-#include<ctime>
#include<cstdio>
#include<cstring>
#include<cstdlib>
#include<fstream>
#include<sstream>
#include<vector>
-
-#include "boost/random.hpp"
+#include<pthread.h>
#include "utils.h"
+#include "my_assert.h"
+#include "sampling.h"
#include "Model.h"
#include "SingleModel.h"
using namespace std;
+struct Params {
+ int no, nsamples;
+ FILE *fo;
+ engine_type *engine;
+ double *pme_c, *pve_c; //posterior mean and variance vectors on counts
+ double *pme_theta;
+};
+
+
struct Item {
int sid;
double conprb;
}
};
+int nThreads;
+
int model_type;
int m, M, N0, N1, nHits;
double totc;
-int BURNIN, CHAINLEN, GAP;
+int BURNIN, NSAMPLES, GAP;
char imdName[STRLEN], statName[STRLEN];
char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
char cvsF[STRLEN];
Refs refs;
GroupInfo gi;
-vector<double> theta, pme_theta, pme_c, eel;
-
-vector<int> s, z;
+vector<int> s;
vector<Item> hits;
-vector<int> counts;
-bool quiet;
+vector<double> theta;
+
+vector<double> pme_c, pve_c; //global posterior mean and variance vectors on counts
+vector<double> pme_theta, eel;
-vector<double> arr;
+bool var_opt;
+bool quiet;
-boost::mt19937 rng(time(NULL));
-boost::uniform_01<boost::mt19937> rg(rng);
+Params *paramsArray;
+pthread_t *threads;
+pthread_attr_t attr;
+void *status;
+int rc;
void load_data(char* reference_name, char* statName, char* imdName) {
ifstream fin;
//load thetaF
sprintf(thetaF, "%s.theta",statName);
fin.open(thetaF);
- if (!fin.is_open()) {
- fprintf(stderr, "Cannot open %s!\n", thetaF);
- exit(-1);
- }
+ general_assert(fin.is_open(), "Cannot open " + cstrtos(thetaF) + "!");
fin>>tmpVal;
- if (tmpVal != M + 1) {
- fprintf(stderr, "Number of transcripts is not consistent in %s and %s!\n", refF, thetaF);
- exit(-1);
- }
- theta.clear(); theta.resize(M + 1);
+ general_assert(tmpVal == M + 1, "Number of transcripts is not consistent in " + cstrtos(refF) + " and " + cstrtos(thetaF) + "!");
+ theta.assign(M + 1, 0);
for (int i = 0; i <= M; i++) fin>>theta[i];
fin.close();
//load ofgF;
sprintf(ofgF, "%s.ofg", imdName);
fin.open(ofgF);
- if (!fin.is_open()) {
- fprintf(stderr, "Cannot open %s!\n", ofgF);
- exit(-1);
- }
+ general_assert(fin.is_open(), "Cannot open " + cstrtos(ofgF) + "!");
fin>>tmpVal>>N0;
- if (tmpVal != M) {
- fprintf(stderr, "M in %s is not consistent with %s!\n", ofgF, refF);
- exit(-1);
- }
+ general_assert(tmpVal == M, "M in " + cstrtos(ofgF) + " is not consistent with " + cstrtos(refF) + "!");
getline(fin, line);
s.clear(); hits.clear();
N1 = s.size() - 1;
nHits = hits.size();
- if (verbose) { printf("Loading Data is finished!\n"); }
-}
+ totc = N0 + N1 + (M + 1);
-// arr should be cumulative!
-// interval : [,)
-// random number should be in [0, arr[len - 1])
-// If by chance arr[len - 1] == 0.0, one possibility is to sample uniformly from 0...len-1
-int sample(vector<double>& arr, int len) {
- int l, r, mid;
- double prb = rg() * arr[len - 1];
-
- l = 0; r = len - 1;
- while (l <= r) {
- mid = (l + r) / 2;
- if (arr[mid] <= prb) l = mid + 1;
- else r = mid - 1;
- }
-
- if (l >= len) { printf("%d %lf %lf\n", len, arr[len - 1], prb); }
- assert(l < len);
-
- return l;
+ if (verbose) { printf("Loading Data is finished!\n"); }
}
+// assign threads
void init() {
- int len, fr, to;
+ int quotient, left;
+ char outF[STRLEN];
+ char splitF[STRLEN];
- arr.clear();
- z.clear();
- counts.clear();
+ quotient = NSAMPLES / nThreads;
+ left = NSAMPLES % nThreads;
- z.resize(N1);
- counts.resize(M + 1, 1); // 1 pseudo count
- counts[0] += N0;
+ sprintf(cvsF, "%s.countvectors", imdName);
+ paramsArray = new Params[nThreads];
+ threads = new pthread_t[nThreads];
- for (int i = 0; i < N1; i++) {
- fr = s[i]; to = s[i + 1];
- len = to - fr;
- arr.resize(len);
- for (int j = fr; j < to; j++) {
- arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
- if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
- }
- z[i] = hits[fr + sample(arr, len)].sid;
- ++counts[z[i]];
+ for (int i = 0; i < nThreads; i++) {
+ paramsArray[i].no = i;
+
+ paramsArray[i].nsamples = quotient;
+ if (i < left) paramsArray[i].nsamples++;
+
+ sprintf(outF, "%s%d", cvsF, i);
+ paramsArray[i].fo = fopen(outF, "w");
+
+ paramsArray[i].engine = engineFactory::new_engine();
+ paramsArray[i].pme_c = new double[M + 1];
+ memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
+ paramsArray[i].pve_c = new double[M + 1];
+ memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
+ paramsArray[i].pme_theta = new double[M + 1];
+ memset(paramsArray[i].pme_theta, 0, sizeof(double) * (M + 1));
}
- totc = N0 + N1 + (M + 1);
+ // output task splitting information
+ sprintf(splitF, "%s.split", imdName);
+ FILE *fo = fopen(splitF, "w");
+ fprintf(fo, "%d", nThreads);
+ for (int i = 0; i < nThreads; i++) fprintf(fo, " %d", paramsArray[i].nsamples);
+ fprintf(fo, "\n");
+ fclose(fo);
- if (verbose) { printf("Initialization is finished!\n"); }
+ /* set thread attribute to be joinable */
+ pthread_attr_init(&attr);
+ pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+
+ if (verbose) { printf("Initialization finished!"); }
}
-void writeCountVector(FILE* fo) {
+//sample theta from Dir(1)
+void sampleTheta(engine_type& engine, vector<double>& theta) {
+ gamma_dist gm(1);
+ gamma_generator gmg(engine, gm);
+ double denom;
+
+ theta.assign(M + 1, 0);
+ denom = 0.0;
+ for (int i = 0; i <= M; i++) {
+ theta[i] = gmg();
+ denom += theta[i];
+ }
+ assert(denom > EPSILON);
+ for (int i = 0; i <= M; i++) theta[i] /= denom;
+}
+
+void writeCountVector(FILE* fo, vector<int>& counts) {
for (int i = 0; i < M; i++) {
fprintf(fo, "%d ", counts[i]);
}
fprintf(fo, "%d\n", counts[M]);
}
-void Gibbs(char* imdName) {
- FILE *fo;
- int fr, to, len;
+void* Gibbs(void* arg) {
+ int len, fr, to;
+ int CHAINLEN;
+ Params *params = (Params*)arg;
- sprintf(cvsF, "%s.countvectors", imdName);
- fo = fopen(cvsF, "w");
- assert(CHAINLEN % GAP == 0);
- fprintf(fo, "%d %d\n", CHAINLEN / GAP, M + 1);
- //fprintf(fo, "%d %d\n", CHAINLEN, M + 1);
+ vector<double> theta;
+ vector<int> z, counts;
+ vector<double> arr;
+
+ uniform01 rg(*params->engine);
+
+ // generate initial state
+ sampleTheta(*params->engine, theta);
- pme_c.clear(); pme_c.resize(M + 1, 0.0);
- pme_theta.clear(); pme_theta.resize(M + 1, 0.0);
+ z.assign(N1, 0);
+
+ counts.assign(M + 1, 1); // 1 pseudo count
+ counts[0] += N0;
+
+ for (int i = 0; i < N1; i++) {
+ fr = s[i]; to = s[i + 1];
+ len = to - fr;
+ arr.assign(len, 0);
+ for (int j = fr; j < to; j++) {
+ arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
+ if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
+ }
+ z[i] = hits[fr + sample(rg, arr, len)].sid;
+ ++counts[z[i]];
+ }
+
+ // Gibbs sampling
+ CHAINLEN = 1 + (params->nsamples - 1) * GAP;
for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
for (int i = 0; i < N1; i++) {
--counts[z[i]];
fr = s[i]; to = s[i + 1]; len = to - fr;
- arr.resize(len);
+ arr.assign(len, 0);
for (int j = fr; j < to; j++) {
arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
}
- z[i] = hits[fr + sample(arr, len)].sid;
+ z[i] = hits[fr + sample(rg, arr, len)].sid;
++counts[z[i]];
}
if (ROUND > BURNIN) {
- if ((ROUND - BURNIN - 1) % GAP == 0) writeCountVector(fo);
- for (int i = 0; i <= M; i++) {
- pme_c[i] += counts[i] - 1;
- pme_theta[i] += counts[i] / totc;
+ if ((ROUND - BURNIN - 1) % GAP == 0) {
+ writeCountVector(params->fo, counts);
+ for (int i = 0; i <= M; i++) {
+ params->pme_c[i] += counts[i] - 1;
+ params->pve_c[i] += (counts[i] - 1) * (counts[i] - 1);
+ params->pme_theta[i] += counts[i] / totc;
+ }
}
}
- if (verbose) { printf("ROUND %d is finished!\n", ROUND); }
+ if (verbose && ROUND % 100 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
}
- fclose(fo);
+
+ return NULL;
+}
+
+void release() {
+// char inpF[STRLEN], command[STRLEN];
+ string line;
+
+ /* destroy attribute */
+ pthread_attr_destroy(&attr);
+ delete[] threads;
+
+ pme_c.assign(M + 1, 0);
+ pve_c.assign(M + 1, 0);
+ pme_theta.assign(M + 1, 0);
+ for (int i = 0; i < nThreads; i++) {
+ fclose(paramsArray[i].fo);
+ delete paramsArray[i].engine;
+ for (int j = 0; j <= M; j++) {
+ pme_c[j] += paramsArray[i].pme_c[j];
+ pve_c[j] += paramsArray[i].pve_c[j];
+ pme_theta[j] += paramsArray[i].pme_theta[j];
+ }
+ delete[] paramsArray[i].pme_c;
+ delete[] paramsArray[i].pve_c;
+ delete[] paramsArray[i].pme_theta;
+ }
+ delete[] paramsArray;
+
for (int i = 0; i <= M; i++) {
- pme_c[i] /= CHAINLEN;
- pme_theta[i] /= CHAINLEN;
+ pme_c[i] /= NSAMPLES;
+ pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
+ pme_theta[i] /= NSAMPLES;
}
- if (verbose) { printf("Gibbs is finished!\n"); }
+ /*
+ // combine files
+ FILE *fo = fopen(cvsF, "a");
+ for (int i = 1; i < nThreads; i++) {
+ sprintf(inpF, "%s%d", cvsF, i);
+ ifstream fin(inpF);
+ while (getline(fin, line)) {
+ fprintf(fo, "%s\n", line.c_str());
+ }
+ fin.close();
+ sprintf(command, "rm -f %s", inpF);
+ int status = system(command);
+ general_assert(status == 0, "Fail to delete file " + cstrtos(inpF) + "!");
+ }
+ fclose(fo);
+ */
}
template<class ModelType>
void calcExpectedEffectiveLengths(ModelType& model) {
- int lb, ub, span;
- double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = sigma_{j=1}^{i}pdf[i]*(lb+i)
+ int lb, ub, span;
+ double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = \sigma_{j=1}^{i}pdf[i]*(lb+i)
- model.getGLD().copyTo(pdf, cdf, lb, ub, span);
- clen = new double[span + 1];
- clen[0] = 0.0;
- for (int i = 1; i <= span; i++) {
- clen[i] = clen[i - 1] + pdf[i] * (lb + i);
- }
-
- eel.clear();
- eel.resize(M + 1, 0.0);
- for (int i = 1; i <= M; i++) {
- int totLen = refs.getRef(i).getTotLen();
- int fullLen = refs.getRef(i).getFullLen();
- int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
- int pos2 = max(min(totLen, ub) - lb, 0);
-
- if (pos2 == 0) { eel[i] = 0.0; continue; }
+ model.getGLD().copyTo(pdf, cdf, lb, ub, span);
+ clen = new double[span + 1];
+ clen[0] = 0.0;
+ for (int i = 1; i <= span; i++) {
+ clen[i] = clen[i - 1] + pdf[i] * (lb + i);
+ }
+
+ eel.assign(M + 1, 0.0);
+ for (int i = 1; i <= M; i++) {
+ int totLen = refs.getRef(i).getTotLen();
+ int fullLen = refs.getRef(i).getFullLen();
+ int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
+ int pos2 = max(min(totLen, ub) - lb, 0);
+
+ if (pos2 == 0) { eel[i] = 0.0; continue; }
- eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
- assert(eel[i] >= 0);
- if (eel[i] < MINEEL) { eel[i] = 0.0; }
- }
+ eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
+ assert(eel[i] >= 0);
+ if (eel[i] < MINEEL) { eel[i] = 0.0; }
+ }
- delete[] pdf;
- delete[] cdf;
- delete[] clen;
+ delete[] pdf;
+ delete[] cdf;
+ delete[] clen;
}
template<class ModelType>
for (int i = 1; i <= M; i++)
if (eel[i] < EPSILON) pme_theta[i] = 0.0;
else denom += pme_theta[i];
- if (denom <= 0) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
+
+ general_assert(denom >= EPSILON, "No Expected Effective Length is no less than " + ftos(MINEEL, 6) + "?!");
+
for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
denom = 0.0;
tau[i] = pme_theta[i] / eel[i];
denom += tau[i];
}
- if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
- //assert(denom > 0);
+
+ general_assert(denom >= EPSILON, "No alignable reads?!");
+
for (int i = 1; i <= M; i++) {
tau[i] /= denom;
}
//isoform level results
sprintf(outF, "%s.iso_res", imdName);
fo = fopen(outF, "a");
- if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
+ general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
+
for (int i = 1; i <= M; i++)
fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
for (int i = 1; i <= M; i++)
fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
+
fclose(fo);
//gene level results
sprintf(outF, "%s.gene_res", imdName);
fo = fopen(outF, "a");
- if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
+ general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
+
for (int i = 0; i < m; i++) {
double sumC = 0.0; // sum of pme counts
int b = gi.spAt(i), e = gi.spAt(i + 1);
if (verbose) { printf("Gibbs based expression values are written!\n"); }
}
-
int main(int argc, char* argv[]) {
if (argc < 7) {
- printf("Usage: rsem-run-gibbs reference_name sample_name sampleToken BURNIN CHAINLEN GAP [-q]\n");
+ printf("Usage: rsem-run-gibbs-multi reference_name sample_name sampleToken BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
exit(-1);
}
BURNIN = atoi(argv[4]);
- CHAINLEN = atoi(argv[5]);
+ NSAMPLES = atoi(argv[5]);
GAP = atoi(argv[6]);
sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
load_data(argv[1], statName, imdName);
+ nThreads = 1;
+ var_opt = false;
quiet = false;
- if (argc > 7 && !strcmp(argv[7], "-q")) {
- quiet = true;
+
+ for (int i = 7; i < argc; i++) {
+ if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
+ if (!strcmp(argv[i], "--var")) var_opt = true;
+ if (!strcmp(argv[i], "-q")) quiet = true;
}
verbose = !quiet;
+ assert(NSAMPLES > 1); // Otherwise, we cannot calculate posterior variance
+
+ if (nThreads > NSAMPLES) {
+ nThreads = NSAMPLES;
+ printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
+ }
+
+ if (verbose) printf("Gibbs started!\n");
+
init();
- Gibbs(imdName);
+ for (int i = 0; i < nThreads; i++) {
+ rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(¶msArray[i]));
+ pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0)!");
+ }
+ for (int i = 0; i < nThreads; i++) {
+ rc = pthread_join(threads[i], &status);
+ pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0)!");
+ }
+ release();
+
+ if (verbose) printf("Gibbs finished!\n");
sprintf(modelF, "%s.model", statName);
FILE *fi = fopen(modelF, "r");
- if (fi == NULL) { fprintf(stderr, "Cannot open %s!\n", modelF); exit(-1); }
- fscanf(fi, "%d", &model_type);
+ general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
+ assert(fscanf(fi, "%d", &model_type) == 1);
fclose(fi);
switch(model_type) {
case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;
}
+ if (var_opt) {
+ char varF[STRLEN];
+
+ sprintf(varF, "%s.var", statName);
+ FILE *fo = fopen(varF, "w");
+ general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
+ for (int i = 0; i < m; i++) {
+ int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
+ for (int j = b; j < e; j++) {
+ fprintf(fo, "%s\t%d\t%.15g\t%.15g\n", refs.getRef(j).getName().c_str(), number_of_isoforms, pme_c[j], pve_c[j]);
+ }
+ }
+ fclose(fo);
+ }
+
return 0;
}
projects / rsem.git / blobdiff