From 76f8aab64d9a74abf4004e4ed965e5ab25e62e5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Chlo=C3=A9=20Muller?= <chloe.muller@student-cs.fr> Date: Wed, 29 Jan 2020 09:02:03 +0100 Subject: [PATCH] =?UTF-8?q?je=20sais=20pas=20ce=20qu'il=20s'est=20pass?= =?UTF-8?q?=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .DS_Store | Bin 6148 -> 6148 bytes RotTable.py | 54 +++++++++++--- Traj3D.py | 6 ++ __pycache__/Initialisation.cpython-37.pyc | Bin 1840 -> 0 bytes __pycache__/RotTable.cpython-36.pyc | Bin 2085 -> 2132 bytes __pycache__/RotTable.cpython-37.pyc | Bin 2086 -> 2577 bytes __pycache__/Traj3D.cpython-36.pyc | Bin 1976 -> 1976 bytes __pycache__/Traj3D.cpython-37.pyc | Bin 1958 -> 1931 bytes __pycache__/croisement.cpython-37.pyc | Bin 0 -> 2386 bytes __pycache__/individu.cpython-37.pyc | Bin 0 -> 1936 bytes __pycache__/population.cpython-37.pyc | Bin 0 -> 6259 bytes algogenetique.py | 38 ++++++++++ croisement.py | 61 +++++++++++++--- 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"TG",\ + "CC": "GG",\ + "CG": "CG",\ + "GA": "TC",\ + "GC": "GC",\ + "TA": "TA"\ + } # get the angles in each axis (x, y, z), considering the deviation def __init__(self): self.rot_table = {} @@ -34,13 +65,18 @@ class RotTable: # get a random deviation, considering the "limits" given in the last 3 columns # of __ORIGINAL_ROT_TABLE def alea(self): - for dinucleotide in RotTable.__ORIGINAL_ROT_TABLE: + for dinucleotide in RotTable.__SOUS_CORRESPONDANCE: for i in range(2): - self.rot_table[dinucleotide][i] += numpy.random.uniform(low = -RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3], high= RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3]) + delta = numpy.random.uniform(low = -RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3], high= RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3]) + self.rot_table[dinucleotide][i] += delta + self.rot_table[RotTable.__SOUS_CORRESPONDANCE[dinucleotide]][i] += delta # return __ORIGINAL_ROT_TABLE def orta(self): return self.__ORIGINAL_ROT_TABLE + + def corr(self): + return self.__CORRESPONDANCE ################### # WRITING METHODS # @@ -53,17 +89,17 @@ class RotTable: ################### def getTwist(self, dinucleotide): - return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][0] + return self.rot_table[dinucleotide][0] def getWedge(self, dinucleotide): - return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][1] + return self.rot_table[dinucleotide][1] def getDirection(self, dinucleotide): - return RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][2] + return self.rot_table[dinucleotide][2] ################### -# table1 = RotTable() -# print(table1.orta()) +#table1 = RotTable() +#print(table1.orta()) -# print(table1.rot_table["AA"]) +# print(table1.rot_table) diff --git a/Traj3D.py b/Traj3D.py index eee7181..92cc972 100644 --- a/Traj3D.py +++ b/Traj3D.py @@ -65,3 +65,9 @@ class Traj3D: ax.plot(x,y,z) plt.show() plt.savefig(filename) + +# from RotTable import RotTable +# table = RotTable() +# test = Traj3D() +# 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numpy +import RotTable +from individu import Individu +from population import Population, afficher +import croisement +from Traj3D import * +from random import random +import matplotlib.pyplot as plt + + + +def main(N,tmax,pmutation, proportion,brin="plasmid_8k.fasta"): + '''lineList = [line.rstrip('\n') for line in open(brin)] + brin = ''.join(lineList[1:])''' + L=[] + People=Population(N) + for i in range(tmax): + print(i) + max=0 + best=None + People.reproduction(p = proportion, proba_mutation= pmutation) + for individu in People.indiv: + if individu.score>max: + best=individu + max=individu.score + L.append(max) + + plt.plot([i for i in range(tmax)], L) + plt.show() + return(best) + + +main(100,100,0,50) + + + diff --git a/croisement.py b/croisement.py index 48a399f..96f85a8 100644 --- a/croisement.py +++ b/croisement.py @@ -26,30 +26,71 @@ def croisement_un_point(parent1, parent2): enfant1 = Individu(RotTable()) enfant2 = Individu(RotTable()) comp = 0 - point_crois= numpy.random.random_integers(0,16) + point_crois= numpy.random.random_integers(0,8) for doublet in ROT_TABLE: + if doublet == "GA": + break if comp < point_crois: enfant1.table.rot_table[doublet] = parent1.table.rot_table[doublet] + correspondent_doublet1 = enfant1.table.corr()[doublet] + enfant1.table.rot_table[correspondent_doublet1] = parent1.table.rot_table[correspondent_doublet1] + enfant1.table.rot_table[correspondent_doublet1][2] *= -1 + enfant2.table.rot_table[doublet] = parent2.table.rot_table[doublet] + correspondent_doublet2 = enfant2.table.corr()[doublet] + enfant2.table.rot_table[correspondent_doublet2] = parent2.table.rot_table[correspondent_doublet2] + enfant2.table.rot_table[correspondent_doublet2][2] *= -1 + else : enfant1.table.rot_table[doublet] = parent2.table.rot_table[doublet] + correspondent_doublet1 = enfant1.table.corr()[doublet] + enfant1.table.rot_table[correspondent_doublet1] = parent2.table.rot_table[correspondent_doublet1] + enfant1.table.rot_table[correspondent_doublet1][2] *= -1 + enfant2.table.rot_table[doublet] = parent1.table.rot_table[doublet] + correspondent_doublet2 = enfant2.table.corr()[doublet] + enfant2.table.rot_table[correspondent_doublet2] = parent1.table.rot_table[correspondent_doublet1] + enfant2.table.rot_table[correspondent_doublet2][2] *= -1 + comp += 1 return enfant1, enfant2 def croisement_deux_points(parent1, parent2): - enfant1 = RotTable() - enfant2 = RotTable() + enfant1 = Individu(RotTable()) + enfant2 = Individu(RotTable()) comp = 0 - point_crois1= numpy.random.random_integers(0,16) - point_crois2= numpy.random.random_integers(0,16) + point_crois1= numpy.random.random_integers(0,8) + point_crois2= numpy.random.random_integers(0,8) for doublet in ROT_TABLE: if comp < min(point_crois1,point_crois2) or comp > max(point_crois1,point_crois2): - enfant1.rot_table[doublet] = parent1.rot_table[doublet] - enfant2.rot_table[doublet] = parent2.rot_table[doublet] + enfant1.table.rot_table[doublet] = parent1.table.rot_table[doublet] + correspondent_doublet1 = enfant1.table.corr()[doublet] + enfant1.table.rot_table[correspondent_doublet1] = parent1.table.rot_table[correspondent_doublet1] + enfant1.table.rot_table[correspondent_doublet1][2] *= -1 + + enfant2.table.rot_table[doublet] = parent2.table.rot_table[doublet] + correspondent_doublet2 = enfant2.table.corr()[doublet] + enfant2.table.rot_table[correspondent_doublet2] = parent2.table.rot_table[correspondent_doublet2] + enfant2.table.rot_table[correspondent_doublet2][2] *= -1 + else : - enfant1.rot_table[doublet] = parent2.rot_table[doublet] - enfant2.rot_table[doublet] = parent1.rot_table[doublet] + enfant1.table.rot_table[doublet] = parent2.table.rot_table[doublet] + correspondent_doublet1 = enfant1.table.corr()[doublet] + enfant1.table.rot_table[correspondent_doublet1] = parent2.table.rot_table[correspondent_doublet1] + enfant1.table.rot_table[correspondent_doublet1][2] *= -1 + + enfant2.table.rot_table[doublet] = parent1.table.rot_table[doublet] + correspondent_doublet2 = enfant2.table.corr()[doublet] + enfant2.table.rot_table[correspondent_doublet2] = parent1.table.rot_table[correspondent_doublet1] + enfant2.table.rot_table[correspondent_doublet2][2] *= -1 comp += 1 - return enfant1, enfant2 \ No newline at end of file + return enfant1, enfant2 + +# parent1 = Individu(RotTable()) +# parent2 = Individu(RotTable()) +# print("parent1: ", parent1.table.rot_table) +# print("parent2: ", parent2.table.rot_table) +# enfant1, enfant2 = croisement_un_point(parent1, parent2) +# print("enfant1: ", enfant1.table.rot_table) +# print("enfant2: ", enfant2.table.rot_table) \ No newline at end of file diff --git a/first_plot.png b/first_plot.png new file mode 100644 index 0000000000000000000000000000000000000000..0e536fb530ea40bc82a9395940755ad27a030609 GIT binary patch literal 2412 zcmeAS@N?(olHy`uVBq!ia0y~yU}|7sV0^&A#=yW}dhyN^1_lO}VkgfK4h{~E8jh3> z1_lPs0*}aI1_u5_5N2FqzdVzHfx)uGHKHUqKdq!Zu_%=xH?gE3C%+^oGfAN=wWv5V zKTp9(&rr`uM<Ju6q`*pFAE7`mzbIYbl>6ri1_q9ko-U3d6?5KRGh}2?;5lG$VE^-n zOnquxRb}VT=rAxCoqNx~z;Mr~fq}u0O@Kk+7y}c-5eWx|1_@>k27zP-MusFF1qO#6 zMizz+!%;<}K`@#MMl-@_Suk20j@AgHl_Fi+1$t_g?0c3k-;~6_z`)??>gTe~DWM4f DIVz$A literal 0 HcmV?d00001 diff --git a/individu.py b/individu.py index 0bc68e4..2419381 100644 --- a/individu.py +++ b/individu.py @@ -1,7 +1,7 @@ from RotTable import RotTable -from Traj3D import * +from Traj3D import Traj3D import numpy as np -from math import sqrt +from math import sqrt, inf from random import random P1 = 0.015 @@ -10,27 +10,36 @@ class Individu(): def __init__(self, table): self.table = table - self.score = None + self.score = self.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") def evaluate(self, brin): traj = Traj3D() - traj.compute(brin, self.table) + + numb_ajout = 3 + + fisrt_seq = brin[0:numb_ajout] + last_seq = brin[-numb_ajout:] + + traj.compute(last_seq + 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] - first_nucleotide = traj_array[0, 0:3] - last_nucleotide = traj_array[-1, 0:3] - distance = sqrt(sum((first_nucleotide - last_nucleotide) ** 2)) + 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) - first_name = brin[0] - last_name = brin[-1] + list_distance += [distance_first_nuc, distance_last_nuc] - rot_computed = self.table.rot_table[last_name+first_name] - rot_traj = first_nucleotide - last_nucleotide - # print(rot_traj) - # print(rot_computed) - diff_angle = sum(abs(rot_computed - rot_traj)) - self.score = 1/(distance + diff_angle) + self.score = 1/max(list_distance) + + return 1/max(list_distance) def mutation(self, proba = P1): @@ -39,10 +48,14 @@ class Individu(): for coord in range(3): tir = random() if tir < proba : - # print("mutation", doublet, coord) - # print("table", table_rotations[doublet][coord]) 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]) - # print("table", table_rotations[doublet][coord]) + 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) @@ -52,3 +65,9 @@ class Individu(): # 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) diff --git a/inutile.py b/inutile.py index 1a2947e..420a646 100644 --- a/inutile.py +++ b/inutile.py @@ -31,7 +31,7 @@ class table_rotation(rotation): self.dict = {doublet : rotation(doublet) for doublet in ORIGINAL_ROT_TABLE} table1 = table_rotation() -print(table1.dict["AA"].x) +# print(table1.dict["AA"].x) #table1.dict --> {'AA': <__main__.rotation object at 0x000001A722E1BAC8>, 'AC': <__main__.rotation object at 0x000001A722E1BB00>, 'AG': <__main__.rotation object at 0x000001A729A66A58>, 'AT': <__main__.rotation object at 0x000001A729A66A20>, 'CA': <__main__.rotation object at 0x000001A729A669E8>, 'CC': <__main__.rotation object at 0x000001A729A66A90>, 'CG': <__main__.rotation object at 0x000001A729A66B00>, 'CT': <__main__.rotation object at 0x000001A729A66B70>, 'GA': <__main__.rotation object at 0x000001A729B88D68>, 'GC': <__main__.rotation object at 0x000001A729B88DA0>, 'GG': <__main__.rotation object at 0x000001A729B88DD8>, 'GT': <__main__.rotation object at 0x000001A729B88E10>, 'TA': <__main__.rotation object at 0x000001A729B88E48>, 'TC': <__main__.rotation object at 0x000001A729B88E80>, 'TG': <__main__.rotation object at 0x000001A729B88EB8>, 'TT': <__main__.rotation object at 0x000001A729B88EF0>} #table1.dict["AA"] ---> <__main__.rotation object at 0x000001A722E1BAC8> (qui est l'object rotation) diff --git a/population.py b/population.py index fdcb337..828caac 100644 --- a/population.py +++ b/population.py @@ -1,8 +1,9 @@ -import random -from random import random, randint, randrange + +from random import * from individu import Individu from RotTable import RotTable -from croisement import * +from croisement import croisement_un_point, croisement_deux_points +import copy class Population: def __init__(self,n): @@ -13,8 +14,30 @@ class Population: """Fonction qui renvoie une nouvelle instance de population a partir d'une liste d'individus""" self.n = len(liste_individus) self.indiv = liste_individus + for i in range(0,self.n): + self.indiv[i].evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") + return self + def selection_p_best(self,p=None): + if p==None: + p=(self.n)//2 + + def tri_rapide_aux(tableau,debut,fin): + if debut < fin-1: + positionPivot=partitionner(tableau,debut,fin) + tri_rapide_aux(tableau,debut,positionPivot) + tri_rapide_aux(tableau,positionPivot+1,fin) + + def tri_rapide(tableau): + tri_rapide_aux(tableau,0,len(tableau)) + + liste_individus=self.indiv + tri_rapide(liste_individus) + individus_selectionnes = [element for element in liste_individus[:p]] + self = self.modifier_population(individus_selectionnes) + + def selection_duel_pondere(self,p=None): if p == None : p = (self.n)//2 @@ -31,7 +54,7 @@ class Population: y=self.indiv[t] vu.add(t) vu.add(m) - p=random(0,1) + p=random() if p>x.score/(x.score+y.score): newself.append(y) else: @@ -42,25 +65,32 @@ class Population: def selection_duel(self,p=None): if p == None : p = (self.n)//2 - newself=[] + meilleur = self.indiv[0] + for individu in self.indiv : + if meilleur.score < individu.score: + print("meilleur, individu: ", meilleur.score, individu.score) + meilleur = individu + newself = [meilleur] vu=set() t=randrange(0,self.n) - m=randrange(0,self.n) + m=randrange(0,self.n) + non_vu = [i for i in range(0, self.n)] while len(newself)<p: - while m in vu: - m=randrange(0,self.n) - while t in vu: - t=randrange(0,self.n) + m = choice(non_vu) + non_vu.remove(m) + t = choice(non_vu) + non_vu.remove(t) + x=self.indiv[m] y=self.indiv[t] - vu.add(t) - vu.add(m) - if x.score<=y.score: + if x.score>=y.score: newself.append(x) else: newself.append(y) self = self.modifier_population(newself) + + def selection_par_rang(self,p = None): if p == None : p = (self.n)//2 @@ -115,33 +145,40 @@ class Population: while len(newself)<p: m=m=randrange(0, self.n) x=self.indiv[m] - p=random(0,1) + p=random() if p<=x.score/somme: newself.append(x) self = self.modifier_population(newself) - def reproduction(self,selection=None,enfant=croisement_un_point, p = None): + def reproduction(self,proba_mutation = None, selection=None,enfant=croisement_un_point, p = None): + if proba_mutation == None : + proba_mutation = 0.001 if selection == None : selection = self.selection_duel if p == None : p = (self.n)//2 vieille_taille = self.n selection(p) - newself = list(self.indiv) + newself = [element for element in self.indiv] while len(newself)<vieille_taille: m=randrange(0,self.n) t=randrange(0,self.n) - x=newself[m] - y=newself[t] + x=copy.deepcopy(newself[m]) + y=copy.deepcopy(newself[t]) couple_enfant = enfant(x,y) + for child in couple_enfant : + child.mutation(proba_mutation) + child.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") newself.append(couple_enfant[0]) newself.append(couple_enfant[1]) self = self.modifier_population(newself) + def afficher(popu): for individu in popu.indiv : print("\n individu \n") print(individu.table.rot_table) + print ("score", individu.score) def test(): popu = Population(4) @@ -149,16 +186,11 @@ def test(): for individu in popu.indiv : individu.evaluate("AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA") afficher(popu) - # popu.selection_par_rang() - # print("\n SELECTION PAR RANG \n") - # afficher(popu) - popu.reproduction() + popu.reproduction(selection = popu.selection_duel) print("\n REPRODUCTION \n") afficher(popu) -test() - - +#test() diff --git a/selection_par_rang.py b/selection_par_rang.py deleted file mode 100644 index ded5567..0000000 --- a/selection_par_rang.py +++ /dev/null @@ -1,45 +0,0 @@ -from random import random - -def creer_population(self, liste_individus): - self.n = len(liste_individus) - self.indiv = set(liste_individus) - return self - -def selection_par_rang(self, p = n//2): - set_individus = self.indiv - n = self.n - - def partitionner(tableau,debut,fin): - echanger(tableau,debut,random.randint(debut,fin-1)) - partition=debut - for i in range(debut+1,fin): - if tableau[i].score<tableau[debut].score: - partition+=1 - echanger(tableau,i,partition) - echanger(tableau,debut,partition) - return partition - - def tri_rapide_aux(tableau,debut,fin): - if debut < fin-1: - positionPivot=partitionner(tableau,debut,fin) - tri_rapide_aux(tableau,debut,positionPivot) - tri_rapide_aux(tableau,positionPivot+1,fin) - - def tri_rapide(tableau): - tri_rapide_aux(tableau,0,len(tableau)) - - liste = list(set_individus) - tri_rapide(liste) - individus_selectionnes = [] - - for _ in range(p): - curseur = random()*n*(n+1)/2 - j = 1 - while j*(j+1)/2 < curseur : - j+=1 - #on doit prendre l'individu avec le jème score - individus_selectionnes.append(liste[j]) - self = creer_population(self, liste_individus) - - - \ No newline at end of file -- 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