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/*
*
* Compute posterior variance of samples.
*
*
*/
#include<cmath>
using namespace std;
#include "ArgumentParser.h"
#include "misc.h"
#include "PosteriorSamples.h"
#include "common.h"
extern "C" int getVariance(int *argc,char* argv[]){
string programDescription=
"Estimates variance of MCMC samples from 1 or multiple replicates.\n\
[sample Files] should contain transposed MCMC samples from replicates.";
// Set options {{{
ArgumentParser args(programDescription,"[sampleFiles]",1);
args.addOptionS("o","outFile","outFileName",1,"Name of the output file.");
args.addOptionB("l","log","log",0,"Use logged values.");
args.addOptionS("t","type","type",0,"Type of variance, possible values: [sample,sqDif] for sample variance or squared difference.","sample");
args.addOptionS("","norm","normalization",0,"Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).");
if(!args.parse(*argc,argv)){return 0;}
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
bool doLog=args.flag("log"),logged=false;
// }}}
long i,j,r,N,RN,M=0;
Conditions cond;
if(! (cond.init("NONE", args.args(), &M, &N))){
error("Main: Failed loading MCMC samples.\n");
return 1;
}
if(doLog){
logged = true;
if(cond.logged()){
doLog=false;
if(args.verbose)message("Samples are already logged, computing mean.\n");
}else{
if(args.verbose)message("Using logged values.\n");
}
}else{
if(args.verbose)message("NOT using logged values.\n");
if(cond.logged())logged=true;
}
if(args.isSet("normalization")){
if(! cond.setNorm(args.getTokenizedS2D("normalization"))){
error("Main: Applying normalization constants failed.\n");
return 1;
}
}
RN=cond.getRN();
if((args.getS("type")=="sqDif")&&(RN>2)&&(args.verbose)){//{{{
i=0;
while(args.args()[i]=="C")i++;
message("using only: %s ",(args.args()[i]).c_str());
i++;
while(args.args()[i]=="C")i++;
message("%s\n",(args.args()[i]).c_str());
}//}}}
if(args.verbose)message("replicates: %ld samples: %ld transcripts: %ld\n",RN,N,M);
ofstream outFile(args.getS("outFileName").c_str());
if(! outFile.is_open()){
error("Main: File write failed!\n");
return 1;
}
vector<double> mean(M),var(M);
vector<double> tr,tr2;
double m,mSq,count,sqDif;
bool good=true;
if(args.getS("type")=="sample"){ //{{{
for(j=0;j<M;j++){
if((j%10000==0)&&(j>0)&&args.verbose)message("%ld\n",j);
m = mSq = count = 0;
for(r=0;r<RN;r++){
if(cond.getTranscript(r,j,tr,N/RN)){
for(i=0;i<N/RN;i++){
if(doLog){
tr[i]=tr[i]<=0?ns_misc::LOG_ZERO:log(tr[i]);
}
m+=tr[i];
mSq += tr[i]*tr[i];
}
count+=N/RN;
}else{
warning("Error at %ld %ld\n",j,r);
}
// message("%ld %ld\n",m,count);
}
if(count==0){
warning("no samples for transcript: %ld.\n",j);
//for(i,Sof(tr))message("%lf "=0;i,Sof(tr))message("%lf "<tr[i];i,Sof(tr))message("%lf "++);
mean[j] = -47;
var[j] = -47;
}else{
mean[j] = m / count;
var[j] = mSq/count - m*m/(count*count);
}
}//}}}
}else{ // "sqDif" {{{
for(j=0;j<M;j++){
if((j%10000==0)&&(j>0)&&args.verbose)message("%ld\n",j);
m = sqDif = 0;
if(RN==1){
if(! cond.getTranscript(0,j,tr,N)){
mean[j] = -47;
var[j] = -47;
good=false;
continue;
}
tr2.resize(N/2);
for(i=0;i<N/2;i++)
tr2[i]=tr[i+N/2];
}else{
if(! (cond.getTranscript(0,j,tr,N/2)&&
cond.getTranscript(1,j,tr2,N/2))){
mean[j] = -47;
var[j] = -47;
good=false;
continue;
}
}
if(good){
for(i=0;i<N/2;i++){
if(doLog){
tr[i]=tr[i]<=0?ns_misc::LOG_ZERO:log(tr[i]);
tr2[i]=tr2[i]<=0?ns_misc::LOG_ZERO:log(tr2[i]);
}
m+=tr[i]+tr2[i];
sqDif+=(tr[i]-tr2[i])*(tr[i]-tr2[i]);
}
mean[j] = m / N;
var[j] = sqDif / N; // == ( sqDif / (N/2) ) / 2
}
}
} //}}}
cond.close();
outFile<<"# Transcripts mean expression and "<<args.getS("type")<<" variance."<<endl;
outFile<<"# files: ";
for(r=0;r<RN;r++)outFile<<args.args()[r]<<" ";
outFile<<endl;
if(logged)outFile<<"# L -> values logged"<<endl;
outFile<<"# M "<<M<<endl;
(outFile<<scientific).precision(9);
for(i=0;i<M;i++){
if((mean[i]==-47)&&(var[i]==-47))outFile<<"NaN 0 "<<endl;
else outFile<<mean[i]<<" "<<var[i]<<endl;
}
outFile.close();
if(args.verbose)message("DONE\n");
return 0;
}
#ifndef BIOC_BUILD
int main(int argc,char* argv[]){
return getVariance(&argc,argv);
}
#endif
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