seqrev.cc

unix或linux下的DNA分析软件源码 其功能如下 1. Edit up to 256 peptide or DNA sequences simultaneously. 2. Transla

//--------------------------------------------------------//
//    seqrev.cc                                           //
//    Finds opposite strand for a DNA sequence            //
//    Latest revision: 09-21-2000                         //
//--------------------------------------------------------//

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


int main(int argc, char **argv)
{
   int index = 0;
   int a,b,k;
   FILE *fp1, *fp2;
   char file1[128], file2[128];
   char s1[1000000];
   char junk[1024];

   printf("Seqrev - finds opposite strand for a DNA sequence\n");
   printf("Sequence file:"); fflush(stdout);
   scanf("%s",file1);
   printf("Output file:  "); fflush(stdout);
   scanf("%s",file2);

   if((fp1=fopen(file1,"rb")) == NULL) 
   {  printf("\nUnable to open file xxx%sxxx\n",file1);
      exit(1);
   }
   if((fp2=fopen(file2,"wb")) == NULL) 
   {  printf("\nUnable to open file xxx%sxxx\n",file2);
      exit(1);
   }

   printf("Original sequence\n");
   while(!feof(fp1))
   {
      b = fgetc(fp1);
      if(b=='#') fgets(junk,1024,fp1);  // comment
      b = toupper(b);
      switch(b)
      {  case 'U': a = 'A'; break;
         case 'T': a = 'A'; break;
         case 'A': a = 'T'; break;
         case 'G': a = 'C'; break;
         case 'C': a = 'G'; break;
         case 'N': a = 'N'; break;
         default: a = ' ';
      }
      if(a == 'A' || a == 'T' || a == 'U' || a == 'C' || a == 'G' || a == 'N')
      { 
         s1[index++] = a;
         printf("%c",b);
      }
   }
   printf("\n\n");

   printf("Reversed sequence\n");
   for(k=index-1;k>=0;k--)
   {  a = s1[k];
      printf("%c",a);
      fputc(a,fp2);
   }
   printf("\n\nReverse (%d bases) saved in %s\n",index,file2);

   fclose(fp1);
   fclose(fp2);
   return 0;
}