Problem collecting large string of data

Hello to all,

I am having difficulty trying to build a large string (approx 5 million characters) from a large input file (approx. 11 MB). The program compiles fine, it just doesn't stop running. Here is my code:

Code:

main( int argc, char **argv )
    {
        FILE *input ; 
        FILE *output ;
        char buffer[1000] ;        
        int i = 0 ;
        char c ;
         
        char *seqData ;
        seqData = (char *)malloc(10000000) ;
        
       
  /*      char t1, t2, t3, t4 ;
        int index ; 
        int tupleCount[4][4][4][4] ; */
                
        if( ! ( input = fopen( argv[1], "r" ) ) )
            { 
                printf( "COULD NOT OPEN FILE %s - Exit!\n", argv[1]) ; 
                exit(1) ; 
            }        

        while(fgets(buffer, 1000, input))
                        {
                        // start obtaining bases after ORIGIN
                        if(strstr(buffer, "ORIGIN")) 
                            {                                                  
                               int i = 0 ;
                               while((c=getchar()) != '/')
                                    {
                                    if(c >= 'a' && c <= 'z')
                                        {
                                        seqData[i++] = c ;
                                        }
                                    }                            
                            }           
                        }
        
        /*for( index = 0 ; index < strlen(seqData) - 3 ; ++index )
            {
                t1 = seqData[index] ;
                t2 = seqData[index + 1] ;
                t3 = seqData[index + 2] ;
                t4 = seqData[index + 3] ;
                 count the different 4-mers 
            }*/
                      
        
        printf("Here is the sequence:\n" ) ;     
        return(0) ;
    }

Any help would be great. Please keep in mind that I am a newbie to programming.

Please keep in mind that starting new threads on exactly the same topic is unlikely to make you popular. Segmentation fault

Now please, let us continue our discussion in your other thread. What did you not understand about the replies?

[edit] I'm sorry, I just noticed that you have changed you code, to use malloc() now. You still should have used the same thread, but I'll reply to this one now . . . .

Code:

                               int i = 0 ;
                               while((c=getchar()) != '/')
                                    {
                                    if(c >= 'a' && c <= 'z')
                                        {
                                        seqData[i++] = c ;
                                        }
                                    }

I think perhaps you should declare i outside the loops. As it is, the elements of seqData will be overwritten with each new occurrence of ORIGIN. Perhaps this is what you wanted; in that case, you should do something with seqData before it is overwritten.

I'd suggest using islower() from <ctype.h> instead of "if(c >= 'a' && c <= 'z')". It's easier to use and read, and more portable too.

Don't forget to free() the memory when you're done with it! Try adding

Code:

free(seqData);

right before your return 0.

Another thing: perhaps your while loop with getchar() should be parsing buffer instead?

4-mers? twomers will be offended! Your program is twice as big as he is. [/edit]

Actually, I think the getchar() problem is why your program hangs.

Code:

while((c=getchar()) != '/')

You just keep reading and reading until you get a '/'. If you happened to encounter EOF (End Of File) before you got a '/', you'd get an infinite loop. A quick fix for this would be:

Code:

int c;
while((c = getchar()) != '/' && c != EOF)

I've made c an int because EOF can only be stored in an int -- don't worry, it doesn't affect the rest of your code.

In addition -- d'oh! -- getchar() reads from the keyboard, not the file input. To read from the file input, use getc(input) instead of getchar().

But I think the main problem is that you're reading from the file/screen/whatever instead of parsing buffer further. Perhaps you should store the position that "ORIGIN" was found and continue parsing the line with sscanf() or something after that? I'm not sure if you're expecting ORIGIN on a line of its own or what.

Thank you for the help dwks. Everything is running fine. The issue with the tag ORIGIN is that this is where in the file I must start collecting characters. The files it acts on all have a standardized architecture.

Again, thanks for the help. I'll catch you later when I know I will need help with a 4-D array