Skip to content
Snippets Groups Projects
Select Git revision
  • master default
  • revert-562809b6
  • Data
  • Chloe2
  • EtudedutempsLoic
  • Chloe3
  • carlos
  • rodrigo
  • gauthier
  • Loicproj
  • Loic2
  • Loic
  • Chloe
  • table_rotation
14 results
Blame Permalink
individu.py 6.03 KiB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129 






from RotTable import RotTable
from Traj3D import Traj3D
import numpy as np
from math import sqrt, inf
from random import random, choice

P1 = 0.015

class Individu():
    ''' Un individu est caractérisé par sa table de rotations (individu.table)'''
    def __init__(self, table):
        lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
        brin = ''.join(lineList[1:])
        self.table = table
        lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
        self.brin = ''.join(lineList[1:])
        #self.brin = "AAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCCAGTAAACGAAAAAACCGCCTGGGGAGGCGGTTTAGTCGAA"
        self.score = None

    def evaluate(self):
        ''' Evalue le score d'un individu sur un nombre numb_ajout de points'''
        
        
        traj = Traj3D()

        numb_ajout = 6

        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 = traj.getTraj()

        list_distance = []

        begining = traj_array[0:2*numb_ajout]
        end = traj_array[-2*numb_ajout:]

        for i in range(numb_ajout):

                nuc_coordonate_beg = begining[i]
                nuc_coordonate_end = end[i]
                distance_nuc = np.linalg.norm(nuc_coordonate_beg - nuc_coordonate_end, ord=2)
                list_distance += [distance_nuc]


        self.score = max(list_distance)

        #return max(list_distance)


    def mutation(self, proba = P1):
        table_rotations = self.table.rot_table
        for doublet in sorted(table_rotations.keys()) :
            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 = 1):
        table_rotations = self.table.rot_table
        table_rotation_not_seen = [i for i in sorted(table_rotations.keys())]
        table_rotation_not_seen = table_rotation_not_seen[:8]

        tir = random()
        if tir < proba :
            for i in range(0,number_of_mutations):
                
                doublet = choice(table_rotation_not_seen)
                table_rotation_not_seen.remove(doublet)

                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]


    def mutation_close_values(self, proba = P1, number_of_mutations = 1):
        table_rotations = self.table.rot_table
        table_rotation_not_seen = [i for i in sorted(table_rotations.keys())]
        table_rotation_not_seen = table_rotation_not_seen[:8]

        tir = random()
        if tir < proba :
            for i in range(0,number_of_mutations):

                doublet = choice(table_rotation_not_seen)
                table_rotation_not_seen.remove(doublet)

                for coord in range(3):
                    value = table_rotations[doublet][coord] + np.random.normal(0, self.table.orta()[doublet][coord + 3]/15)
                    if value > self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3]:
                        value = self.table.orta()[doublet][coord] + self.table.orta()[doublet][coord + 3]
                    elif value < self.table.orta()[doublet][coord] - self.table.orta()[doublet][coord + 3]:
                        value = self.table.orta()[doublet][coord] - self.table.orta()[doublet][coord + 3]
                    table_rotations[doublet][coord] = value
                    
                    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()
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)