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individu.py 4.58 KiB
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from RotTable import RotTable
from Traj3D import Traj3D
import numpy as np
from math import sqrt, inf
from random import random

P1 = 0.015

class Individu():

    def __init__(self, table):
        self.table = table
        lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
        self.brin = ''.join(lineList[1:])
        #self.brin = "AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA"
        self.score = self.evaluate()

    def evaluate(self):
        traj = Traj3D()

        numb_ajout = 3

        fisrt_seq = self.brin[0:numb_ajout]
        last_seq = self.brin[-numb_ajout:]

        traj.compute(last_seq + self.brin + fisrt_seq, self.table)
        traj_array = np.array(traj.getTraj())
        list_distance = []

        for i in range(numb_ajout):
                first_nuc_coordonate = traj_array[numb_ajout+i, 0:3]
                first_nuc_coordonate_compute = traj_array[-(numb_ajout-i), 0:3]
                
                last_nuc_coordonate = traj_array[-(2*numb_ajout-i), 0:3]
                last_nuc_coordonate_compute = traj_array[i, 0:3]

                distance_first_nuc = np.linalg.norm(first_nuc_coordonate - first_nuc_coordonate_compute, ord=2)
                distance_last_nuc = np.linalg.norm(last_nuc_coordonate - last_nuc_coordonate_compute, ord=2)

                list_distance += [distance_first_nuc, distance_last_nuc]


        self.score = max(list_distance)

        return max(list_distance)


    def mutation(self, proba = P1):
        table_rotations = self.table.rot_table
        for doublet in table_rotations :
            for coord in range(3):
                tir = random()
                if tir < proba :
                    table_rotations[doublet][coord] =np.random.uniform(low = self.table.orta()[doublet][coord] - self.table.orta()[doublet][coord + 3], high = self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3])
                    doublet2 = self.table.corr()[doublet]
                    if coord == 0 or coord == 1 :
                        table_rotations[doublet2][coord] = table_rotations[doublet][coord]
                    else :
                        #sur l'axe z il y a un moins
                        table_rotations[doublet2][coord] = - table_rotations[doublet][coord]

    def mutation_with_numbers(self, proba = P1, number_of_mutations = 5):
        table_rotations = self.table.rot_table
        for i in range(0,number_of_mutations):
            tir = random()
            if tir < proba :
                doubletNumber = randrange(0,8)
                counter = 0
                for doublet in table_rotations:
                    if counter==doubletNumber:
                        break
                    counter+=1
                for coord in range(3):
                    table_rotations[doublet][coord] =np.random.uniform(low = self.table.orta()[doublet][coord] - self.table.orta()[doublet][coord + 3], high = self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3])
                    doublet2 = self.table.corr()[doublet]
                    if coord == 0 or coord == 1 :
                        table_rotations[doublet2][coord] = table_rotations[doublet][coord]
                    else :
                        #sur l'axe z il y a un moins
                        table_rotations[doublet2][coord] = - table_rotations[doublet][coord]

# individu1 = Individu(RotTable())
# print(individu1.table.rot_table)
# individu1.mutation()

# table = RotTable()
# test = Individu(table)
# test.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA")
# print(test.score)


# qqun=Individu(RotTable())
# qqun.table.rot_table={'AA': [35.576558502141, 7.433901511509349, -154], 'AC': [33.22048222654215, 5.25191751302917, 143], 'AG': [26.446029097301288, 6.052240462237622, -2], 'AT': [30.47045254036881, 1.333716025628036, 0], 'CA': [34.00734209585039, 33.70710613604862, -64], 'CC': [33.61019622767888, 3.713127032109607, -57], 'CG': [29.664061041382677, 6.725155507162601, 0], 'CT': [26.446029097301288, 6.052240462237622, 2], 'GA': [36.655773481637176, 10.45337581740701, 120], 'GC': [42.26984493493484, 3.5310453395352823, 180], 'GG': [33.61019622767888, 3.713127032109607, -57], 'GT': [33.22048222654215, 5.25191751302917, 143], 'TA': [36.951508786388914, -2.5174751178033303, 0], 'TC': [36.655773481637176, 10.45337581740701, -120], 'TG': [34.00734209585039, 33.70710613604862, -64], 'TT': [35.576558502141, 7.433901511509349, -154]}
# qqun.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA")
# print(qqun.score)