import random
import os
import csv
# Function that counts number of dissimilarities
# between two sequences
def diss(x, y):
n = 0
for a, b in zip(x, y):
if a != b:
n += 1
return (n)
# Function that mutates a string (Dna) Gen times.
# On average 0.75 mutations per generation, as the resampling will
# pick the existing nucleotide in one out of four times.
def mutate(Dna, Gen):
# Store a copy of the original DNA sequence that
# the mutated sequence can be compared to.
Dna_o = Dna[:]
Len = len(Dna)
Dis = []
# For loop that mutates the sequence Gen times and calculates the
# dissimilarity after each mutation.
for _ in range(Gen):
# Random location for mutation
Mut = random.randint(0, Len-1)
# Randomly selected nucleotide
Dna[Mut] = random.choice(['A', 'T', 'G', 'C'])
# Calculate proportional dissimalirity
Dis.append(diss(Dna, Dna_o)/Len)
# Print proportional dissimilarities.
return (Dis)
# Iterate (repeat) the mutate function i times
# Outputs a nested list
def mutate_i(Dna, Gen, i):
Mat = []
for _ in range(i):
Mat.append(mutate(Dna, Gen))
return (Mat)
# Function for helping export simulation result as CSV file.
def export_mutate(Mutate_mat, Filename="mutation_simulation.csv"):
# Add a count of the generations
Mutate_mat.insert(0, list(range(1, len(Mutate_mat[0])+1)))
# Transpose the list (swap rows and columns)
Mutate_mat = list(map(list, zip(*Mutate_mat)))
# Add headers
header = ["Generation"]
for i in range(1, len(Mutate_mat[0])):
header.append("sim_" + str(i))
Mutate_mat.insert(0, header)
# Export simulation data as a CSV file that can be imported to
# Google Sheets
with open(Filename, 'w') as csvfile:
csvwriter = csv.writer(csvfile, delimiter=',')
csvwriter.writerows(Mutate_mat)
# Print the path to the CSV file
return (os.path.join(os.getcwd(), Filename))
# # # Simulation start
# Original DNA sequence
Dna = list("ATGC" * 4)
# Set random seed so the simulation is repeatable
random.seed(1)
# Generate four simulations, each ten generations long
Mutate_mat = mutate_i(Dna, 12, 4)
# Export simulation results
export_mutate(Mutate_mat)
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