From c9581fda79bf01880720190b7845a3e848e60d90 Mon Sep 17 00:00:00 2001
From: Kappes Marques Rodrigo <rodrigo.kappes@student-cs.fr>
Date: Thu, 30 Jan 2020 09:58:00 +0100
Subject: [PATCH] Cleaned croisement and RotTable
---
__pycache__/RotTable.cpython-37.pyc | Bin 2578 -> 2578 bytes
__pycache__/croisement.cpython-37.pyc | Bin 2680 -> 2064 bytes
__pycache__/individu.cpython-37.pyc | Bin 3877 -> 3877 bytes
__pycache__/population.cpython-37.pyc | Bin 5102 -> 5249 bytes
croisement.py | 43 +++++++++-----------------
individu.py | 1 +
population.py | 3 --
7 files changed, 15 insertions(+), 32 deletions(-)
diff --git a/__pycache__/RotTable.cpython-37.pyc b/__pycache__/RotTable.cpython-37.pyc
index 97c7b449f729cb4937feb17325b1d5876ee76f4e..a2a8357d3008572384c7dcf2386e0a1d32d1e2de 100644
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diff --git a/__pycache__/croisement.cpython-37.pyc b/__pycache__/croisement.cpython-37.pyc
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diff --git a/__pycache__/individu.cpython-37.pyc b/__pycache__/individu.cpython-37.pyc
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diff --git a/__pycache__/population.cpython-37.pyc b/__pycache__/population.cpython-37.pyc
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diff --git a/croisement.py b/croisement.py
index 95119ec..e9942ef 100644
--- a/croisement.py
+++ b/croisement.py
@@ -2,37 +2,22 @@ import numpy
from RotTable import RotTable
from individu import Individu
-ROT_TABLE = {\
- "AA": [35.62, 7.2, -154, 0.06, 0.6, 0],\
- "AC": [34.4, 1.1, 143, 1.3, 5, 0],\
- "AG": [27.7, 8.4, 2, 1.5, 3, 0],\
- "AT": [31.5, 2.6, 0, 1.1, 2, 0],\
- "CA": [34.5, 3.5, -64, 0.9, 34, 0],\
- "CC": [33.67, 2.1, -57, 0.07, 2.1, 0],\
- "CG": [29.8, 6.7, 0, 1.1, 1.5, 0],\
- "CT": [27.7, 8.4, -2, 1.5, 3, 0],\
- "GA": [36.9, 5.3, 120, 0.9, 6, 0],\
- "GC": [40, 5, 180, 1.2, 1.275, 0],\
- "GG": [33.67, 2.1, 57, 0.07, 2.1, 0],\
- "GT": [34.4, 1.1, -143, 1.3, 5, 0],\
- "TA": [36, 0.9, 0, 1.1, 2, 0],\
- "TC": [36.9, 5.3, -120, 0.9, 6, 0],\
- "TG": [34.5, 3.5, 64, 0.9, 34, 0],\
- "TT": [35.62, 7.2, -154, 0.06, 0.6, 0]\
- }
-
-
def croisement_un_point(parent1, parent2):
'''Croise les tables de rotation des parents pour former deux enfants en respectant les symétries du problème'''
''' Retourne deux enfants'''
+
enfant1 = Individu(RotTable())
enfant2 = Individu(RotTable())
comp = 0
point_crois= numpy.random.random_integers(0,8)
- list_dinucleotides = sorted(ROT_TABLE)
+ list_dinucleotides = sorted(RotTable().orta())
+
+ #We look at the list of sorted dinucleotides and create the crossover
for doublet in list_dinucleotides:
if doublet == "GA":
break
+
+ #If it have a value smaller than the generated number it wont do the crossover
if comp < point_crois:
enfant1.table.rot_table[doublet] = parent1.table.rot_table[doublet]
correspondent_doublet1 = enfant1.table.corr()[doublet]
@@ -44,6 +29,7 @@ def croisement_un_point(parent1, parent2):
enfant2.table.rot_table[correspondent_doublet2] = parent2.table.rot_table[correspondent_doublet2]
enfant2.table.rot_table[correspondent_doublet2][2] *= -1
+ #If it have a value bigger than the generated number it will crossover
else :
enfant1.table.rot_table[doublet] = parent2.table.rot_table[doublet]
correspondent_doublet1 = enfant1.table.corr()[doublet]
@@ -62,13 +48,19 @@ def croisement_un_point(parent1, parent2):
def croisement_deux_points(parent1, parent2):
''' Croise les tables de rotationd des deux parents en croisant à deux points et respectant les symétries du problème'''
''' Retourne deux enfants'''
+
enfant1 = Individu(RotTable())
enfant2 = Individu(RotTable())
comp = 0
point_crois1= numpy.random.random_integers(0,8)
point_crois2= numpy.random.random_integers(0,8)
list_dinucleotides = sorted(ROT_TABLE)
+
+ #We look at the list of sorted dinucleotides and create the crossover
for doublet in list_dinucleotides:
+
+ #If it have a value smaller than the first generated number it wont do the crossover
+ #unless it have a value bigger than the second generated number
if comp < min(point_crois1,point_crois2) or comp > max(point_crois1,point_crois2):
enfant1.table.rot_table[doublet] = parent1.table.rot_table[doublet]
correspondent_doublet1 = enfant1.table.corr()[doublet]
@@ -80,6 +72,7 @@ def croisement_deux_points(parent1, parent2):
enfant2.table.rot_table[correspondent_doublet2] = parent2.table.rot_table[correspondent_doublet2]
enfant2.table.rot_table[correspondent_doublet2][2] *= -1
+ #If it have a value is located in between the generated values it will do the crossover
else :
enfant1.table.rot_table[doublet] = parent2.table.rot_table[doublet]
correspondent_doublet1 = enfant1.table.corr()[doublet]
@@ -92,11 +85,3 @@ def croisement_deux_points(parent1, parent2):
enfant2.table.rot_table[correspondent_doublet2][2] *= -1
comp += 1
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/individu.py b/individu.py
index c6b3ba2..abb27b1 100644
--- a/individu.py
+++ b/individu.py
@@ -8,6 +8,7 @@ P1 = 0.015
class Individu():
''' Un individu est caractérisé par sa table de rotations (individu.table)'''
+
def __init__(self, table):
self.table = table
lineList = [line.rstrip('\n') for line in open("plasmid_8k.fasta")]
diff --git a/population.py b/population.py
index c576750..2c89349 100644
--- a/population.py
+++ b/population.py
@@ -95,12 +95,10 @@ class Population:
for _ in range(p-1):
curseur = random()*n*(n+1)/2
- # print("curseur", curseur)
j = 1
while j*(j+1)/2 < curseur :
j+=1
#on doit prendre l'individu avec le jème score
- # print("individus selectionés", individus_selectionnes)
individus_selectionnes.append(liste_individus[j-1])
self = self.modifier_population(individus_selectionnes)
@@ -164,7 +162,6 @@ class Population:
def afficher(popu):
for individu in popu.indiv :
print("\n individu \n")
- # print(individu.table.rot_table)
print ("score", individu.score)
--
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