fighting heavywatal#20

hamazaki1990/allelechangewf.csv

@@ -0,0 +1 @@
+0.09999999999999998,0.19999999999999996,0.19999999999999996,0.19999999999999996,0.4,0.6,0.5,0.5,0.8,0.8,0.9,1.0

hamazaki1990/individual.py

@@ -1,3 +1,6 @@
+from decimal import Decimal
+
+
 class Individual:
     def __init__(self, n, f=1.0):
         self._id = n
@@ -11,19 +14,14 @@ def get_fitness(self):
 
     def __repr__(self):
         return str(self._id)
-
-    def is_not_fixed(self):
-        for x in range(1, len(self._inds)):
-            if self._inds[0] != self._inds[x]:
-                return True
-        else:
-            return False
+        return Decimal(self._fitness)
 
 
 def main():
     ind = Individual(42)
     print(ind.get_id())
     print(ind.get_fitness())
 
+
 if __name__ == '__main__':
     main()

hamazaki1990/population.py

@@ -16,12 +16,12 @@ def __init__(self, n, mutantrate=0, s=0):
         wild_inds = [Individual(x) for x in range(num_mutant, n)]
         self._inds = mutant_inds + wild_inds
 
-    def print_ids(self):
-        print(self._inds)
+    def get_ids(self):
+        return self._inds
 
-    def print_fitness(self):
+    def get_fitnesses(self):
         fitness = [x.get_fitness() for x in self._inds]
-        print(fitness)
+        return fitness
 
     def next_genwf(self):
         fitness = [x.get_fitness() for x in self._inds]
@@ -46,45 +46,59 @@ def is_not_fixed(self):
         else:
             return False
 
+    def mutation_is_not_fixed(self):
+        fitness = [x.get_fitness() for x in self._inds]
+        for x in range(1, len(fitness)):
+            if fitness[0] != fitness[x]:
+                return True
+        else:
+            return False
+
 
 def main():
     p1_1 = Population(10)
-    p1_1.print_ids()
-    p1_1.print_fitness()
+    print(p1_1.get_ids())
+    print(p1_1.get_fitnesses())
     print(p1_1.is_not_fixed())
+    print(p1_1.mutation_is_not_fixed())
 
     for x in range(20):
         p1_1.next_genwf()
-        p1_1.print_ids()
-        p1_1.print_fitness()
+        print(p1_1.get_ids())
+        print(p1_1.get_fitnesses())
     print(p1_1.is_not_fixed())
+    print(p1_1.mutation_is_not_fixed())
 
     p1_2 = Population(10, 0.3, 0.2)
-    p1_2.print_ids()
-    p1_2.print_fitness()
+    print(p1_2.get_ids())
+    print(p1_2.get_fitnesses())
+    print(p1_2.is_not_fixed())
+    print(p1_2.mutation_is_not_fixed())
 
     for x in range(20):
         p1_2.next_genwf()
-        p1_2.print_ids()
-    p1_2.print_fitness()
+        print(p1_2.get_ids())
+    print(p1_2.get_fitnesses())
+    print(p1_2.is_not_fixed())
+    print(p1_2.mutation_is_not_fixed())
 
     p2_1 = Population(10)
-    p2_1.print_ids()
-    p2_1.print_fitness()
+    print(p2_1.get_ids())
+    print(p2_1.get_fitnesses())
 
     for x in range(20):
         p2_1.next_genmo()
-        p2_1.print_ids()
-        p2_1.print_fitness()
+        print(p2_1.get_ids())
+    print(p2_1.get_fitnesses())
 
     p2_2 = Population(10, 0.3, 0.2)
-    p2_2.print_ids()
-    p2_2.print_fitness()
+    print(p2_2.get_ids())
+    print(p2_2.get_fitnesses())
 
     for x in range(20):
         p2_2.next_genmo()
-        p2_2.print_ids()
-    p2_2.print_fitness()
+        print(p2_2.get_ids())
+    print(p2_2.get_fitnesses())
 
 
 if __name__ == '__main__':

hamazaki1990/visualize.py

@@ -1,37 +1,35 @@
+import csv
 import pandas as pd
 from population import Population
 
 
-def calculate_ave(seq):
-    return sum(seq)/len(seq)
-
-
-def calculate_var(seq):
-    ave = calculate_ave(seq)
-    sqd = [(seq[x] - ave)**2 for x in range(len(seq))]
-    return sum(sqd)/len(seq)
-
-
-def change_allelewf(Population):
-    fixprocess = [Population._inds]
-    while Population.is_not_fixed():
-        Population.next_genwf()
-        fixprocess.append(Population._inds)
+def change_allelewf(population):
+    fit_list = population.get_fitnesses()
+    fixprocess = [1 - fit_list.count(1.0)/len(fit_list)]
+    while population.mutation_is_not_fixed():
+        population.next_genwf()
+        fit_list = population.get_fitnesses()
+        mutantrate = 1 - fit_list.count(1.0)/len(fit_list)
+        fixprocess.append(mutantrate)
     return fixprocess
 
 
-def change_allelemo(Population):
-    fixprocess = [Population._inds]
-    while Population.is_not_fixed():
-        Population.next_genmo()
-        fixprocess.append(Population._inds)
+def change_allelemo(population):
+    fit_list = population.get_fitnesses()
+    fixprocess = [1 - fit_list.count(1.0)/len(fit_list)]
+    while population.mutation_is_not_fixed():
+        population.next_genmo()
+        fit_list = population.get_fitnesses()
+        mutantrate = 1 - fit_list.count(1.0)/len(fit_list)
+        fixprocess.append(mutantrate)
     return fixprocess
 
 
-p1 = Population(10)
-data = pd.DataFrame(change_allelewf(p1))
-print(data)
+csvfile1 = open("allelechangewf.csv", "w", encoding="utf-8")
+writer = csv.writer(csvfile1)
+p1 = Population(10, 0.1, 0.5)
+writer.writerow(change_allelewf(p1))
+
 
-p2 = Population(10)
-data = pd.DataFrame(change_allelemo(p2))
-print(data)
+p2 = Population(10, 0.1, 0.5)
+print(change_allelemo(p2))

hamazaki1990/visualize.r

@@ -0,0 +1,7 @@
+install.packages("tidyverse")
+library("tidyverse")
+allelefreq=read_csv("~/github/practice-py/hamazaki1990/allelechangewf.csv", col_names = FALSE)
+names(allelefreq)=c("generation","derived_allele_frequency")
+freqprot=ggplot(allelefreq, x=generation, y=derived_allele_frequency)
+freqprot=freqprot+geom_line()
+print(freqprot)