Spot#

class panorama.region.Spot(spot_id)#

Bases: Spot

Represents a spot in a pangenome.

__delitem__(name)#

Delete the region for the given name

Parameters:

name – Name of the wanted region

Raises:

  • KeyError – Name does not exist in the spot

  • TypeError – Name is not a string

__getitem__(name)#

Get the region with the given name

Parameters:

name – Name of the wanted region

Return type:

Region

Returns:

Region in the spot for the given name

Raises:

  • KeyError – Name does not exist in the spot

  • TypeError – Name is not a string

__init__(spot_id)#

Constructor method.

Parameters:

spot_id (int) – The identifier of the spot.

__len__()#

Get the number of regions in the spot

Return type:

int

__repr__()#

Spot representation

Return type:

str

__setitem__(name, region)#

Set the region belonging to the spot

Parameters:

  • name (str) – Name of the region

  • region (Region) – Region to add in the spot

Raises:

KeyError – Name of the region is already in the spot for a different region

__str__()#

String representation of the spot

_get_content()#

Creates the _uniqContent object if it was never computed.

Return type:

Dict[Region, Set[Region]]

Returns:

RGP groups that have identical gene content

_get_ordered_set()#

Creates the _uniqSyn object if it was never computed. Return it in any case

Return type:

Dict[Region, Set[Region]]

Returns:

RGP groups that have an identical synteny

_mk_uniq_content()#

cluster RGP into groups that have identical gene content

_mk_uniq_ordered_set_obj()#

cluster RGP into groups that have an identical synteny

add(region)#

Add a region to the spot. Alias more readable for setitem

Parameters:

region (Region) – Region to add in the spot

Raises:

TypeError – Region is not an instance Region

add_metadata(metadata, metadata_id=None)#

Add metadata to metadata getter

Parameters:

  • metadata (Metadata) – metadata value to add for the source

  • metadata_id (int) – metadata identifier

Raises:

AssertionError – Source or metadata is not with the correct type

Return type:

None

borders(set_size, multigenics)#

Extracts all the borders of all RGPs belonging to the spot

Parameters:

  • set_size – Number of genes to get

  • multigenics – pangenome graph multigenic persistent families

Returns:

Families that bordering spot

property conserved: bool#

Check if the spot is conserved between pangenomes.

Returns:

bool – True if the spot is conserved, False otherwise.

count_uniq_content()#

Get a counter of uniq RGP and number of identical RGP (in terms of gene family content)

Return type:

dict

Returns:

Dictionary with a representative rgp as the key and number of identical rgp as value

count_uniq_ordered_set()#

Get a counter of uniq RGP and number of identical RGP (in terms of synteny content)

Returns:

Dictionary with a representative rgp as the key and number of identical rgp as value

del_metadata_by_attribute(**kwargs)#

Remove a source from the feature

del_metadata_by_source(source)#

Remove a source from the feature

Parameters:

source (str) – Name of the source to delete

Raises:

  • AssertionError – Source is not with the correct type

  • KeyError – Source does not belong in the MetaFeature

property families: Generator[GeneFamily, None, None]#

Get the gene families in the RGP

Returns:

Family in the spot

formatted_metadata_dict()#

Format metadata by combining source and field values.

Given an object with metadata, this function creates a new dictionary where the keys are formatted as ‘source_field’.

Return type:

Dict[str, List[str]]

Returns:

A dictionary with formatted metadata.

formatted_metadata_dict_to_string(separator='|')#

Format metadata by combining source and field values.

Given an object with metadata, this function creates a new dictionary where the keys are formatted as ‘source_field’. In some cases, it is possible to have multiple values for the same field, in this situation, values are concatenated with the specified separator.

Parameters:

separator (str) – The separator used to join multiple values for the same field (default is ‘|’).

Return type:

Dict[str, str]

Returns:

A dictionary with formatted metadata.

get(name)#

Get a region by its name. Alias more readable for getitem

Parameters:

name (str) – Name of the region

Return type:

Region

Returns:

Wanted region

get_metadata(source, metadata_id=None)#

Get metadata from metadata getter by its source and identifier

Parameters:

  • source (str) – source of the metadata

  • metadata_id (int) – metadata identifier

Raises:

KeyError – No metadata with ID or source is found

Return type:

Metadata

get_metadata_by_attribute(**kwargs)#

Get metadata by one or more attribute

Return type:

Generator[Metadata, None, None]

Returns:

Metadata searched

get_metadata_by_source(source)#

Get all the metadata feature corresponding to the source

Parameters:

source (str) – Name of the source to get

Return type:

Optional[Dict[int, Metadata]]

Returns:

List of metadata corresponding to the source

Raises:

AssertionError – Source is not with the correct type

get_uniq_content()#

Get an Iterable of all the unique rgp (in terms of gene family content) in the spot

Return type:

Set[Region]

Returns:

Iterable of all the unique rgp (in terms of gene family content) in the spot

get_uniq_ordered_set()#

Get an Iterable of all the unique syntenies in the spot

Return type:

Set[Region]

Returns:

Iterable of all the unique syntenies in the spot

get_uniq_to_rgp()#

Get dictionary with a representing RGP as the key, and all identical RGPs as value

Return type:

Dict[Region, Set[Region]]

Returns:

Dictionary with a representing RGP as the key, and set of identical RGPs as value

has_metadata()#

Does the feature has some metadata associated.

Return type:

bool

Returns:

True if it has metadata else False

has_source(source)#

Check if the source is in the metadata feature

Parameters:

source (str) – name of the source

Return type:

bool

Returns:

True if the source is in the metadata feature else False

max_metadata_by_source()#

Get the maximum number of metadata for one source

Return type:

Tuple[str, int]

Returns:

Name of the source with the maximum annotation and the number of metadata corresponding

property metadata: Generator[Metadata, None, None]#

Generate metadata in gene families

Returns:

Metadata from all sources

property number_of_families: int#

Get the number of different families in the spot

Returns:

Number of families

property number_of_metadata: int#

Get the number of metadata associated to feature

property number_of_organisms#

Get the number of organisms that contain the spot.

Returns:

int – The number of organisms.

property organisms: Generator[Organism, None, None]#

Generator of the organisms that contain the spot.

Yields:

Organism – The next organism that contains the spot.

property regions: Generator[Region, None, None]#

Generates the regions in the spot

Returns:

Regions in the spot

remove(name)#

Remove a region by its name. Alias more readable for delitem

Parameters:

name (str) – Name of the region

property sources: Generator[str, None, None]#

Get all metadata source in gene family

Returns:

Metadata source

spot_2_families()#

Add to Gene Families a link to spot