Question

dna01.txt

3. [Bonus Problem] DNA Subsequence 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 instance:s 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 GTA appears 2 times

ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA

Answer 1

The answer is as follows:

The code is as follows:

#include <stdio.h>
#include <string.h>

void main( int argc, char *argv[] ) {

   char *filename;
   char *data;
   char *sequence;
   FILE *fp;
   int count = 0;

   filename = argv[1];
   data = argv[2];
   fp = fopen(filename, "r");
   if (fp != NULL){
      fscanf(fp, "%s",sequence);
      fclose(fp);
      while(sequence = strstr(sequence, data))
      {
         count++;
         sequence++;
      }
      printf("%s appears %d times\n", data, count);
   }
   else {
       printf("Error in opening file\n");
   }
  
}