biopython

v1.71.0

biopython v1.71.0 Bio.GA.Organism.Organism

Represent a single individual in a population.

Attributes:

  • genome — The genome of the organism. This is a Bio.MutableSeq object that has the sequence of the genome, and the alphabet describing all elements that can be a part of the genome.
  • fitness — The calculate fitness of the organism. This fitness is based on the last time it was calculated using the fitness_calculator. So… the fitness could potentially be out of date with the real genome if you are not careful to recalculate it after changes with recalculate_fitness()

Link to this section Summary

Functions

__eq__()

Compare organisms by their genomes (as strings of letters)

__ge__()

Compare organisms by their genomes (as strings of letters)

__gt__()

Compare organisms by their genomes (as strings of letters)

__init__()

Initialize an organism

__le__()

Compare organisms by their genomes (as strings of letters)

__lt__()

Compare organisms by their genomes (as strings of letters)

__ne__()

Compare organisms by their genomes (as strings of letters)

__str__()

Provide a string output for debugging

copy()

Return a copy of the organism

recalculate_fitness()

Calculate and reset the fitness of the current genome

Link to this section Functions

Link to this function __eq__()

Compare organisms by their genomes (as strings of letters).

Link to this function __ge__()

Compare organisms by their genomes (as strings of letters).

Link to this function __gt__()

Compare organisms by their genomes (as strings of letters).

Link to this function __init__()

Initialize an organism.

Arguments:

  • genome — A MutableSeq object representing the sequence of the genome.
  • fitness_calculator — A function that will calculate the fitness of the organism when given the organisms genome.
  • start_fitness - the starting fitness corresponding with the given genome. If not supplied, the fitness will be calculated using fitness_calculator.
Link to this function __le__()

Compare organisms by their genomes (as strings of letters).

Link to this function __lt__()

Compare organisms by their genomes (as strings of letters).

Link to this function __ne__()

Compare organisms by their genomes (as strings of letters).

Link to this function __str__()

Provide a string output for debugging.

Link to this function copy()

Return a copy of the organism.

This makes it easy to duplicate an organism before changing it.

Link to this function recalculate_fitness()

Calculate and reset the fitness of the current genome.

This should be called after the genome is updated to ensure that fitness always stays in sync with the current genome.