CSC231 Homework 8 2017

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Problem #1: Programming in C

Write a C program that receives 3 DNA strings on the command line, one called marker1, one called marker2 and one called DNA, and which zaps the bases (characters) in DNA that sit between marker1 and marker2, replacing them with dashes.
Here are some examples of how the solution program operates:

231b@aurora ~ $ ./hw8_1 AGC ACC ACCGGGGGAGCCAAAGCTTTTTACCTT
ACCGGGGG-----------------TT
 
231b@aurora ~ $ ./hw8_1 AGCA ACC ACCGGGGGAGCCAAAGCTTTTTACCTT
ACCGGGGGAGCCAAAGCTTTTTACCTT

231b@aurora ~ $ ./hw8_1 AGC AT ACCGGGGGAGCCAAAGCTTTTTACCTT
ACCGGGGGAGCCAAAGCTTTTTACCTT

231b@aurora ~ $ ./hw8_1 AC TG ACACACACGGGGGGTGTGTGTG
----------------TGTGTG

231b@aurora ~ $  ./hw8_1 AC TG TGACACACACGGGGGGTGTGTGTG
TG----------------TGTGTG

Notes

When the first or second markers are not found in the DNA, the program outputs the original DNA string.

When the first marker appears several time, the first occurrence is the one used.

When the second marker appears several times, its first occurrence after an occurrence of the first marker is used.

Starting Seed

Start with this skeleton program, and call it hw8_1.c.

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


void main( int argc, char *argv[] ) {
  char *marker1, *marker2, *DNA;
  char *fileName;

  if (argc < 4 ) {
    printf( "syntax: %s marker1 marker2 DNA\n", argv[0] );
    return;
  }

  marker1 = argv[1];
  marker2 = argv[2];
  DNA     = argv[3];
  
  //--- print the markers and DNA ---
  /* (for debugging purpose)
  printf( "Marker1 = %s\n", marker1 );
  printf( "Marker2 = %s\n", marker2 );
  if ( strlen( DNA ) > 80 )
    printf( "DNA     = %.*s...%s (%d bases)\n\n",
          10, DNA, DNA+((int)strlen(DNA)-10), 
	  (int) strlen( DNA) );
  else
    printf( "DNA     = %s\n\n", DNA );
  */

  //--- add your code below this point ---


}

You should uncomment the section print the markers and DNA" to see how the program gets the 3 strings.