strstr() returns null

[Jedd Lim]

Title says it all, every time i run strstr() between the first string and the string to be searched for, I keep getting "null" returned. Code snippet below:

    char sequence1[200];
    char start[] = "AUG";
    char *startcodon;


/*sequence1 is already read in at this point*/

    startcodon = strstr(sequence1, start);
    printf("startcodon: %s\n", startcodon);
    position = startcodon - sequence1;
    printf("Position of start codon sequence 1: %d\n", position);

It's part of a homework assignment to accept any RNA sequence (characters A,U,G,C), search for "AUG," and to print/remember its position in the string. And yes, I did check the forum guidelines on asking for homework help.

[laserlight]

Well, I did a simulation, and it appears that you are mistaken:

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

int main(void)
{
    char sequence1[200];
    char start[] = "AUG";
    char *startcodon;

    /* simulate reading into sequence1 */
    int position;
    strcpy(sequence1, "CCCAUGCCC");
    /* end simulation */

    /*sequence1 is already read in at this point*/

    startcodon = strstr(sequence1, start);
    printf("startcodon: %s\n", startcodon);
    position = startcodon - sequence1;
    printf("Position of start codon sequence 1: %d\n", position);

    return 0;
}

Compiling and running the above program, I get the output:

startcodon: AUGCCC
Position of start codon sequence 1: 3

So, the problem likely lies with code that you did not show, e.g., the code that reads into sequence1.

[Jedd Lim]

Hmm okay, thanks, I didn't think that that could have caused the issue. If I'm writing this portion right, would it not cause any issue issue since it's set to write to the string until the '\n' character is entered then add the '\0' termination character?

    printf("Enter RNA sequence one:\n");
    while (position1 < 198 && letter1 != '\n')
    {
        letter1 = getchar();
        if(toupper(letter1) == 'A')
        {
            sequence1[position1] = letter1;
            position1 = position1 + 1;
        }
        else if(toupper(letter1) == 'C')
        {
            sequence1[position1] = letter1;
            position1 = position1 + 1;
        }
        else if(toupper(letter1) == 'G')
        {
            sequence1[position1] = letter1;
            position1 = position1 + 1;
        }
        else if(toupper(letter1) == 'U')
        {
            sequence1[position1] = letter1;
            position1 = position1 + 1;
        }
    }
    sequence1[position1] = '\0'; /*termination of string*/

(*yeah, it's a bit bulky, reused it from a previous sequence reader)

[laserlight]

You should check for EOF too for terminating the loop. Furthermore, you should avoid magic numbers and unnecessary repetition. For example:

#include SEQUENCE_SIZE 200

/* ... */

char sequence1[SEQUENCE_SIZE];
int position1;

printf("Enter RNA sequence one:\n");
while (position1 < SEQUENCE_SIZE - 1 && (letter1 = getchar()) != EOF && letter1 != '\n')
{
    letter1 = toupper(letter1);
    if (letter1 == 'A' || letter1 == 'C' || letter1 == 'G' || letter1 == 'U')
    {
        sequence1[position1++] = letter1;
    }
}
sequence1[position1] = '\0'; /*termination of string*/

[Jedd Lim]

Ohh ok thank you for the help.
The code works properly now, I just am unsure of exactly why the EOF mattered. (I'm relatively new to programming in general, just the basics are down).

[WoodSTokk]

@laserlight

Your position1 start with garbage value. It should be initialize with zero.
(but i think you know that ;-)

[laserlight]

Yes, that is obvious. It was given an initial value of 0, but unfortunately the change appears to have been omitted after editing, copying and pasting. Since Jedd Lim apparently fixed it, I saw no reason to edit my example code.