ConservedSpots#

class panorama.region.ConservedSpots(identifier, *spots)#

Bases: object

Represents a set of conserved spots across multiple pangenomes.

__init__(identifier, *spots)#

Constructor method.

Parameters:

  • identifier (int) – The identifier of the conserved spots set.

  • *spots (Spot) – The spots to add to the conserved set.

add(spot)#

Add a spot to the conserved set of spots.

Parameters:

spot (Spot) – The spot to add to the object.

Raises:

  • AssertionError – If the spot is not an instance of the Spot class.

  • KeyError – If the spot already exists in the conserved spots with the same ID.

Return type:

None

get(spot_id, pangenome_name)#

Get a spot from the conserved set of spots.

Parameters:

  • spot_id (int) – The identifier of the spot.

  • pangenome_name (str) – The name of the pangenome from which the spot belongs.

Returns:

Spot – The spot with the given id and pangenome.

Raises:

  • AssertionError – If the spot id is not an integer.

  • KeyError – If the spot is not in the conserved set of spots.

Return type:

Spot

pangenomes()#

Get the list of pangenomes where the conserved spot belongs.

Returns:

List[str] – The list of pangenome names.

Return type:

List[str]

property spots: Generator[Spot, None, None]#

Generator of the spots in the conserved object.

Yields:

Spot – The next spot in the conserved object.