Vini2

import java.util.concurrent.locks.Condition;
import java.util.concurrent.locks.Lock;
import java.util.concurrent.locks.ReentrantLock;
import static java.lang.Thread.sleep;
import java.util.Random;

/*
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 * To change this template file, choose Tools | Templates
 * and open the template in the editor.

Vini2

import java.util.Random;

/**
 *
 * @author Vijini
 */

//Main class
public class SimpleDemoGA {

Vini2

class Individual {
    int fitness = 0;
    int geneLength = 5;
    int[] genes = new int[5];

    public Individual() {
        Random rn = new Random();
        //Set genes randomly for each individual
        for (int i = 0; i < geneLength; i++) {
            genes[i] = rn.nextInt() % 2;

Vini2

import java.util.Stack;
import java.util.StringTokenizer;

/*
 * To change this license header, choose License Headers in Project Properties.
 * To change this template file, choose Tools | Templates
 * and open the template in the editor.
 */
/**
 *

Vini2

# Read the file and get the DNA string
file = open('sample_dna.txt', 'r')
dna = file.read()

# Print the original DNA string
print "DNA String: ", dna

# Print the count of each letter
print "Count of A: ", dna.count("A")
print "Count of C: ", dna.count("C")

Vini2

# Read the file and get the DNA string
file = open("sample_dna.txt", "r")
dna = file.read()

# Print the original DNA string
print "DNA String: ", dna

# Create dictionary of complementing nucleobase pairs
comp_pairs = {"A" : "T", "T" : "A", "G" : "C", "C" : "G"}

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# Read the file and get the DNA string
file = open('sample_dna.txt', 'r')
dna = file.read()
print "DNA: ", dna

rna = ""

# Generate the RNA string
for i in dna:
    # Replace all occurrences of T with U

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# Read the file and get the RNA string
file = open('sample_rna.txt', 'r')
rna = file.read()

print "RNA String: ", rna

# RNA codon table
rna_codon = {"UUU" : "F", "CUU" : "L", "AUU" : "I", "GUU" : "V",
           "UUC" : "F", "CUC" : "L", "AUC" : "I", "GUC" : "V",
           "UUA" : "L", "CUA" : "L", "AUA" : "I", "GUA" : "V",

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# Read the file and get the DNA string
file = open('sample_dna.txt', 'r')
dna = file.read()

print "DNA Sequence: ", dna

# DNA codon table
protein = {"TTT" : "F", "CTT" : "L", "ATT" : "I", "GTT" : "V",
           "TTC" : "F", "CTC" : "L", "ATC" : "I", "GTC" : "V",
           "TTA" : "L", "CTA" : "L", "ATA" : "I", "GTA" : "V",

Vini2

# Import pairwise2 module
from Bio import pairwise2

# Import format_alignment method
from Bio.pairwise2 import format_alignment

# Define two sequences to be aligned
X = "ACGGGT"
Y = "ACG"