Revision e6a0334445b5755bb52a0d2209120ee4e251e7b4 authored by Joao Sollari Lopes on 13 November 2017, 18:32:56 UTC, committed by Joao Sollari Lopes on 13 November 2017, 18:32:56 UTC
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abc.c
/*
@author: joao lopes
@workplace: Reading University
@date: 1st May 2009
NBB - based on Mark's genparmf.c and genparmfS.c
*/
#include "abc.h"
/*
This function calculates the number of topologies according to the npop
@param npop - numer of populations
@result number of topologies
*/
int notop(int npop);
/*
This function frees the memory used for the DNA sequence data simulations
@param nloc - number of loci
@param na - number of diferente sequencies
@param val - all the diferente sequencies by loci
@param ltype - DNA type per loci
*/
void freeMem(int nloc, int *na,char ***val,char * ltype);
/*
Start of the ABC program. Simulates coordenated points (summary_statistics, parameters) to be
used in an Aproximate Bayesian Computation model to estimate the true values of a genealogical tree.
@arg .prs input filename
@arg .ssz input filename
@arg .sst input filename
@arg .dat output filename
@arg print or not the .len and .frq files of every genetic tree (0-don't print; 1-print)
@arg print or not the .mut (0-don't print; 1-print)
@arg print or not the .rec (0-don't print; 1-print)
*/
int main(int argc, char* argv[]){
int csamp,cpop,cpop2,cloc,cevt,i,cSTR, //iterators
foundSTR, //check if STR's are present
foundSNP, //check if SNP's are present
nrSTR, //number of linked STR's
npop, //nr. populations
nloc, //nr. loci
nevt, //nr. time events
nstats_aux, //auxiliar to get the nr. of summary statistics used
nstats, //nr. of summary statistics used
nparams, //nr. of parameters used
printIt, //print or not the information about frequency of haplotyes, sizes of haplotypes, number of diferent sizes, number of loci
printMut, //print or not to a file the mutation rate of each locus
printRec, //print or not to a file the recombination rate of each locus
cut, //auxiliar to work around strings
homesize, //size of the path from where the program is being run
outsize, //size of output filename
started, //auxiliar to help print lsstats2 into the file
lsstats[MAXSSTATS], //list of the sstats (0 - absent; 1 - present)
*sampleSTR; //sample sizes of the linked STR's
double ploidySTR; //ploidy of the linked STR's
long citer, //iterator
niter; //nr. iterations
char type, //type of analysis
*lsstats2[MAXSSTATS] = {"H","varL","k_M","curL","sH_M","NmH","pi","S","k_S","sH_S","avMFS","sdMFS","NmS","privS","S(1)"},
*home, //path where the program is being run
*path, //path to which the output files are going to be store in
*outline1, //stores parameters informations
*outline2, //stores summstats informations
*name_dat, //output filename
*name_inf, //output filename
*name_mut, //output filename
*name_rec; //output filename
FILE *inp_prs, //pntr to .prs
*inp_ssz, //pntr to .ssz
*inp_sst, //pntr to .ssz
*out_mut, //pntr to .mut
*out_rec, //pntr to .rec
*out_dat, //pntr to .dat
*out_inf; //pntr to .txt
time_t startClock, //time_t when the program starts
endClock; //time_t when the program ends
struct params pm; //struct that stores the parameter set values
struct data data; //struct that stores the data of a genetic tree
const struct tm *startTime, //struct time when the program starts
*endTime; //struct time when the program ends
if(!(argc == 8))
printerr("needs .prs file, .ssz file, .sst file, output filename (no extension), printIt, printMut, printRec");
time( &startClock ); // Get time in seconds
startTime = localtime( &startClock ); // Convert time to struct tm form
inp_prs = fopen(argv[1],"r"); //input .prs
if(inp_prs == NULL)
printerr("cannot open .prs file");
inp_ssz = fopen(argv[2],"r"); //input .ssz
if(inp_ssz == NULL)
printerr("cannot open .ssz file");
inp_sst = fopen(argv[3],"r"); //input .sst
if(inp_sst == NULL)
printerr("cannot open .sst file");
/*get the path from where the progam is being run*/
homesize = strlen(argv[0])+ 5;
home = (char *)malloc(homesize*sizeof(char));
strcpy(home,argv[0]);
for(cut=-1,i=homesize-1 ; home[i]!='/' && home[i]!='\\' && i >= 0 ; cut++,i--){
home[i]='\0';
}
home = realloc(home,(homesize-cut)*sizeof(char));
/*get the path to output files*/
outsize = strlen(argv[4]) + 5;
path = (char *)malloc(outsize*sizeof(char));
strcpy(path,argv[4]);
for(cut=-1,i=outsize-1 ; path[i]!='/' && path[i]!='\\' && i >= 0 ; cut++,i--){
path[i]='\0';
}
path = realloc(path,(outsize-cut)*sizeof(char));
name_dat = (char *)malloc(outsize*sizeof(char));
strcpy(name_dat,argv[4]);
out_dat = fopen(strcat(name_dat,".dat"),"w"); //output .dat
free(name_dat);
if(out_dat == NULL)
printerr("cannot create .dat file");
name_inf = (char *)malloc(outsize*sizeof(char));
strcpy(name_inf,argv[4]);
out_inf = fopen(strcat(name_inf,".txt"),"w"); //output info.txt
if(out_inf == NULL)
printerr("cannot create .txt file");
free(name_inf);
printIt = atoi(argv[5]); //value of printIt
printMut = atoi(argv[6]); //value of printMut
printRec = atoi(argv[7]); //value of printRec
fscanf(inp_prs,"%d %lf %d %d",&pm.niter,&pm.gent,&pm.npop,&pm.nloc);
pm.nevt = pm.npop - 1;
pm.ntop = notop(pm.npop);
npop = pm.npop;
nloc = pm.nloc;
niter = pm.niter;
nevt = pm.nevt;
if(npop>1){
pm.mig = (double **)malloc(nevt*sizeof(double*));
pm.tev = (double *)malloc(nevt*sizeof(double));
}
pm.mu = (double *)malloc(nloc*sizeof(double));
pm.rec = (double *)malloc(nloc*sizeof(double));
pm.ploidy = (double *)malloc(nloc*sizeof(double));
pm.type = (char *)malloc((nloc+1)*sizeof(char));
pm.nsamp = (int **)malloc(nloc*sizeof(int *));
for(cloc=0;cloc<nloc;++cloc)
pm.nsamp[cloc] = (int *)malloc(npop*sizeof(int));
for(cevt=0;cevt<nevt;cevt++)
pm.mig[cevt] = (double *)malloc(npop*sizeof(double));
pm.psize = (double **)malloc((nevt+1)*sizeof(double*));
for(cevt=0;cevt<=nevt;cevt++)
pm.psize[cevt] = (double *)malloc(npop*sizeof(double));
for(cloc=0 ; cloc<nloc ; cloc++)
fscanf(inp_prs,"%lf",&pm.ploidy[cloc]);
foundSTR = 0;
foundSNP = 0;
for(cloc=0 ; cloc<nloc ; cloc++){
fscanf(inp_prs,"%s",&pm.type[cloc]);
if(pm.type[cloc]=='m'||pm.type[cloc]=='M')
foundSTR = 1;
if(pm.type[cloc]=='s'||pm.type[cloc]=='S')
foundSNP = 1;
}
for(cloc=0;cloc<nloc;++cloc){
for(cpop=0;cpop<npop;++cpop){
if(EOF == fscanf(inp_ssz,"%d",&(pm.nsamp[cloc][cpop])))
printerr("reading .ssz file");
}
}
fclose(inp_ssz);
for(i=0; i<MAXSSTATS; i++){
while(getc(inp_sst)!='#');
if(EOF == fscanf(inp_sst,"%d",&lsstats[i]))
printerr("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;
//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 ; 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,"Simulate - 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,"Priors file : %s\n",argv[1]);
fprintf(out_inf,"Sample Sizes file: %s\n",argv[2]);
fprintf(out_inf,"SummaryStatistics file: %s\n\n",argv[3]);
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 ",pm.type[cloc]);
fprintf(out_inf,"\nScalar of the loci analysed: ");
for(cloc=0 ; cloc<nloc ; cloc++)
fprintf(out_inf,"%.2lf ",pm.ploidy[cloc]);
fprintf(out_inf,"\nGeneration time (in years): %g\n\n",pm.gent);
fprintf(out_inf,"RUN INFORMATION\n");
fprintf(out_inf,"---------------------------\n");
fprintf(out_inf,"Number of geneological trees created: %d\n\n",niter);
/*Reads the topology type*/
fscanf(inp_prs,"%d",&P_top.type);
if(npop > 2){
fprintf(out_inf,"Populational tree topology:\n");
//uniform distribution along the number of different topologies
if(P_top.type == 0)
fprintf(out_inf,"- Prior distribution (Topol): uniform(0,%d)\n",pm.ntop);
//read values from file
else if(P_top.type == 1){
P_top.p = (double*)malloc(sizeof(double));
fscanf(inp_prs,"%lf ",&P_top.p[0]);
fprintf(out_inf,"- Fixed Topology: %.0lf\n",P_top.p[0]);
}
//discriminate the join events
else if(P_top.type == 2){
P_top.p = (double*)malloc(2*nevt*sizeof(double));
for(i=0 ; i<2*nevt ; i++){
fscanf(inp_prs,"%lf ",&P_top.p[i]);
}
fprintf(out_inf,"- Fixed Topology: (");
for(i=0 ; i<2*nevt ; i++){
fprintf(out_inf,"%.0lf",P_top.p[i]);
if(i%2==0)
fprintf(out_inf,",");
else if(i!=2*nevt-1)
fprintf(out_inf,")(");
}
fprintf(out_inf,")\n");
}
//uniform distribution along the number of different topologies (with specific marker)
else if(P_top.type == 3){
P_top.p = (double*)malloc(sizeof(double));
fscanf(inp_prs,"%lf ",&P_top.p[0]);
fprintf(out_inf,"- Prior distribution (Topol): uniform(0,%d) [with Model marker:%.0lf]\n",pm.ntop,P_top.p[0]);
}
//read values from file (with specific marker)
else if(P_top.type == 4){
P_top.p = (double*)malloc(2*sizeof(double));
fscanf(inp_prs,"%lf ",&P_top.p[0]);
fscanf(inp_prs,"%lf ",&P_top.p[1]);
fprintf(out_inf,"- Fixed Topology: %.0lf [with Model marker:%.0lf]\n",P_top.p[0],P_top.p[1]);
}
//discriminate the join events (with specific marker)
else if(P_top.type == 5){
P_top.p = (double*)malloc((1+(2*nevt))*sizeof(double));
for(i=0 ; i<2*nevt ; i++){
fscanf(inp_prs,"%lf ",&P_top.p[i]);
}
fscanf(inp_prs,"%lf ",&P_top.p[2*nevt]);
fprintf(out_inf,"- Fixed Topology: (");
for(i=0 ; i<2*nevt ; i++){
fprintf(out_inf,"%.0lf",P_top.p[i]);
if(i%2==0)
fprintf(out_inf,",");
else if(i!=2*nevt-1)
fprintf(out_inf,")(");
}
fprintf(out_inf,") [with Model marker:%.0lf]\n",P_top.p[2*nevt]);
}
else
printerr("wrong topology prior type");
}
if(npop<=2){
fprintf(out_inf,"Populational tree topology:\n");
if(P_top.type == 0)
fprintf(out_inf,"- Single topology\n");
else if(P_top.type == 3){
P_top.p = (double*)malloc(sizeof(double));
fscanf(inp_prs,"%lf ",&P_top.p[0]);
fprintf(out_inf,"- Single topology [with Model marker:%.0lf]\n",P_top.p[0]);
}
else if(P_top.type == 1 || P_top.type == 2 || P_top.type == 4 || P_top.type == 5)
printerr("with 1 or 2 pops only topology prior type 0 or 3 can be used");
else
printerr("wrong topology prior type");
}
/*Reads the Populations'Ne priors*/
P_psize = (struct prior **)malloc((nevt+1)*sizeof(struct prior *));
fprintf(out_inf,"Efective population size:\n");
for(cevt=0;cevt<=nevt;++cevt){
P_psize[cevt] = (struct prior *)malloc(npop*sizeof(struct prior));
for(cpop=0;cpop<npop;++cpop){
fscanf(inp_prs,"%d",&P_psize[cevt][cpop].type);
//uniformly between 2 limits
if(P_psize[cevt][cpop].type == 1){
P_psize[cevt][cpop].p = (double*)malloc(2*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (Ne%d): uniform(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (NeAnc%d): uniform(",cevt);
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_psize[cevt][cpop].p[i]);
if(i==1)
fprintf(out_inf,"%.0lf)\n",P_psize[cevt][cpop].p[i]);
else
fprintf(out_inf,"%.0lf,",P_psize[cevt][cpop].p[i]);
}
}
//use generalized gamma
else if(P_psize[cevt][cpop].type == 2){
P_psize[cevt][cpop].p = (double*)malloc(4*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (Ne%d): generalized gamma(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (NeAnc%d): generalized gamma(",cevt);
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_psize[cevt][cpop].p[i]);
if(i==3)
fprintf(out_inf,"%.0lf)\n",P_psize[cevt][cpop].p[i]);
else
fprintf(out_inf,"%.0lf,",P_psize[cevt][cpop].p[i]);
}
}
else
printerr("wrong Ne priors");
//each anc pop is just done once
if(cevt > 0)
break;
}
}
if(npop>1){
/*Reads the events'time priors*/
P_t = (struct prior *)malloc(nevt*sizeof(struct prior));
fprintf(out_inf,"Time events:\n");
for(cevt=0;cevt<nevt;++cevt){
fscanf(inp_prs,"%d",&P_t[cevt].type);
//use uniform distribution
if(P_t[cevt].type == 1){
P_t[cevt].p = (double*)malloc(2*sizeof(double));
if(cevt>0){
fprintf(out_inf,"- Prior distribution (tev%d): tev%d + uniform(",cevt+1,cevt);
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==1)
fprintf(out_inf,"%.0lf)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%.0lf,",P_t[cevt].p[i]);
}
}
else{
fprintf(out_inf,"- Prior distribution (tev%d): uniform(",cevt+1);
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==1)
fprintf(out_inf,"%.0lf)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%.0lf,",P_t[cevt].p[i]);
}
}
}
//use generalized gamma
else if(P_t[cevt].type == 2){
P_t[cevt].p = (double*)malloc(4*sizeof(double));
if(cevt>0){
fprintf(out_inf,"- Prior distribution (tev%d): tev%d + generalized gamma(",cevt+1,cevt);
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%g,",P_t[cevt].p[i]);
}
}
else{
fprintf(out_inf,"- Prior distribution (tev%d): generalized gamma(",cevt+1);
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%g,",P_t[cevt].p[i]);
}
}
}
//use uniform distribution (all tev)
else if(P_t[cevt].type == 3){
P_t[cevt].p = (double*)malloc(2*sizeof(double));
fprintf(out_inf,"- Prior distribution (all tev): uniform(");
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==1)
fprintf(out_inf,"%.0lf)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%.0lf,",P_t[cevt].p[i]);
}
if(cevt!=0)
printerr("if using tev type 3 prior, define prior only once");
break;
}
//use generalized gamma (all tev)
else if(P_t[cevt].type == 4){
P_t[cevt].p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- Prior distribution (all tev): generalized gamma(");
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_t[cevt].p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_t[cevt].p[i]);
else
fprintf(out_inf,"%g,",P_t[cevt].p[i]);
}
if(cevt!=0)
printerr("if using tev type 4 prior, define prior only once");
break;
}
else
printerr("wrong tev priors");
}
/*Reads the migration priors*/
P_mig = (struct prior **)malloc(nevt*sizeof(struct prior *));
fprintf(out_inf,"Migration rates:\n");
for(cevt=0;cevt<nevt;++cevt){
P_mig[cevt] = (struct prior *)malloc(npop*sizeof(struct prior));
for(cpop=0;cpop<npop;++cpop){
fscanf(inp_prs,"%d",&P_mig[cevt][cpop].type);
//no migration
if(P_mig[cevt][cpop].type == 0){
P_mig[cevt][cpop].p = (double*)malloc(2*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- mig%d: No migration\n",cpop+1);
else
fprintf(out_inf,"- migAnc%d: No migration\n",cevt);
}
//uniform
else if(P_mig[cevt][cpop].type == 1){
P_mig[cevt][cpop].p = (double*)malloc(2*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (mig%d): uniform(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (migAnc%d): uniform(",cevt);
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_mig[cevt][cpop].p[i]);
if(i==1)
fprintf(out_inf,"%g)\n",P_mig[cevt][cpop].p[i]);
else
fprintf(out_inf,"%g,",P_mig[cevt][cpop].p[i]);
}
}
//generalized gamma
else if(P_mig[cevt][cpop].type == 2){
P_mig[cevt][cpop].p = (double*)malloc(4*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (mig%d): generalized gamma(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (migAnc%d): generalized gamma(",cevt);
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_mig[cevt][cpop].p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_mig[cevt][cpop].p[i]);
else
fprintf(out_inf,"%g,",P_mig[cevt][cpop].p[i]);
}
}
//uniform on number of migrants
else if(P_mig[cevt][cpop].type == 3){
P_mig[cevt][cpop].p = (double*)malloc(2*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (mig%d): uniform(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (migAnc%d): uniform(",cevt);
for(i=0;i<2;++i){
fscanf(inp_prs,"%lf",&P_mig[cevt][cpop].p[i]);
if(i==1)
fprintf(out_inf,"%g) on emigrants number\n",P_mig[cevt][cpop].p[i]);
else
fprintf(out_inf,"%g,",P_mig[cevt][cpop].p[i]);
}
}
//generalized gamma on number of migrants
else if(P_mig[cevt][cpop].type == 4){
P_mig[cevt][cpop].p = (double*)malloc(4*sizeof(double));
if(cevt==0)
fprintf(out_inf,"- Prior distribution (mig%d): generalized gamma(",cpop+1);
else
fprintf(out_inf,"- Prior distribution (migAnc%d): generalized gamma(",cevt);
for(i=0;i<4;++i){
fscanf(inp_prs,"%lf",&P_mig[cevt][cpop].p[i]);
if(i==3)
fprintf(out_inf,"%g) on emigrants number\n",P_mig[cevt][cpop].p[i]);
else
fprintf(out_inf,"%g,",P_mig[cevt][cpop].p[i]);
}
}
else
printerr("wrong migration prior type");
//each anc pop is just done once
if(cevt > 0)
break;
}
}
}
else{
fprintf(out_inf,"Time events:\n");
fprintf(out_inf,"- No time events -\n");
fprintf(out_inf,"Migration rates:\n");
fprintf(out_inf,"- No migration -\n");
}
/*Reads the mutation rates (Microsatelites)*/
fprintf(out_inf,"Mutation rates (Microsatelites):\n");
fscanf(inp_prs,"%d",&P_mutM.type);
//no mutation present
if(P_mutM.type == 0){
P_mutM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- No mutation -\n");
}
//lognormal distribution
else if(P_mutM.type == 1){
P_mutM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: lognormal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_mutM.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_mutM.p[i]);
else
fprintf(out_inf,"%g,",P_mutM.p[i]);
}
}
//normal distribution
else if(P_mutM.type == 2){
P_mutM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: normal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_mutM.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_mutM.p[i]);
else
fprintf(out_inf,"%g,",P_mutM.p[i]);
}
}
else{
printerr("wrong mutation prior type (Microsatelite)");
}
/*Reads the mutation rates (Sequence data)*/
fprintf(out_inf,"Mutation rates (Sequence data):\n");
fscanf(inp_prs,"%d",&P_mutS.type);
//no mutation present
if(P_mutS.type == 0){
P_mutS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- No mutation -\n");
}
//lognormal distribution
else if(P_mutS.type == 1){
P_mutS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: lognormal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_mutS.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_mutS.p[i]);
else
fprintf(out_inf,"%g,",P_mutS.p[i]);
}
}
//normal distribution
else if(P_mutS.type == 2){
P_mutS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: normal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_mutS.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_mutS.p[i]);
else
fprintf(out_inf,"%g,",P_mutS.p[i]);
}
}
else{
printerr("wrong mutation prior type (Sequence data)");
}
/*Reads the recombination rates (Microsatelites)*/
fprintf(out_inf,"Recombination rates (Microsatelites):\n");
fscanf(inp_prs,"%d",&P_recM.type);
//no recombination present
if(P_recM.type == 0){
P_recM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- No recombination -\n");
}
//lognormal distribution
else if(P_recM.type == 1){
P_recM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: lognormal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_recM.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_recM.p[i]);
else
fprintf(out_inf,"%g,",P_recM.p[i]);
}
}
//normal distribution
else if(P_recM.type == 2){
P_recM.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: normal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_recM.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_recM.p[i]);
else
fprintf(out_inf,"%g,",P_recM.p[i]);
}
}
else{
printerr("wrong recombination prior type (Microsatelite");
}
/*Reads the recombination rates (Sequence data)*/
fprintf(out_inf,"Recombination rates (Sequence data):\n");
fscanf(inp_prs,"%d",&P_recS.type);
//no recombination present
if(P_recS.type == 0){
P_recS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- No recombination -\n");
}
//lognormal distribution
else if(P_recS.type == 1){
P_recS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: lognormal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_recS.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_recS.p[i]);
else
fprintf(out_inf,"%g,",P_recS.p[i]);
}
}
//normal distribution
else if(P_recS.type == 2){
P_recS.p = (double*)malloc(4*sizeof(double));
fprintf(out_inf,"- HiperPrior distribution: normal(");
for(i=0;i<4;i++){
fscanf(inp_prs,"%lf ",&P_recS.p[i]);
if(i==3)
fprintf(out_inf,"%g)\n",P_recS.p[i]);
else
fprintf(out_inf,"%g,",P_recS.p[i]);
}
}
else{
printerr("wrong recombination prior type (Sequence data)");
}
/*Reads the migration weights*/
if(npop>2){
fprintf(out_inf,"Migration weights matrix:\n");
fscanf(inp_prs,"%d",&M_migw.type);
//no use of migration weights
if(M_migw.type == 0){
fprintf(out_inf,"- No migration weights in use -\n");
}
//use of migration weights
else if(M_migw.type == 1){
if(P_top.type==0 || P_top.type==3)
printerr("to use migration weights matrix, topology must be defined (option 1,2,4 or 5)");
M_migw.m = (double***)malloc(npop*sizeof(double**));
for(cpop=0; cpop<npop; cpop++){
fprintf(out_inf,"- %d:\n", cpop);
M_migw.m[cpop] = (double**)malloc(nevt*sizeof(double*));
for(cevt=0; cevt<nevt; cevt++){
M_migw.m[cpop][cevt] = (double*)malloc(npop*sizeof(double));
for(cpop2=0; cpop2<npop; cpop2++){
fscanf(inp_prs,"%lf",&M_migw.m[cpop][cevt][cpop2]);
if(cpop2==0)
fprintf(out_inf," %6.4g ",M_migw.m[cpop][cevt][cpop2]);
else
fprintf(out_inf,"%6.4g ",M_migw.m[cpop][cevt][cpop2]);
}
fprintf(out_inf,"\n");
}
fprintf(out_inf,"\n");
}
}
else
printerr("wrong migration weights matrix related option");
}
fclose(inp_prs);
/*counting the number of parameters*/
nparams=0;
if(npop>1){
if(P_top.type==3||P_top.type==4||P_top.type==5)
nparams++;
if(foundSTR)
nparams+=2;
if(foundSNP)
nparams+=2;
if(foundSTR)
nparams+=2;
if(foundSNP)
nparams+=2;
nparams+= 1+(npop-1)+(2*npop-1)+(2*npop-2);
}
else{
if(P_top.type==3)
nparams++;
if(foundSTR)
nparams+=2;
if(foundSNP)
nparams+=2;
if(foundSTR)
nparams+=2;
if(foundSNP)
nparams+=2;
nparams+= 1+(2*npop-1);
}
//check if there are too many nparams+nstats
if((nparams+nstats)*niter>MAXDATA)
printerr(".dat file would be too big to be analyzed");
/*check if the STR's loci are linked*/
if(foundSTR && P_recM.type != 0){
//join all the STR loci
nrSTR = 0;
sampleSTR = (int*)malloc(nloc*sizeof(int));
for(cloc=0,i=0;cloc<nloc;cloc++){
if(pm.type[cloc]=='m'||pm.type[cloc]=='M'){
if(nrSTR==0){
ploidySTR = pm.ploidy[cloc];
for(cpop=0; cpop<npop; cpop++)
sampleSTR[cpop] = pm.nsamp[cloc][cpop];
}
else if(ploidySTR != pm.ploidy[cloc])
printerr("when using rec with STR all loci must have the same scalar");
else
for(cpop=0;cpop<npop; cpop++)
if(sampleSTR[cpop] != pm.nsamp[cloc][cpop])
printerr("when using rec with STR all loci must have the same samples per population");
nrSTR++;
}
else{
pm.type[i] = pm.type[cloc];
pm.ploidy[i] = pm.ploidy[cloc];
for(cpop=0;cpop<npop;cpop++){
pm.nsamp[i][cpop] = pm.nsamp[cloc][cpop];
}
i++;
}
}
for(cSTR=0; cSTR<nrSTR; cSTR++){
pm.type[i+cSTR] = 'm';
pm.ploidy[i+cSTR] = ploidySTR;
for(cpop=0;cpop<npop;cpop++){
pm.nsamp[i+cSTR][cpop] = sampleSTR[cpop];
}
}
}
else
nrSTR = 1;
pm.nrSTR=nrSTR;
/*write second part of the .txt output file*/
fprintf(out_inf,"\nOUTPUT FILES:\n");
fprintf(out_inf,"-------------------------------\n");
if(printIt)
for(citer=0;citer<niter;citer++)
fprintf(out_inf,"Simulation data file %d: %sdata%d.len\n",citer+1,path,citer);
if(printMut)
fprintf(out_inf,"Mutation rates file: %s.mut\n",argv[4]);
if(printRec)
fprintf(out_inf,"Recombination rates file: %s.rec\n",argv[4]);
fprintf(out_inf,"Data file: %s.dat\n",argv[4]);
fprintf(out_inf,"%d parameters [top",nparams);
if(P_top.type==3||P_top.type==4||P_top.type==5)
fprintf(out_inf,"|marker");
if(foundSTR)
fprintf(out_inf,"|avMutM|sdMutM");
if(foundSNP)
fprintf(out_inf,"|avMutS|sdMutS");
if(foundSTR)
fprintf(out_inf,"|avRecM|sdRecM");
if(foundSNP)
fprintf(out_inf,"|avRecS|sdRecS");
if(npop>1){
for(cevt=0;cevt<nevt;++cevt)
fprintf(out_inf,"|t%d",cevt+1);
for(cevt=0;cevt<=nevt;++cevt){
for(cpop=0;cpop<npop;cpop++){
if(cevt==0)
fprintf(out_inf,"|Ne%d",cpop+1);
else
fprintf(out_inf,"|NeA%d",cevt);
if(cevt > 0)
break;
}
}
for(cevt=0;cevt<nevt;++cevt){
for(cpop=0;cpop<npop;cpop++){
if(cevt==0)
fprintf(out_inf,"|mig%d",cpop+1);
else
fprintf(out_inf,"|migA%d",cevt);
if(cevt > 0)
break;
}
}
}
else
fprintf(out_inf,"|Ne1");
fprintf(out_inf,"]\n%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));
data.nsamp = pm.nsamp;
data.npop = npop;
data.nloc = nloc;
data.tsamp = (int *)malloc(nloc*sizeof(int));
for(cloc=0; cloc<nloc; cloc++){
data.tsamp[cloc]=0;
for(cpop=0; cpop<npop; cpop++)
data.tsamp[cloc]+=data.nsamp[cloc][cpop];
}
data.Nmax = (int *)malloc(nloc*sizeof(int *));
data.ldna = (int *)malloc(nloc*sizeof(int *));
data.freq = (int ***)malloc(nloc*sizeof(int **));
if(foundSTR){
data.valM = (int **)malloc(nloc*sizeof(int *));
}
if(foundSNP){
data.valS = (char ***)malloc(nloc*sizeof(char **));
data.lsites = (int *)malloc(nloc*sizeof(int *));
}
for(cloc = 0;cloc<nloc;++cloc){
data.Nmax[cloc] = 0;
data.freq[cloc] = (int **)malloc(npop*sizeof(int *));
for(cpop=0;cpop<npop;++cpop){
data.freq[cloc][cpop] = (int *)malloc(data.tsamp[cloc]*sizeof(int));
}
if(foundSTR)
data.valM[cloc] = (int *)malloc(sizeof(int));
if(foundSNP){
data.lsites[cloc] = 0;
data.valS[cloc] = (char **)malloc(data.tsamp[cloc]*sizeof(char *));
}
}
/*check if the mutation rates are going to be recorded*/
if(printMut){
name_mut = (char *)malloc(outsize*sizeof(char));
strcpy(name_mut,argv[4]);
out_mut = fopen(strcat(name_mut,".mut"),"w"); //output .mut
if(out_mut == NULL)
printerr("cannot create .mut file");
free(name_mut);
}
/*check if the recombination rates are going to be recorded*/
if(printRec){
name_rec = (char *)malloc(outsize*sizeof(char));
strcpy(name_rec,argv[4]);
out_rec = fopen(strcat(name_rec,".rec"),"w"); //output .rec
if(out_rec == NULL)
printerr("cannot create .rec file");
free(name_rec);
}
outline1 = (char*)malloc(nparams*15*sizeof(char));
if(nstats!=0)
outline2 = (char*)malloc(nstats*15*sizeof(char));
else
outline2 = (char*)malloc(15*sizeof(char));
/*Generate all the genetic trees*/
opengfsr(home);
printf("\n--\nNumber of Genetic trees to be simulated: %d\n",niter);
printf("\nStarting of ABC program...\n ");
for(citer=0;citer<niter;++citer){
sampPriors(&pm,outline1,out_mut,out_rec,printMut,printRec,foundSTR,foundSNP,pm.type);
sampLikelihood(&pm,&data,printIt,citer,path);
summStats(&data,lsstats,outline2,foundSTR,foundSNP,pm.type);
freeMem(nloc,data.tsamp,data.valS,pm.type);
fprintf(out_dat,"%s%s",outline1,outline2);
if(citer!=0 && citer%RecIter==0){
printf("\nGenetic trees simulated so far: %d\n",citer);
}
}
printf("\n...simulations ending\n");
printf("\nGenetic trees simulated: %d\n--\n",citer);
closegfsr(home);
/*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*/
if(foundSTR && P_recM.type != 0)
free(sampleSTR);
freetree(nloc - pm.nrSTR + 1,npop,nevt);
free(home);
free(path);
if(npop>1){
if(P_t[0].type==1||P_t[0].type==2){
for(cevt=0;cevt<nevt;cevt++){
free(pm.mig[cevt]);
free(P_t[cevt].p);
}
}
else{
for(cevt=0;cevt<nevt;cevt++){
free(pm.mig[cevt]);
}
free(P_t[0].p);
}
for(cevt=0;cevt<nevt;++cevt){
for(cpop=0;cpop<npop;++cpop){
free(P_mig[cevt][cpop].p);
if(cevt>0)
break;
}
free(P_mig[cevt]);
}
free(pm.mig);
free(pm.tev);
free(P_t);
free(P_mig);
}
if(npop>2){
if(M_migw.type==1){
for(cpop=0; cpop<npop; cpop++){
for(cevt=0; cevt<nevt; cevt++)
free(M_migw.m[cpop][cevt]);
free(M_migw.m[cpop]);
}
free(M_migw.m);
}
}
free(P_mutM.p);
free(P_mutS.p);
free(P_recM.p);
free(P_recS.p);
free(pm.mu);
free(pm.rec);
free(pm.ploidy);
free(pm.type);
for(cloc=0;cloc<nloc;++cloc)
free(pm.nsamp[cloc]);
free(pm.nsamp);
for(cevt=0;cevt<=nevt;++cevt){
for(cpop=0;cpop<npop;++cpop){
free(P_psize[cevt][cpop].p);
if(cevt>0)
break;
}
free(P_psize[cevt]);
free(pm.psize[cevt]);
}
if(P_top.type!=0)
free(P_top.p);
free(P_psize);
free(pm.psize);
free(outline2);
free(outline1);
free(data.Nmax);
free(data.ldna);
free(data.tsamp);
for(cloc = 0;cloc<nloc;++cloc){
for(cpop=0;cpop<npop;++cpop)
free(data.freq[cloc][cpop]);
free(data.freq[cloc]);
}
free(data.freq);
if(foundSNP){
for(cloc = 0;cloc<nloc;++cloc)
free(data.valS[cloc]);
free(data.valS);
free(data.lsites);
}
if(foundSTR){
for(cloc = 0;cloc<nloc;++cloc)
free(data.valM[cloc]);
free(data.valM);
}
/*close files*/
fclose(out_dat);
fclose(out_inf);
if(printMut)
fclose(out_mut);
if(printRec)
fclose(out_rec);
} //end of main
int notop(int n){
int i,
prod;
prod=1;
for(i=2;i<=n;i++)
prod*=combinations(i,2);
return prod;
}// end of notop
void freeMem(int nloc, int *tsamp,char ***val,char *ltype){
int cloc,cdna; //iterators
for(cloc=0 ; cloc<nloc ; cloc++){
if(ltype[cloc]=='s'||ltype[cloc]=='S'){
for(cdna=0;cdna<tsamp[cloc];++cdna){
if(val[cloc][cdna]!=NULL){
free(val[cloc][cdna]);
val[cloc][cdna] = NULL;
}
}
}
}
} //end of freeMem
Computing file changes ...
