How To Generate Dna K-Mers Of A Given Length In C?

Question

[User 4000]

how to generate DNA k-mers of a given length? For example, if the k=2, there should be 4^2=16 k-mers.I need to know how we can do in C language.

[narendrareddy.k97]

can i know what here input is when i run this code the output was using main k size. how get output For example, if the k=2, there should be 4^2=16 k-mers.

[Ram]

Don't add answers unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. When you say "this code", we have no idea what you're talking about. Reply to the appropriate answer with your comment.

[narendrareddy.k97]

IN this below when i run code it saying output as using main k size so here what is the input and i want output when k=1,2,3.

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

#define SET_BASE(a) dna[pos]=a;recursive(dna,pos+1,k)

static void recursive(
    char* dna,
    const int pos,
    const int k)
    {
    if(pos==k)
        {
        fputs(dna,stdout);
        fputc('\n',stdout);
        return;
        }
    SET_BASE('A');
    SET_BASE('T');
    SET_BASE('G');
    SET_BASE('C');
    }

int main(int argc,char** argv)
    {
    char* dna;
    int k;
    if(argc!=2)
        {
        fprintf(stderr,"Usage %s k-size\n",argv[0]);
        return EXIT_FAILURE;
        }
    k=atoi(argv[1]);
    if(k<=0)
        {
        fprintf(stderr,"Bad k-size:%s\n",argv[1]);
        return EXIT_FAILURE;
        }
    dna=(char*)malloc(sizeof(char)*(k+1));
    if(dna==0)
        {
        fprintf(stderr,"Out of memory k=%s\n",argv[1]);
        return EXIT_FAILURE;
        }
    dna[k]=0;
    recursive(dna,0,k);
    free(dna);
    return EXIT_SUCCESS;
    }

[Ram]

Hi,

You were supposed to add a comment, not an answer. Please stop adding answers or your account will be temporarily suspended.

Answer 1

[lh3]

For k<=31:

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

int main(int argc, char *argv[])
{
    int i, k;
    unsigned long long x, y;
    if (argc == 1) {
        fprintf(stderr, "Usage: %s <k>\n", argv[0]);
        return 1;
    }
    k = atoi(argv[1]);
    for (x = 0; x < 1ULL<<(2*k); ++x) {
        for (i = 0, y = x; i < k; ++i, y >>= 2)
            putchar("ACGT"[y&3]);
        putchar('\n');
    }
    return 0;
}

[lh3]

Writing such things is part of my routine work. If you were working on alignment etc. on a daily base, you would certainly know these tiny tricks as well. You know a lot I do not know well. :)

[Pierre Lindenbaum]

Heng, why do I feel completely stupid each time you answer on biostar :-) ?

[lh3]

Writing such things is part of routine work. If you were working on alignment etc. on a daily base, you would certainly know these tiny tricks as well. You know a lot I do not know well. :)

[Pierre Lindenbaum]

I hope you'll receive the 2012 Franklin Award. You have my vote :-)

[lh3]

Thank you very much, Pierre. I am not sure if I have contributed enough, but I really hope biosciences to be open.

[Pierre Lindenbaum]

congrats! :-) http://www.bio-itworld.com/2012/03/14/broads-heng-li-wins-2012-benjamin-franklin-award.html

[lh3]

Thank you, Pierre. :-)

Answer 2

[Pierre Lindenbaum]

Sounds like a homework, but I can't resist to code in C ;-)

Recursion is the way.

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

#define SET_BASE(a) dna[pos]=a;recursive(dna,pos+1,k)

static void recursive(
    char* dna,
    const int pos,
    const int k)
    {
    if(pos==k)
        {
        fputs(dna,stdout);
        fputc('\n',stdout);
        return;
        }
    SET_BASE('A');
    SET_BASE('T');
    SET_BASE('G');
    SET_BASE('C');
    }

int main(int argc,char** argv)
    {
    char* dna;
    int k;
    if(argc!=2)
        {
        fprintf(stderr,"Usage %s k-size\n",argv[0]);
        return EXIT_FAILURE;
        }
    k=atoi(argv[1]);
    if(k<=0)
        {
        fprintf(stderr,"Bad k-size:%s\n",argv[1]);
        return EXIT_FAILURE;
        }
    dna=(char*)malloc(sizeof(char)*(k+1));
    if(dna==0)
        {
        fprintf(stderr,"Out of memory k=%s\n",argv[1]);
        return EXIT_FAILURE;
        }
    dna[k]=0;
    recursive(dna,0,k);
    free(dna);
    return EXIT_SUCCESS;
    }