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main.cpp
319 lines (280 loc) · 9.81 KB
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main.cpp
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#include "main.h"
//req_GobalParameter
restrict req_restrict;
ptt ptts[1000000];
int pi;
site psb_site[1000000];
int ini;
site in_site[1000000];
char str[NUM_CHROMOSOME][GENE_LEN];
char wai[NUM_CHROMOSOME][GENE_LEN];
bool cmp_in_site(site a,site b){
return a.score>b.score;
}
bool cmp_by_index(site a,site b){
return a.index<b.index;
}
int readLine(FILE *file){
char ch;
while(fscanf(file,"%c",&ch)==1) if(ch=='\n') return 1;
return 0;
}
cJSON *Create_array_of_anything(cJSON **objects,int num)
{
int i;cJSON *prev, *root=cJSON_CreateArray();
for (i=0;i<num;i++)
{
if (!i) root->child=objects[i];
else prev->next=objects[i], objects[i]->prev=prev;
prev=objects[i];
}
return root;
}
//R=A,G; M=A,C; W=A,T; S=C,G; K=G,T; Y=C,T; H=A,C,T; V=A,C,G; B=C,G,T; D=A,G,T; N=A,G,C,T
int check_pam(const char *str,const char *pam){
for(;*pam;pam++,str++){
if(*pam=='R' && (*str=='A' || *str=='G')) continue;
if(*pam=='M' && (*str=='A' || *str=='C')) continue;
if(*pam=='W' && (*str=='A' || *str=='T')) continue;
if(*pam=='S' && (*str=='C' || *str=='G')) continue;
if(*pam=='K' && (*str=='G' || *str=='T')) continue;
if(*pam=='Y' && (*str=='C' || *str=='T')) continue;
if(*pam=='H' && (*str=='A' || *str=='C' || *str=='T')) continue;
if(*pam=='V' && (*str=='A' || *str=='C' || *str=='G')) continue;
if(*pam=='B' && (*str=='C' || *str=='G' || *str=='T')) continue;
if(*pam=='D' && (*str=='A' || *str=='G' || *str=='T')) continue;
if(*pam=='N' || *pam=='n') continue;
if(*pam==*str) continue;
return 0;
}
return 1;
}
char dna_rev_char(char ch){
if(ch=='A' || ch=='a') return 'T';
if(ch=='T' || ch=='t') return 'A';
if(ch=='C' || ch=='c') return 'G';
if(ch=='G' || ch=='g') return 'C';
return 'N';
}
char *dna_rev(char *sr,const char *s,int len){
int i;
for(i=0;i<len;i++){
sr[i]=dna_rev_char(s[len-i-1]);
}
sr[i]=0;
return sr;
}
char *NomoreSpace(char *str){
int i,j;
int mark=0;
for(i=0,j=0;str[i];i++){
if(str[i]=='\"') mark=1-mark;
if(mark || (str[i]!=' ' && str[i]!='\n' && str[i]!='\t')) str[j++]=str[i];
}
str[j]=0;
return str;
}
char *_NomoreSpace(char *str){
return str;
}
int check_req(cJSON *request){
int clt=3;
int i;
char cl[][10]={"pam","specie","rfc"};
for(i=0;i<clt;i++){
if(cJSON_GetObjectItem(request,cl[i])==NULL) break;
}
return i<clt;
}
void onError(const char *msg){
char *p;
cJSON *root_error=cJSON_CreateObject();
cJSON_AddNumberToObject(root_error,"status",1);
cJSON_AddStringToObject(root_error,"message",msg);
printf("%s\n",NomoreSpace(p=cJSON_Print(root_error)));
free(p);
}
char argv_default[]="{\"specie\":\"E.coli\",\"kind\":\"E.coli K12-MG1655\",\"location\":\"1:1..500\",\"pam\":\"NGG\",\"rfc\":\"100010\"}";
int main(int args,char *argv[]){
const int smallOutputNumber=-1;
int i,j;
cJSON *root;
int num_chromosome;
int req_type=1;
char buffer[30];
char req_gene[20]={0};
cJSON *msg;
char req_kind[50]="E.coli K12-DH10B";
pi=0;
ini=0;
req_restrict.rfc10=0;
req_restrict.rfc12=0;
req_restrict.rfc12a=0;
req_restrict.rfc21=0;
req_restrict.rfc23=0;
req_restrict.rfc25=0;
char *req_str=argv_default;
if(args==2) req_str=argv[1];
cJSON *request=cJSON_Parse(req_str);
if(check_req(request)){
onError("illegal args");
return 0;
}
i=1;
j=1;
cJSON *cJSON_temp;
cJSON_temp=cJSON_GetObjectItem(request,"type");
if(cJSON_temp) req_type=cJSON_temp->valueint;
char req_pam[PAM_LEN+1];
int req_pam_len;
strcpy(req_pam,cJSON_GetObjectItem(request,"pam")->valuestring);
req_pam_len=(int)strlen(req_pam);
char req_specie[30];
struct return_struct rs;
int ptts_num;
int len[NUM_CHROMOSOME];
strcpy(req_specie,cJSON_GetObjectItem(request,"specie")->valuestring);
if(strcmp(req_specie,"SARS")==0){
rs=info_readin(PTT_SARS,ptts,str,wai,NULL);
}else if(strcmp(req_specie,"E.coli")==0){
cJSON_temp=cJSON_GetObjectItem(request,"kind");
if(cJSON_temp) strcpy(req_kind,cJSON_temp->valuestring);
rs=info_readin(PTT_ECOLI,ptts,str,wai,req_kind);
}else if(strcmp(req_specie,"Saccharomycetes")==0){
rs=info_readin(PTT_SACCHAROMYCETES,ptts,str,wai,NULL);
}else{
onError("no specie");
return 0;
}
ptts_num=rs.ptts_num;
num_chromosome=rs.num_chromosome;
for(i=1;i<=num_chromosome;i++) len[i]=rs.len[i];
double req_r1=0.65;
cJSON_temp=cJSON_GetObjectItem(request,"gene");
if(cJSON_temp){
req_r1=cJSON_GetObjectItem(request,"r1")->valuedouble;
}
cJSON_temp=cJSON_GetObjectItem(request,"gene");
int req_id,req_gene_start,req_gene_end;
if(cJSON_temp){
strcpy(req_gene,cJSON_temp->valuestring);
for(int i=0;i<ptts_num;i++){
if(strcmp(req_gene,ptts[i].gene)==0){
req_id=ptts[i].chromosome;
req_gene_start=ptts[i].s;
req_gene_end=ptts[i].t;
break;
}
}
}else{
char req_location[20];
strcpy(req_location,cJSON_GetObjectItem(request,"location")->valuestring);
sscanf(req_location,"%d:%d..%d",&req_id,&req_gene_start,&req_gene_end);
}
char req_rfc[10];
strcpy(req_rfc,cJSON_GetObjectItem(request,"rfc")->valuestring);
req_restrict.rfc10=req_rfc[0]-48;
req_restrict.rfc12=req_rfc[1]-48;
req_restrict.rfc12a=req_rfc[2]-48;
req_restrict.rfc21=req_rfc[3]-48;
req_restrict.rfc23=req_rfc[4]-48;
req_restrict.rfc25=req_rfc[5]-48;
generate_filename(buffer,req_specie,req_kind,req_pam,req_type);
dc_init(buffer);
/*
This part above is for read in JSON-style request.
The result stored in req_specie, req_pam, req_gene_start, req_gene_end, rfc and so on.
At the same time, it reads in ptt file for specie,
and also open files.
*/
for(int id=1;id<=num_chromosome;id++){
for(i=LEN;i<len[id]-req_pam_len;i++){ // All possible gRNAs, +direction
if(check_pam(str[id]+i,req_pam)){
psb_site[pi].index=i;
psb_site[pi].strand='+';
psb_site[pi].chromosome=id;
for(j=0;j<req_pam_len;j++) psb_site[pi].pam[j]=(str[id]+i)[j];
psb_site[pi].pam[j]=0;
for(j=0;j<LEN;j++) psb_site[pi].nt[j]=(str[id]+i-LEN)[j];
psb_site[pi].nt[j]=0;
pi++;
}
}
char req_pam_rev[PAM_LEN];
int last=-1;
dna_rev(req_pam_rev,req_pam,req_pam_len);
for(i=0;i<len[id]-LEN-req_pam_len;i++){ // All possible gRNAs, -direction
if(check_pam(str[id]+i,req_pam_rev)){
psb_site[pi].index=i+req_pam_len-1;
psb_site[pi].strand='-';
psb_site[pi].chromosome=id;
if(req_pam_len!=last){
last=req_pam_len;
}
for(j=0;j<req_pam_len;j++) psb_site[pi].pam[j]=dna_rev_char((str[id]+i)[req_pam_len-1-j]);
psb_site[pi].pam[j]=0;
for(j=0;j<LEN;j++) psb_site[pi].nt[j]=dna_rev_char((str[id]+i+req_pam_len)[LEN-j-1]);
psb_site[pi].nt[j]=0;
pi++;
}
}
}
for(i=0;i<pi;i++){
fflush(stdout);
if(psb_site[i].chromosome!=req_id) continue;
if(psb_site[i].strand=='+'){
if(psb_site[i].index<req_gene_start || psb_site[i].index+req_pam_len-1>req_gene_end) continue;
for(j=psb_site[i].index-LEN;j<psb_site[i].index+req_pam_len-1;j++){
if(wai[req_id][j]!=1) break;
}
if(j<psb_site[i].index+req_pam_len-1) j=0;
else j=1;
}else{
if(psb_site[i].index-req_pam_len+1<req_gene_start || psb_site[i].index>req_gene_end) continue;
for(j=psb_site[i].index-req_pam_len+1;j<psb_site[i].index+LEN;j++){
if(wai[req_id][j]!=1) break;
}
if(j<psb_site[i].index+LEN) j=0;
else j=1;
}
if(j){
score(i,&ini,req_type,req_r1);
}
}
dc_save();
sort(in_site,in_site+ini,cmp_in_site); // Sort & Output
root=cJSON_CreateObject();
cJSON_AddNumberToObject(root,"status",0);
msg=cJSON_CreateObject();
cJSON_AddStringToObject(msg,"specie",req_specie);
cJSON_AddStringToObject(msg,"kind",req_kind);
cJSON_AddStringToObject(msg,"gene",req_gene);
sprintf(buffer,"%d:%d..%d",req_id,req_gene_start,req_gene_end);
cJSON_AddStringToObject(msg,"location",buffer);
cJSON_AddItemToObject(root,"message",msg);
vector<cJSON*> list;
list.clear();
for(i=0;i<ini && i!=smallOutputNumber;i++){
cJSON *ans=cJSON_CreateObject();
sprintf(buffer,"#%d",i+1);
cJSON_AddStringToObject(ans,"key",buffer);
sprintf(buffer,"%s%s",in_site[i].nt,in_site[i].pam);
cJSON_AddStringToObject(ans,"grna",buffer);
sprintf(buffer,"%d:%d",in_site[i].chromosome,in_site[i].index);
cJSON_AddStringToObject(ans,"position",buffer);
char xs[2];
xs[0]=in_site[i].strand;
xs[1]=0;
cJSON_AddStringToObject(ans,"strand",xs);
cJSON_AddNumberToObject(ans,"total_score",(int)in_site[i].score);
cJSON_AddNumberToObject(ans,"Sspe",(int)(req_r1*in_site[i].Sspe_nor));
cJSON_AddNumberToObject(ans,"Seff",(int)((1.0-req_r1)*in_site[i].Seff_nor));
cJSON_AddNumberToObject(ans,"count",in_site[i].count);
cJSON_AddItemToObject(ans,"offtarget",in_site[i].otj);
list.push_back(ans);
}
cJSON_AddItemToObject(root,"result",Create_array_of_anything(&(list[0]),list.size()));
printf("%s\n",NomoreSpace(argv[0]=cJSON_Print(root)));
free(argv[0]);
return 0;
}