A DNA sequence is a sequence of some combination of the characters A (adenine),

Question

A DNA sequence is a sequence of some combination of the characters A (adenine), C (cytosine), G (guanine), and T (thymine) which correspond to the four nucleobases that make up DNA. Given a long DNA sequence it is often necessary to compute the number of instances of a certain subsequence. For this exercise, you will develop a program that processes a DNA sequence from a file and, given a subsequences, searches the DNA sequence and counts the number of times s appears. As an example, consider the following sequence: GGAAGTAGCAGGCCGCATGCTTGGAGGTAAAGTTCATGGTTCCCTGGCCC If we were to search for the subsequence GTA, it appears twice. You will write a program (place your source in a file named dnaSearch.c) that takes, as command line inputs, an input file name and a valid DNA (sub)sequence. That is, it should be callable from the command line as follows: /dnaSearch dna01.txt GTA What you will submit via handin: dnaSearch.c.

Explanation / Answer

Hi Let me know if you need more information:-

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#include <iostream>
#include <stdio.h>
#include <string>
#include <fstream>
using namespace std;
int main(int argc, char **argv) {
   ifstream fileInput;
   int offset;
   string search(argv[2]);
   string line;
   //cout << argv[1] << ":" << search << endl;
   int counter = 0;

   fileInput.open(argv[1]);
   if (fileInput.is_open()) {
       while (!fileInput.eof()) {
           getline(fileInput, line);
           int offset = 0;
           while(offset <line.size()){
           if ((offset = line.find(search, offset)) != string::npos) {
               //cout<<"offset"<<offset<<endl;
               offset = offset + search.size();
               counter++;
           }else{
               offset= line.size();
           }
           }
       }
       fileInput.close();
   }
   cout << search << " appears " << counter << " times " << endl;
}

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INPUT:-

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INPUT: GGAAGTAGCAGGCCGCATGCTTGGAGGTAAAGTTCATGGTTCCCTGGCCC

OUTPUT:-

GTA appears 2 times

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INPUT 2: GGAAGTAGCAGGCCGCATGCTTGGAGGTAAAGTTCATGGTTCCCTGTAGCCC

OUTPUT:-

GTA appears 3 times

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INPUT 3: ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTGTACCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA

OUTPUT:-

GTA appears 14 times

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Thanks

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