CSC231 Homework 8 2017

Page under construction!

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.

When found, the two markers are also zapped with dashes.

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.

Testing Your Program

I have made the executable version of the solution available. It should already be in your PATH, so you don't need to copy it. To perform a batch test of your program against the solution, create two batch files. The first one is given below:

#! /bin/bash
# Your name
# Tests the hw8_1 program by feeding it different markers and DNA strings.
# The output is fed in "cat -v" which will display unprintable (junk) characters.

echo AGC ACC ACCGGGGGAGCCAAAGCTTTTTACCTT
./hw8_1 AGC ACC ACCGGGGGAGCCAAAGCTTTTTACCTT | cat -v 

echo AGCA ACC ACCGGGGGAGCCAAAGCTTTTTACCTT
./hw8_1 AGCA ACC ACCGGGGGAGCCAAAGCTTTTTACCTT | cat -v

echo AGC AT ACCGGGGGAGCCAAAGCTTTTTACCTT
./hw8_1 AGC AT ACCGGGGGAGCCAAAGCTTTTTACCTT | cat -v

echo AC TG ACACACACGGGGGGTGTGTGTG
./hw8_1 AC TG ACACACACGGGGGGTGTGTGTG | cat -v

echo AC TG TGACACACACGGGGGGTGTGTGTG
./hw8_1 AC TG TGACACACACGGGGGGTGTGTGTG | cat -v