C语言计算fastq文件GC含量

C语言小练习：计算非压缩fastq格式的GC含量

 

 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 }

posted @ 2020-09-21 14:38  un-define  阅读(318)  评论(0)    收藏  举报