Daniel Spångber's C code, when reading whole file, and using table to count. See http://saml.rilspace.org/node/248
#include <stdio.h> | |
#include <stdlib.h> | |
#define MAXFLEN 70000000 /* Larger than the file. */ | |
int main() | |
{ | |
char *m=malloc(MAXFLEN); | |
char tablegc[256]; | |
char tableat[256]; | |
int gc=0; | |
int at=0; | |
FILE *f=fopen("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa","r"); | |
int items=fread(m,1,MAXFLEN,f); /* Read the whole file into memory. */ | |
char *ptr=m; | |
int nums, i; | |
while (*ptr++!='\n'); /* Find end of first line. */ | |
for (i=0; i<256; i++) | |
tablegc[i]=0; | |
for (i=0; i<256; i++) | |
tableat[i]=0; | |
tableat['A']=1; | |
tableat['T']=1; | |
tablegc['C']=1; | |
tablegc['G']=1; | |
nums=items-(ptr-m); | |
for (i=0; i<nums; i++) { | |
char c=*ptr++; | |
at+=tableat[(int)c]; | |
gc+=tablegc[(int)c]; | |
} | |
fclose(f); | |
free(m); | |
int total = at + gc; | |
printf("%.10f\n",(100.*gc)/total); | |
return 0; | |
} |
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