Convert to Antisense sequence

Guy St.C. Slater.. gslater at hgmp.mrc.ac.uk
Tue Dec 1 13:38:52 EST 1998


You might want to watch out for the other IUPAC nucleotide symbols
(especially N).

See http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html for a full list.

The (ahem) C snippet below will handle these cases when
generating a reverse complement of a fasta format file. 

HTH,

Guy.

/* START */
#include <stdio.h>

char *comp =
  "----------\n--------------------------------------------------"
  "----TVGH--CD--M-KN---YSAABW-R-------tvgh--cd--m-kn---ysaabw-r-";

int rev(int ch){
    if((ch == '>') || (ch == EOF))
        return ungetc(ch, stdin);
    rev(getchar());
    putchar(comp[ch]);
    return ch;
    }

int main(){
    int ch;
    do { while(((ch = getchar()) != '\n') && (ch != EOF))
            putchar(ch);
    } while(rev(ch) != EOF);
    return 0;
    }

/* STOP */

-- 
 ----------------------------------------------------------------------
 Guy St.C. Slater,                             Tel: (+44) 1223 49 45 65
 Human Genome Mapping Project Resource Centre, Fax: (+44) 1223 49 45 12
 Wellcome Trust Genome Campus,            mailto:gslater at hgmp.mrc.ac.uk
 Hinxton, Cambridge, CB10 1SB.      http://www.hgmp.mrc.ac.uk/~gslater/
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