()
```
gene_status (macsypy.gene.GeneStatus object) –
counterpart (list of macsypy.hit.CoreHit) – the other occurence of the gene or exchangeable in the replicon

multi_system¶

Returns:	True if the hit represent a multi_system `macsypy.Gene.ModelGene`, False otherwise.
Return type:	bool

LonerMultiSystem¶

class macsypy.hit.LonerMultiSystem(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

Handle hit which encode for a gene

gene tagged as multi-system
and gene tagged as loner also
and the hit do not clustering with other hits.

__init__(hit, gene_ref=None, gene_status=None, counterpart=None)[source]¶

hit that is outside a cluster, the gene_ref is loner and multi_system

Parameters:

hit (macsypy.hit.CoreHit | macsypy.hit.ModelHit | macsypy.hit.MultiSystem object) – a match between a hmm profile and a replicon
gene_ref (macsypy.gene.ModelGene object) –
The ModelGene link to this hit The ModeleGene have the same name than the CoreGene But one hit can be link to several ModelGene (several Model) To know for what gene this hit play role use the macsypy.gene.ModelGene.alternate_of()
```
hit.gene_ref.alternate_of()
```
gene_status (macsypy.gene.GeneStatus object) –
counterpart (list of macsypy.hit.CoreHit) – the other occurence of the gene or exchangeable in the replicon

HitWeight¶

class macsypy.hit.HitWeight(itself: float = 1, exchangeable: float = 0.8, mandatory: float = 1, accessory: float = 0.5, neutral: float = 0, out_of_cluster: float = 0.7)[source]¶

The weight to compute the cluster and system score see user documentation macsyfinder functionning for further details by default

itself = 1

exchangeable = 0.8

mandatory = 1

accessory = 0.5

neutral = 0

out_of_cluster = 0.7

__weakref__¶: list of weak references to the object (if defined)

get_best_hit_4_func¶

macsypy.hit.get_best_hit_4_func(function, hits, key='score')[source]¶

select the best Loner among several ones encoding for same function

score

i_evalue

profile_coverage

Parameters:	function (str) – the name of the function fulfill by the hits (all hits must have same function) hits (sequence of `macsypy.hit.ModelHit` object) – the hits to filter. key (str) – The criterion used to select the best hit ‘score’, i_evalue’, ‘profile_coverage’
Returns:	the best hit
Return type:	`macsypy.hit.ModelHit` object

sort_model_hits¶

macsypy.hit.sort_model_hits(model_hits)[source]¶

Sort macsypy.hit.ModelHit per function

Parameters:	model_hits – a sequence of `macsypy.hit.ModelHit`
Returns:	dict {str function name: [model_hit, …] }

compute_best_MSHit¶

macsypy.hit.compute_best_MSHit(ms_registry)[source]¶

Parameters:	ms_registry –
Returns:

get_best_hits¶

macsypy.hit.get_best_hits(hits, key='score')[source]¶

If several hits match the same protein, keep only the best match based either on

score

i_evalue

profile_coverage

Parameters:	hits ([ `macsypy.hit.CoreHit` object, …]) – the hits to filter, all hits must match the same protein. key (str) – The criterion used to select the best hit ‘score’, i_evalue’, ‘profile_coverage’
Returns:	the list of the best hits
Return type:	[ `macsypy.hit.CoreHit` object, …]