Region

class panorama.region.Region(name)

Bases: Region

Represents a region in a pangenome.

Parameters:

name (str) – The name of the region.

__delitem__(position)

Remove the gene at the given position

Parameters:

position – Position of the gene

Raises:

KeyError – Gene at the given position does not exist

__eq__(other)

Test whether two Region objects have the same gene families

Parameters:

other (Region) – Another region to test equality of regions

Return type:

bool

Returns:

Equal or not

Raises:

TypeError – Try to compare a region with another type object

__getitem__(position)

Get the gene at the given position

Parameters:

position (int) – Position of the gene

Return type:

Gene

Returns:

Gene in the Region at the given position

Raises:

KeyError – Gene at the given position does not exist

__hash__()

Create a hash value for the region

Return type:

int

__init__(name)

Constructor method.

Parameters:

name (str) – The name of the region.

__len__()

Get the number of genes in the region

Return type:

int

__repr__()

Region representation

Return type:

str

__setitem__(position, gene)

Set a gene by is position in the region

Parameters:

• position (int) – Position of the gene in the contig

• gene (Gene) – Gene to add in the region

Raises:

• TypeError – If the gene is not an instance of Gene.

• ValueError – If the organism or contig of the gene is different from the region.

• KeyError – If another gene already exists at the specified position.

• ValueError – If the position of the gene does not match the provided position.

add(gene)

Add a gene to the region

Parameters:

gene (Gene) – Gene to add

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

property contig: Contig

Get the starter contig link to RGP

Returns:

Contig corresponding to the region

property coordinates: List[Tuple[int]]

Return the coordinates of the region :return: coordinates of the region

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:

Gene families

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.

property genes: Generator[Gene, None, None]

Generate the gene as they are ordered in contigs

Returns:

Genes in the region

get(position)

Get a gene by its position

Parameters:

position (int) – Position of the gene in the contig

Return type:

Gene

Returns:

Wanted gene

Raises:

TypeError – Position is not an integer

get_bordering_genes(n, multigenics, return_only_persistents=True)

Get the bordered genes in the region. Find the n persistent and single copy gene bordering the region. If return_only_persistents is False, the method return all genes included between the n single copy and persistent genes.

Parameters:

• n – Number of genes to get

• multigenics – pangenome graph multigenic persistent families

• return_only_persistents – return only non multgenic persistent genes identify as the region. If False return all genes included between the borders made of n persistent and single copy genes around the region.

Returns:

A list of bordering genes in start and stop position

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_ordered_genes()

Get ordered genes of the region, taking into account the circularity of contigs.

Return type:

List[Gene]

Returns:

A list of genes ordered by their positions in the region.

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

id_counter = 0

identify_rgp_last_and_first_genes()

Identify first and last genes of the rgp by taking into account the circularity of contigs.

Set the attributes _starter: first gene of the region and _stopper: last gene of the region and _coordinates

property is_contig_border: bool

Indicates if the region is bordering a contig

Returns:

True if bordering else False

Raises:

AssertionError – No genes in the regions, it’s not expected

property is_whole_contig: bool

Indicates if the region is an entire contig

Returns:

True if whole contig else False

property length

Get the length of the region

Returns:

Size of the region

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 modules: Set[Module]

Get the modules of gene families in the RGP

Returns:

Modules found in families of the RGP

property number_of_families: int

Get the number of different gene families in the region

Returns:

Number of families

property number_of_metadata: int

Get the number of metadata associated to feature

property organism: Organism

Get the Organism link to RGP

Returns:

Organism corresponding to the region

property overlaps_contig_edge: bool

remove(position)

Remove a gene by its position

Parameters:

position – Position of the gene in the contig

Raises:

TypeError – Position is not an integer

property sources: Generator[str, None, None]

Get all metadata source in gene family

Returns:

Metadata source

property spot: Spot | None

property start: int

Get the starter start link to RGP

Returns:

start position in the contig of the first gene of the RGP

property starter: Gene

Return first gene of the region. If this gene is not identified, it does that first. :return: first gene of the region

property stop: int

Get the stopper stop link to RGP

Returns:

start position in the contig of the last gene of the RGP

property stopper: Gene

Return last gene of the region. If this gene is not identified, it does that first. :return: last gene of the region

string_coordinates()

Return a string representation of the coordinates

Return type:

str