https://github.com/jsollari/popABC
Tip revision: 3ebe7b76043299bc4b6a541b5be0d7012895ca1c authored by Joao Sollari Lopes on 21 November 2017, 15:04:40 UTC
remove binaries folder
remove binaries folder
Tip revision: 3ebe7b7
maketarget.c
/*
@author: joao lopes
@workplace: Reading University
@date: 1th May 2009
NBB - based on Mark's make_target.c and make_targetS.c
*/
#include "maketarget.h"
/*
This funtion uses a freq_tab_length file and creates a output file which contains
the summary statistics of the given file and its sample sizes
@arg input filename (*.len)
@arg input filename (*.sst)
@arg output filename (*.trg AND *.szz)
*/
int main(int argc, char* argv[]){
int cloc, cpop, cpop2, cdna, i, //iterators
dump, //variable just to put the information from data that isn't necessary, dump
started, //auxiliar to help print sstats to the .txt file
foundSTR, //check if STR's are present
foundSNP, //check if SNP's are present
nstats_aux, //auxiliar to calculate the number of summ stats
nstats, //number of summ stats
outsize, //size of output file name
sum, //sample size in one population
nloc, //number of loci
npop, //number of populations
ndna, //number of all the diferent haplotypes
lsstats[MAXSSTATS]; //list of used summary statistics
char c1, //auxiliar
*ltype, //DNA type per loci
*outline, //store the target data summary statistic
*name_inf, //filename of the report file
*name_trg, //name of the output.tfq file
*lsstats2[MAXSSTATS] = {"H","varL","k_M","curL","sH_M","NmH","pi","S","k_S","sH_S","avMFS","sdMFS","NmS","privS","S(1)"},
*name_ssz; //name of the output.out file
FILE *inp_len, //pntr to data file
*inp_sst, //pntr to data file
*out_inf, //pntr to the report file
*out_trg, //pntr to target output file
*out_ssz; //pntr to samp_size output file
time_t startClock, //time_t when the program starts
endClock; //time_t when the program ends
struct data block, //target data
*data; //pntr to target data
const struct tm *startTime, //struct time when the program starts
*endTime; //struct time when the program ends
if(argc != 4)
printerr("needs .len file, .sst file, output filename (no extension)");
inp_len = fopen(argv[1],"r"); //input filename
if(inp_len == NULL)
printerr("cannot open .len file");
inp_sst = fopen(argv[2],"r"); //input .sst
if(inp_sst == NULL)
printerr("cannot open .sst file");
outsize = strlen(argv[3]) + 5;
name_trg = (char *)malloc(outsize*sizeof(char));
name_ssz = (char *)malloc(outsize*sizeof(char));
name_inf = (char *)malloc((outsize+4)*sizeof(char));
strcpy(name_trg,argv[3]);
strcpy(name_ssz,argv[3]);
strcpy(name_inf,argv[3]);
out_trg = fopen(strcat(name_trg,".trg"),"w"); //out_trg filename
if(out_trg == NULL)
printerr("cannot create .trg file");
out_ssz = fopen(strcat(name_ssz,".ssz"),"w"); //out_sps filename
if(out_ssz == NULL)
printerr("cannot create .ssz file");
out_inf = fopen(strcat(name_inf,"_trg.txt"),"w"); //open out_inf
if(out_inf == NULL)
printerr("cannot create .txt file");
for(i=0; i<MAXSSTATS; i++){
while(getc(inp_sst)!='#');
if(EOF == fscanf(inp_sst,"%d",&lsstats[i]))
printerr("error reading .sst file");
}
fclose(inp_sst);
/*check for errors when choosing summary statistics*/
if(npop==1 && (lsstats[5] || lsstats[12] || lsstats[13] || lsstats[14]))
printerr("Following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)");
//if we want to use the Nm_H we have to calculate H
if(lsstats[5]== 1)
lsstats[0] = 1;
//if we want to use the sdMFS we have to calculate mMFS
if(lsstats[11]== 1)
lsstats[10] = 1;
//if we want to use the mMFS, Nm_S, privateS or S(1) we have to calculate S
if(lsstats[10]== 1 || lsstats[12]== 1 || lsstats[13]== 1 || lsstats[14]== 1 )
lsstats[7] = 1;
time( &startClock ); // Get time in seconds
startTime = localtime( &startClock ); // Convert time to struct tm form
/*if # (commentary) run to end of line*/
c1=getc(inp_len);
while(c1 == '#'){
while(!isendline(c1 = getc(inp_len)));
while(isspace(c1=getc(inp_len))||isendline(c1)||c1=='\t');
}
ungetc(c1,inp_len);
fscanf(inp_len,"%d %d",&npop,&nloc);
ltype = (char*)malloc(1+nloc*sizeof(char));
foundSTR = 0;
foundSNP = 0;
for(cloc=0 ; cloc<nloc ; cloc++){
fscanf(inp_len,"%s",<ype[cloc]);
if(ltype[cloc]=='m'||ltype[cloc]=='M')
foundSTR = 1;
if(ltype[cloc]=='s'||ltype[cloc]=='S')
foundSNP = 1;
}
data = █
data->npop = npop;
data->nloc = nloc;
data->ldna = (int *)malloc(nloc*sizeof(int));
data->tsamp = (int *)malloc(nloc*sizeof(int));
data->nsamp = (int **)malloc(nloc*sizeof(int *));
data->freq = (int ***)malloc(nloc*sizeof(int **));
if(foundSTR)
data->valM = (int **)malloc(nloc*sizeof(int *));
if(foundSNP){
data->lsites = (int *)malloc(nloc*sizeof(int));
data->valS = (char ***)malloc(nloc*sizeof(char **));
}
/*run through every locus*/
for(cloc=0;cloc<nloc;++cloc){
data->freq[cloc] = (int **)malloc(npop*sizeof(int *));
data->nsamp[cloc] = (int *)malloc(npop*sizeof(int));
data->tsamp[cloc]=0;
if(foundSNP)
data->lsites[cloc]=0;
if(ltype[cloc]=='m'||ltype[cloc]=='M'){
fscanf(inp_len,"%d",&ndna);
data->ldna[cloc] = ndna;
data->valM[cloc] = (int *)malloc(ndna*sizeof(int));
//run through every population
for(cpop=0;cpop<npop;++cpop){
sum = 0;
data->freq[cloc][cpop] = (int *)malloc(ndna*sizeof(int));
for(cdna=0;cdna<ndna;++cdna){
fscanf(inp_len,"%d",&(data->freq[cloc][cpop][cdna]));
sum += data->freq[cloc][cpop][cdna];
}
data->nsamp[cloc][cpop] = sum;
data->tsamp[cloc]+=sum;
fprintf(out_ssz,"%d ",sum); //out_sps: sum
}
fprintf(out_ssz,"\n");
for(cdna=0;cdna<ndna;++cdna)
fscanf(inp_len,"%d",&(data->valM[cloc][cdna]));
}
else{
fscanf(inp_len,"%d",&ndna);
data->ldna[cloc] = ndna;
data->valS[cloc] = (char **)malloc(ndna*sizeof(char *));
//run through every population
for(cpop=0;cpop<npop;++cpop){
sum = 0;
data->freq[cloc][cpop] = (int *)malloc(ndna*sizeof(int));
for(cdna=0;cdna<ndna;++cdna){
fscanf(inp_len,"%d",&(data->freq[cloc][cpop][cdna]));
sum += data->freq[cloc][cpop][cdna];
}
data->nsamp[cloc][cpop] = sum;
data->tsamp[cloc]+=sum;
fprintf(out_ssz,"%d ",sum); //NT- out_sps: sum
}
fprintf(out_ssz,"\n");
for(cdna=0;cdna<ndna;++cdna)
fscanf(inp_len,"%d",&dump);
fscanf(inp_len,"%d",&(data->lsites[cloc]));
if(data->lsites[cloc]!=0)
for(cdna=0;cdna<ndna;++cdna){
data->valS[cloc][cdna] = (char *)malloc((data->lsites[cloc]+1)*sizeof(char));
fscanf(inp_len,"%d %s ",&dump,data->valS[cloc][cdna]);
}
else
printerr("use of Sequence data locus without information, this should be discarded");
}
}
/*counting the number of summary statistics*/
if(npop>1){
//applied to each population and to the populations pooled together
nstats_aux = 0;
if(foundSTR)
for(i=0 ; i<MAXSSTATS_M ; i++){
if((i==0||i==1||i==2||i==3||i==4) && lsstats[i])
nstats_aux++;
}
if(foundSNP)
for(i=MAXSSTATS_M ; i<MAXSSTATS ; i++){
if((i==6||i==7||i==8||i==9) && lsstats[i])
nstats_aux++;
}
nstats = npop*nstats_aux+(combinations(npop,2))*nstats_aux;
//applied only to each population
nstats_aux = 0;
if(foundSTR)
for(i=0 ; i<MAXSSTATS_M ; i++){
if((i==5) && lsstats[i])
nstats_aux++;
}
if(foundSNP)
for(i=MAXSSTATS_M ; i<MAXSSTATS ; i++){
if((i==10||i==11||i==12||i==13||i==14) && lsstats[i])
nstats_aux++;
}
nstats += npop*nstats_aux;
}
else{
nstats = 0;
if(foundSTR){
for(i=0 ; i<MAXSSTATS_M ; i++){
if(lsstats[i])
nstats++;
}
}
if(foundSNP){
for(i=MAXSSTATS_M ; i<MAXSSTATS ; i++){
if(lsstats[i])
nstats++;
}
}
}
/*writting first part of output to .txt file*/
fprintf(out_inf,"SummData - Mark Beaumont & Joao Lopes\n\n");
fprintf(out_inf," last updated 01/05/09\n\n");
fprintf(out_inf,"INPUT AND STARTING INFORMATION\n");
fprintf(out_inf,"-------------------------------\n");
fprintf(out_inf,"Table file : %s\n",argv[1]);
fprintf(out_inf,"SummaryStatistics file: %s\n\n",argv[2]);
if(foundSTR && !foundSNP){
fprintf(out_inf,"Type of genetic data analysed: microssatelites\n\n");
fprintf(out_inf,"Number of summary statistics: %d\n",nstats);
if(lsstats[0])
fprintf(out_inf," -heterozygosity\n");
if(lsstats[1])
fprintf(out_inf," -variance of alleles length\n");
if(lsstats[2])
fprintf(out_inf," -number of alleles\n");
if(lsstats[3])
fprintf(out_inf," -curtosis of alleles length\n");
if(lsstats[4])
fprintf(out_inf," -Shanon's index\n");
if(lsstats[5])
fprintf(out_inf," -Nm estimator based on H\n");
fprintf(out_inf,"\nMutation model used: single-step model\n\n");
}
else if(foundSNP && !foundSTR){
fprintf(out_inf,"Type of genetic data analysed: dna sequency\n\n");
fprintf(out_inf,"Number of summary statistics: %d\n",nstats);
if(lsstats[6])
fprintf(out_inf," -mean of pairwise differences\n");
if(lsstats[7])
fprintf(out_inf," -number of segregating sites\n");
if(lsstats[8])
fprintf(out_inf," -number of haplotypes\n");
if(lsstats[9])
fprintf(out_inf," -Shanon's index\n");
if(lsstats[10])
fprintf(out_inf," -mean of MFS\n");
if(lsstats[11])
fprintf(out_inf," -stdev of MFS\n");
if(lsstats[12])
fprintf(out_inf," -Nm estimator based on S\n");
if(lsstats[13])
fprintf(out_inf," -private S\n");
if(lsstats[14])
fprintf(out_inf," -S(1)\n");
fprintf(out_inf,"\nMutation model used: infinite-segregated-sites model\n\n");
}
else{
fprintf(out_inf,"Type of genetic data analysed: microssatelites\n");
fprintf(out_inf," dna sequency\n\n");
fprintf(out_inf,"Number of summary statistics: %d\n",nstats);
fprintf(out_inf," Microssatelites:\n");
if(lsstats[0])
fprintf(out_inf," -heterozygosity\n");
if(lsstats[1])
fprintf(out_inf," -variance of alleles length\n");
if(lsstats[2])
fprintf(out_inf," -number of alleles\n");
if(lsstats[3])
fprintf(out_inf," -curtosis of alleles length\n");
if(lsstats[4])
fprintf(out_inf," -Shanon's index\n");
if(lsstats[5])
fprintf(out_inf," -Nm estimator based on H\n");
fprintf(out_inf," Sequence data:\n");
if(lsstats[6])
fprintf(out_inf," -mean of pairwise differences\n");
if(lsstats[7])
fprintf(out_inf," -number of segregating sites\n");
if(lsstats[8])
fprintf(out_inf," -number of haplotypes\n");
if(lsstats[9])
fprintf(out_inf," -Shanon's index\n");
if(lsstats[10])
fprintf(out_inf," -mean of MFS\n");
if(lsstats[11])
fprintf(out_inf," -stdev of MFS\n");
if(lsstats[12])
fprintf(out_inf," -Nm estimator based on S\n");
if(lsstats[13])
fprintf(out_inf," -private S\n");
if(lsstats[14])
fprintf(out_inf," -S(1)\n");
fprintf(out_inf,"\nMutation model used: \n");
fprintf(out_inf," Microssatelites: single-step model\n");
fprintf(out_inf," Sequence data: infinite-segregated-sites model\n\n");
}
fprintf(out_inf,"Number of Modern Populations: %d\n",npop);
fprintf(out_inf,"Number of Loci analysed: %d\n",nloc);
fprintf(out_inf,"Type of the loci analysed: ");
for(cloc=0 ; cloc<nloc ; cloc++)
fprintf(out_inf,"%c ",ltype[cloc]);
fprintf(out_inf,"\n\nOUTPUT FILES:\n");
fprintf(out_inf,"-------------------------------\n");
fprintf(out_inf,"Sample size file: %s.ssz\n",argv[3]);
fprintf(out_inf,"Target file: %s.trg\n",argv[3]);
fprintf(out_inf,"%d summstats [",nstats);
started=0;
if(foundSTR)
for(i=0;i<MAXSSTATS_M;i++){
if(lsstats[i])
for(cpop=0; cpop<npop; cpop++)
if(started)
fprintf(out_inf,"|%s%d",lsstats2[i],cpop+1);
else{
fprintf(out_inf,"%s%d",lsstats2[i],cpop+1);
started=1;
}
}
if(foundSTR)
for(i=0;i<MAXSSTATS_M;i++){
if((i==0||i==1||i==2||i==3||i==4||i==6||i==7||i==8||i==9) && lsstats[i])
for(cpop = 0;cpop <npop;++cpop){
for(cpop2 = cpop+1;cpop2 < npop;++cpop2){
if(started)
fprintf(out_inf,"|%s%d-%d",lsstats2[i],cpop+1,cpop2+1);
else{
fprintf(out_inf,"%s%d-%d",lsstats2[i],cpop+1,cpop2+1);
started=1;
}
}
}
}
if(foundSNP)
for(i=MAXSSTATS_M;i<MAXSSTATS;i++){
if(lsstats[i])
for(cpop=0; cpop<npop; cpop++)
if(started)
fprintf(out_inf,"|%s%d",lsstats2[i],cpop+1);
else{
fprintf(out_inf,"%s%d",lsstats2[i],cpop+1);
started=1;
}
}
if(foundSNP)
for(i=MAXSSTATS_M;i<MAXSSTATS;i++){
if((i==0||i==1||i==2||i==3||i==4||i==6||i==7||i==8||i==9) && lsstats[i])
for(cpop = 0;cpop <npop;++cpop){
for(cpop2 = cpop+1;cpop2 < npop;++cpop2){
if(started)
fprintf(out_inf,"|%s%d-%d",lsstats2[i],cpop+1,cpop2+1);
else{
fprintf(out_inf,"%s%d-%d",lsstats2[i],cpop+1,cpop2+1);
started=1;
}
}
}
}
fprintf(out_inf,"]\n\nRUNTIME:\n");
fprintf(out_inf,"-------------------------------\n");
fprintf(out_inf,"Starting date: %s",asctime(startTime));
outline = malloc(nstats*15*sizeof(char));
summStats(data,lsstats,outline,foundSTR,foundSNP,ltype);
fprintf(out_trg,"%s",outline); //out_trg: outline
/*get ending time and save it to .txt file*/
time( &endClock ); // Get time in seconds
endTime = localtime( &endClock ); // Convert time to struct tm form
fprintf(out_inf,"Ending date: %s\n",asctime(endTime));
fprintf(out_inf,"\nEND OF OUTPUT\n");
/*free stuff*/
free(outline);
free(name_trg);
free(name_ssz);
free(name_inf);
for(cloc=0 ; cloc<nloc ; cloc++){
if(ltype[cloc]=='M'||ltype[cloc]=='m')
free(data->valM[cloc]);
else{
for(cdna=0; cdna<data->ldna[cloc]; cdna++)
free(data->valS[cloc][cdna]);
free(data->valS[cloc]);
}
}
if(foundSTR)
free(data->valM);
if(foundSNP){
free(data->valS);
free(data->lsites);
}
for(cloc=0 ; cloc<nloc ; cloc++){
for(cpop=0 ; cpop<npop ; cpop++)
free(data->freq[cloc][cpop]);
free(data->freq[cloc]);
free(data->nsamp[cloc]);
}
free(data->freq);
free(data->nsamp);
free(data->tsamp);
free(data->ldna);
free(ltype);
/*close files*/
fclose(inp_len);
fclose(out_inf);
fclose(out_trg);
fclose(out_ssz);
}//end of main