output heavywatal#22

hamazaki1990/individual.py

@@ -2,7 +2,7 @@
 
 
 class Individual:
-    mutationrate = 0.01
+    mutationrate = 0.001
 
     def __init__(self, n, f=1.0):
         self._id = n

hamazaki1990/population.py

@@ -1,4 +1,5 @@
 import random
+import copy
 from individual import Individual
 
 
@@ -33,7 +34,8 @@ def next_genwf(self):
         cumsum_fitness = [sum(fitness[:i]) for i in range(1, size + 1)]
         next_generation = []
         for x in range(size):
-            next_inds = roulettechoice(self._inds, cumsum_fitness)
+            current_inds = copy.deepcopy(self._inds)
+            next_inds = roulettechoice(current_inds, cumsum_fitness)
             next_inds.acquire_mutation()
             next_generation.append(next_inds)
         self._inds = next_generation
@@ -43,7 +45,8 @@ def next_genmo(self):
         size = len(self._inds)
         cumsum_fitness = [sum(fitness[:i]) for i in range(1, size + 1)]
         i_dying = random.randrange(size)
-        next_inds = roulettechoice(self._inds, cumsum_fitness)
+        current_inds = copy.deepcopy(self._inds)
+        next_inds = roulettechoice(current_inds, cumsum_fitness)
         next_inds.acquire_mutation()
         self._inds[i_dying] = next_inds
 
@@ -52,15 +55,30 @@ def list_mutation(self):
         m_sites = []
         for x in genotypes:
             m_sites.extend(x)
-        m_sites = sorted(m_sites)
+        m_sites = sorted(list(set(m_sites)))
         m_list = ([[0 for x in range(len(m_sites))]
                   for y in range(len(self._inds))])
         for i in range(len(self._inds)):
             for j in range(len(genotypes[i])):
                 k = m_sites.index(genotypes[i][j])
-                if k != "ValueError":
-                    m_list[i][k] += 1
-        print(m_list)
+                m_list[i][k] += 1
+        return m_list
+
+    def calculate_mutantfreq_per_site(self):
+        genotypes = [x.get_genotype() for x in self._inds]
+        m_sites = []
+        for x in genotypes:
+            m_sites.extend(x)
+        m_sites = sorted(list(set(m_sites)))
+        m_count = [0 for x in range(len(m_sites))]
+        for i in range(len(self._inds)):
+            for j in range(len(genotypes[i])):
+                k = m_sites.index(genotypes[i][j])
+                m_count[k] += 1
+        mutantfreq = [x/len(self._inds) for x in m_count]
+        mutantfreq_per_site = ({m_sites[i]: mutantfreq[i]
+                               for i in range(len(m_sites))})
+        return mutantfreq_per_site
 
     def is_not_fixed(self):
         for x in range(1, len(self._inds)):
@@ -80,7 +98,8 @@ def main():
         p1_1.next_genwf()
         print(p1_1.get_ids())
         print(p1_1.get_genotypes())
-        p1_1.list_mutation()
+        print(p1_1.list_mutation())
+        print(p1_1.calculate_mutantfreq_per_site())
 
     print(p1_1.is_not_fixed())
     p1_1.list_mutation()

hamazaki1990/visualize.py

@@ -2,60 +2,62 @@
 from population import Population
 
 
-def calculate_mutantfreq(population):
-    m_list = population.list_mutation()
-    m_count = [0 for x in range(len(m_list[0]))]
-    for i in m_list:
-        for j in m_list[i]:
-            if i[j] != 0:
-                m_count[j] += 1
-    mutantfreq = [x/len(m_list) for x in m_count]
-    return mutantfreq
-
-
 def change_allelewf(population, generation):
-    t = 0
-    fixprocess = [[t, population.calculate_mutantfreq()]]
+    change_allele = [population.calculate_mutantfreq_per_site()]
     for x in range(generation):
-        t += 1
         population.next_genwf()
-        fixprocess.append([t, population.calculate_mutantfreq()])
-    return fixprocess
-
-
-def change_allelemo(population):
-    t = 0
-    fixprocess = [[t, population.calculate_mutantfreq()]]
-    for x in range(20):
-        t += 1
+        change_allele.append(population.calculate_mutantfreq_per_site())
+    all_mutations = []
+    for x in change_allele:
+        all_mutations.extend(x.keys())
+    all_mutationsites = sorted(list(set(all_mutations)))
+    derived_allelefreq = []
+    for x in range(generation+1):
+        t = [x]
+        t.extend([change_allele[x].get(y, 0.0) for y in all_mutationsites])
+        derived_allelefreq.append(t)
+    return derived_allelefreq
+
+
+def change_allelemo(population, generation):
+    change_allele = [population.calculate_mutantfreq_per_site()]
+    for x in range(generation):
         population.next_genmo()
-        fixprocess.append([t, population.calculate_mutantfreq()])
-    return fixprocess
-
-
-def output_allelechange(filename, population, function):
+        change_allele.append(population.calculate_mutantfreq_per_site())
+    all_mutations = []
+    for x in change_allele:
+        all_mutations.extend(x.keys())
+    all_mutationsites = sorted(list(set(all_mutations)))
+    derived_allelefreq = []
+    for x in range(generation+1):
+        t = [x]
+        t.extend([change_allele[x].get(y, 0.0) for y in all_mutationsites])
+        derived_allelefreq.append(t)
+    return derived_allelefreq
+
+
+def output_allelechange(filename, function, population, generation):
     with open(filename, "w", encoding="utf-8") as outfile:
         writer = csv.writer(outfile)
-        writer.writerow(["generation", "derived_allele_frequency"])
-        fixprocess = function(population)
-        for x in range(len(fixprocess)):
-            writer.writerow(fixprocess[x])
+        m_freq = function(population, generation)
+        num = ["allele" + str(i) + "frequency" for i in range(len(m_freq[0]))]
+        col_name = ["generation"]
+        col_name.extend(num)
+        writer.writerow(col_name)
+        for x in range(len(m_freq)):
+            writer.writerow(m_freq[x])
 
 
 p1_1 = Population(10)
-print(p1_1.get_ids())
-print(p1_1.get_fitnesses())
-print(p1_1.is_not_fixed())
-
-for x in range(10):
-    p1_1.next_genwf()
-    print(p1_1.get_ids())
-    p1_1.get_genotypes()
-    p1_1.list_mutation()
-    print(p1_1.calculate_mutantfreq())
-
-p1 = Population(10, 0.1, 0.2)
-output_allelechange("allelefreqwf.csv", p1, change_allelewf)
-
-p2 = Population(10, 0.1, 0.5)
-output_allelechange("allelefreqmo.csv", p2, change_allelemo)
+fixprocess1 = change_allelewf(p1_1, 10)
+print(fixprocess1)
+
+p1_2 = Population(10)
+fixprocess2 = change_allelemo(p1_2, 20)
+print(fixprocess2)
+
+p1 = Population(100)
+output_allelechange("allelefreqwf.csv", change_allelewf, p1, 100)
+
+p2 = Population(100)
+output_allelechange("allelefreqmo.csv", change_allelemo, p2, 100)