Genome.py

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#!/usr/bin/env python3
""" @brief  Definition of genes as DNA segments having semantics. """
 
#============================================================================#
# EVOLIFE  http://evolife.telecom-paris.fr             Jean-Louis Dessalles  #
# Telecom Paris  2022-04-11                                www.dessalles.fr  #
# -------------------------------------------------------------------------- #
# License:  Creative Commons BY-NC-SA                                        #
#============================================================================#
# Documentation: https://evolife.telecom-paris.fr/Classes                    #
#============================================================================#
 
 
 
 
 
 
import sys
if __name__ == '__main__':  sys.path.append('../..')  # for tests
 
 
 
from Evolife.Genetics.DNA import DNA
 
class Gene:
    """ Actual gene (semantic segment on DNA) with intensity 
        A Gene also knows its locus (position in the list of genes, as defined in genetic map)
    """
 
    def __init__(self, gene_locus, intensity = 0):
        """ A gene knows its intensity and its locus (position in the list of genes, as defined in genetic map)
        """
        self.locus = gene_locus
        self.intensity = intensity
 
    def __str__(self):
        # return ' L' + str(self.locus) + ': ' + MyScenario.get_gene_name(self.locus) + ' ('+ str(self.intensity) + ')'
        return ' L' + str(self.locus) + ': ' + ' ('+ str(self.intensity) + ')'
 
class Genome(DNA):
    """   class Genome: list of genes carried by individuals 
    """
 
    def __init__(self, Scenario):
        self.ScenarioScenario = Scenario
        self.genome = []
        for g in self.ScenarioScenario.GeneMap:
            self.genome.append(Gene(g.locus))
        DNA.__init__(self, self.ScenarioScenario, self.ScenarioScenario.geneMap_length())
 
    def update(self):
        """ gene values are read from DNA and stored in Genes
        """
        for locus in range(0,len(self.ScenarioScenario.GeneMap)):
            (b1,b2) = self.ScenarioScenario.get_gene_boundaries(locus)
            coding = self.ScenarioScenario.get_coding(locus)
            self.genome[locus].intensity = self.read_DNA(b1, b2, coding=coding)
 
    def gene_value(self, name):
        """ absolute intensity addressed trough name
        """
        return self.genome[self.ScenarioScenario.get_locus(name)].intensity
 
    def gene_relative_value(self, name):
        """ relative intensity (between 0 and 100) addressed through name
        """
        return self.locus_relative_value(self.ScenarioScenario.get_locus(name))
 
    def locus_value(self, locus):
        """ absolute intensity addressed trough locus
        """
        return self.genome[locus].intensity
 
    def locus_relative_value(self, locus):
        """ relative intensity (between 0 and 100) addressed through locus
        """
        return 100 * float(self.genome[locus].intensity) / self.ScenarioScenario.locus_range(locus)
 
    def signature(self):
        """ returns all gene relative values - useful for statistics and display
        """
        return [self.locus_relative_value(locus[0]) for locus in enumerate(self.ScenarioScenario.GeneMap)]
        
    def __str__(self):
        return ' || '.join([g.__str__() for g in self.genome])
 
 
if __name__ == "__main__":
    print(__doc__)
    print(Gene.__doc__)
    print(Genome.__doc__ + '\n')
    GG = Genome(Blank=False)
    print(GG)
    print(DNA.__str__(GG))
    GG.update()
    print(GG)
    raw_input('[Return]')
 
 
__author__ = 'Dessalles'