1 #include <stdio.h>

 2 #include <stdlib.h>

 3 #include <string.h>

 4 #define buff 1024

 5

 6 typedef unsigned long long int u_llong;

 7

 8 static void usage(int num,const char *str)

 9 {

10     if(num !=2)

11     {

12         fprintf(stderr,"usage: %s fqFile\n",str);

13         exit(0);

14     }

15 }

16

17 static u_llong* gcN(char base[buff])

18 {

19     base[strlen(base)-1]='\0';

20

21     int i;

22     static u_llong gactn[]={0,0,0,0,0};

23     for(i=0; i<strlen(base); i++)

24     {

25         if(base[i]=='G')

26             gactn[0]++;

27         if(base[i]=='A')

28             gactn[1]++;

29         if(base[i]=='C')

30             gactn[2]++;

31         if(base[i]=='T')

32             gactn[3]++;

33         if(base[i]=='N')

34             gactn[4]++;

35     }

36     return gactn;

37 }

38

39 static void calc(const char *fqfile)

40 {

41     FILE *fq;

42     if((fq=fopen(fqfile,"r")) == NULL)

43     {

44         perror("fopen");

45         exit(1);

46     }

47     //fprintf(stderr,"fq file <%s> open suceed!\n",fqfile);

48

49     char base[buff];

50     char qual=0;

51     u_llong *p=NULL;

52     while((fgets(base,buff,fq))!= NULL)

53     {

54         if(base[0]=='@')

55         {

56             continue;

57         }

58         if(base[0]=='+')

59         {

60             qual=1;

61             continue;

62         }

63         if(qual==1)

64         {

65             qual=0;

66             continue;

67         }

68

69         p=gcN(base); // G A C T N

70     }

71

72     float GClevel,Nlevel;

73     u_llong sum=0;

74     for(int i=0; i<5; i++)

75     {

76         sum+=*(p+i);

77     }

78     GClevel=(float)(*p+*(p+2)) / sum * 100;

79     Nlevel=(float)(*p+4) / sum * 100;

80

81     fprintf(stdout,"G:%lld\tA:%lld\nC:%lld\tT:%lld\nN:%lld\tsum:%lld\n",*p,*(p+1),*(p+2),*(p+3),*(p+4),sum);

82     fprintf(stdout,"GC:%.2f%%\n",GClevel);

83

84     fclose(fq);

85 }

86

87 int main(int argc,const char *argv[])

88 {

89     usage(argc,argv[0]);

90     calc(argv[1]);

91

92     exit(0);

93 }