function to change character to integer

[gkoenig]

hello to all,

I need a function that will change all characters in my string to integers (a to 0, c to 1, g to 2, t to 3)

I know this sounds like a simple operation but, I am new to programming and not fluent in the functions yet.

Thanks

[mike_g]

Example:

char ch = 'd';
int i = ch -'a';

You might also want to convert characters to lowercase first as well.

Edit: you seem to want strange values from the characters. Unless theres some formula for it you might want to have an array holding each characters value, then map the characters position in the array. EG:

int map[26] = {0, 345, 1, 23445, 34, 5436, 2, ..... etc}
char ch = 'g';
int i = map[ch-'a'];

[Codeplug]

How bout a macro

#define DNAbase2int(c) \
    ((c) == 'a' ? 0 : \
     ((c) == 'c' ? 1 : \
      ((c) == 'g' ? 2 : 3)))

gg

[dwks]

How 'bout this?

int DNA2int(char c) {
    static const char *convert = "acgt";
    const char *p = strchr(convert, c);
    return p ? p-convert : -1;
}

It could be even shorter if you don't care about error checking . . . but never mind that, because mike_g's solution is nicer.

BTW: the other way around is easy.

const char *map = "acgt";
char c = map[i];

Or, if you like obfuscation:

char c = "acgt"[i];

Edit: you seem to want strange values from the characters.

As Codeplug's response obscurely hinted, it's probably DNA-related.

[gkoenig]

Thanks for the help. I am sorry to say this but, I am new to programming and some of the techniques you are using I am not that familiar with. I will try to clarify what I am trying to do.

I need to convert a->0, c->1, g->2, t->3. These are the only letters in string (DNA sequence)
I need to convert because later in the program I will be using a 4-D array as a chart to collect a count. Below is my code; hopefully it helps

// A Program to count the count of 4-mers in a nucleotide sequence.

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

main( int argc, char **argv )
    {
        FILE *input ; 
        FILE *outpur ;
        char buffer[1000] ;        
        int i = 0 ;
        int c, tr ;
        int w,x,y,z ;
         
        char *seqData ;
        seqData = (char *)malloc(10000000) ;
        
       
        char t1, t2, t3, t4 ;
        int index ; 
        
        
        // Initialize 4-D array
        int tupleCount[4][4][4][4] ;
        for(w = 0 ; w < 4 ; w++ )
            for(x = 0 ; x < 4 ; x++ )
                for(y = 0 ; y < 4 ; y++ ) 
                    for(z = 0 ; z < 4 ; z++ )
                        {
                            tupleCount[w][x][y][z] ;
                        }
        
        // Open input file to read from        
        if( ! ( input = fopen( argv[1], "r" ) ) )
            { 
                printf( "COULD NOT OPEN FILE %s - Exit!\n", argv[1]) ; 
                exit(1) ; 
            }        
        
        
        // Collect sequence from GenBank file
        while(fgets(buffer, 1000, input))
                        {
                        // start obtaining bases after ORIGIN
                        if(strstr(buffer, "ORIGIN")) 
                            {                                                  
                               while((c=getc(input)) != '/' && c != EOF)
                                    {
                                    if(c >= 'a' && c <= 'z')
                                        {
                                        seqData[i++] = c ;
                                        }
                                    }                            
                            }           
                        }
                        
        // Convert a,c,g,t to 0,1,2,3                
      /*  while(tr=getc(seqData) != EOF)
            {
                        
            } */
        
        
        
        // Scan DNA sequence for each 4-mer 
        for( index = 0 ; index < strlen(seqData) - 3 ; ++index )
            {
                t1 = seqData[index] ;
                t2 = seqData[index + 1] ;
                t3 = seqData[index + 2] ;
                t4 = seqData[index + 3] ;
                
                
                // Accumulate a count to find distribution
                ++tupleCount[t1][t2][t3][t4] ;
                
            }
            
    
         
         
                   
        fclose(input) ;
    
        printf("Here is the distribution of 4-mers:\n\n%s", tupleCount ) ;     
        free(seqData) ; 
        return(0) ;
    }

Thanks

[dwks]

Casting malloc() is usually a bad idea in C -- see the FAQ.

tupleCount[w][x][y][z] ;

Obviously, this does nothing. Presumably you want to initialize that element of the array to something, perhaps 0.

seqData[i++] = c ;

Here's where you want to do the conversion. Well, let's start off with a simple way of doing it. Here's what you said:

I need to convert a->0, c->1, g->2, t->3.

Okay:

if(c == 'a') seqData[i++] = 0;
else if(c == 'c') seqData[i++] = 1;
else if(c == 'g') seqData[i++] = 2;
else if(c == 't') seqData[i++] = 3;
else /* error */;

But wait, that's a lot of "seqData[i++]"'s. Maybe it would be better to do something like this:

int n;
if(c == 'a') n = 0;
else if(c == 'c') n = 1;
else if(c == 'g') n = 2;
else if(c == 't') n = 3;
else n = -1;  /* error */
seqData[i++] = n;

But that could also be a switch statement:

switch(c) {
    case 'a': n = 0; break;
    case 'c': n = 1; break;
    case 'g': n = 2; break;
    case 't': n = 3; break;
    default: n = -1; break;  /* error */
}
seqData[i++] = n;

There are so many ways to do it . . . .