biopython

v1.71.0

biopython v1.71.0 Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover

Perform n-point crossover between genomes at some defined rates.

Ideas on how to use this class:

  • Call it directly ( construct, do_crossover )
  • Use one of the provided subclasses

  • Inherit from it:

    • replace _generate_locs with a more domain specific technique
    • replace _crossover with a more efficient technique for your point-count

Link to this section Summary

Functions

__init__()

Initialize to do crossovers at the specified probability

_crossover()

Generalized Crossover Function

_generate_locs()

Generalized Location Generator

do_crossover()

Potentially do a crossover between the two organisms

Link to this section Functions

Link to this function __init__()

Initialize to do crossovers at the specified probability.

Link to this function _crossover()

Generalized Crossover Function.

Arguments:

  • x (int) - genome number [0|1]

  • no (organism, organism)

    • new organisms
    • locs (int list, int list)

  • lists of locations, [0, +n points+, bound] for each genome (sync’d with x)

Return type: sequence (to replace no[x])

Link to this function _generate_locs()

Generalized Location Generator.

Arguments:

  • bound (int) - upper bound

Returns: [0]+x_0…x_n+[bound] where n=self._npoints-1 and 0 < x_0 < x_1 … < bound

Link to this function do_crossover()

Potentially do a crossover between the two organisms.