11 #include "my_assert.h"
15 #include "SingleModel.h"
16 #include "SingleQModel.h"
17 #include "PairedEndModel.h"
18 #include "PairedEndQModel.h"
21 #include "GroupInfo.h"
29 double *pme_c, *pve_c; //posterior mean and variance vectors on counts
38 Item(int sid, double conprb) {
40 this->conprb = conprb;
47 int m, M, N0, N1, nHits;
49 int BURNIN, NSAMPLES, GAP;
50 char imdName[STRLEN], statName[STRLEN];
51 char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
62 vector<double> pme_c, pve_c; //global posterior mean and variance vectors on counts
63 vector<double> pme_theta, eel;
74 void load_data(char* reference_name, char* statName, char* imdName) {
80 sprintf(refF, "%s.seq", reference_name);
81 refs.loadRefs(refF, 1);
85 sprintf(groupF, "%s.grp", reference_name);
90 sprintf(thetaF, "%s.theta",statName);
92 general_assert(fin.is_open(), "Cannot open " + cstrtos(thetaF) + "!");
94 general_assert(tmpVal == M + 1, "Number of transcripts is not consistent in " + cstrtos(refF) + " and " + cstrtos(thetaF) + "!");
95 theta.assign(M + 1, 0);
96 for (int i = 0; i <= M; i++) fin>>theta[i];
100 sprintf(ofgF, "%s.ofg", imdName);
102 general_assert(fin.is_open(), "Cannot open " + cstrtos(ofgF) + "!");
104 general_assert(tmpVal == M, "M in " + cstrtos(ofgF) + " is not consistent with " + cstrtos(refF) + "!");
107 s.clear(); hits.clear();
109 while (getline(fin, line)) {
110 istringstream strin(line);
114 while (strin>>sid>>conprb) {
115 hits.push_back(Item(sid, conprb));
117 s.push_back(hits.size());
124 totc = N0 + N1 + (M + 1);
126 if (verbose) { printf("Loading Data is finished!\n"); }
134 quotient = NSAMPLES / nThreads;
135 left = NSAMPLES % nThreads;
137 sprintf(cvsF, "%s.countvectors", imdName);
138 paramsArray = new Params[nThreads];
139 threads = new pthread_t[nThreads];
141 for (int i = 0; i < nThreads; i++) {
142 paramsArray[i].no = i;
144 paramsArray[i].nsamples = quotient;
145 if (i < left) paramsArray[i].nsamples++;
147 sprintf(outF, "%s%d", cvsF, i);
148 paramsArray[i].fo = fopen(outF, "w");
150 paramsArray[i].engine = engineFactory::new_engine();
151 paramsArray[i].pme_c = new double[M + 1];
152 memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
153 paramsArray[i].pve_c = new double[M + 1];
154 memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
155 paramsArray[i].pme_theta = new double[M + 1];
156 memset(paramsArray[i].pme_theta, 0, sizeof(double) * (M + 1));
159 /* set thread attribute to be joinable */
160 pthread_attr_init(&attr);
161 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
163 if (verbose) { printf("Initialization finished!"); }
166 //sample theta from Dir(1)
167 void sampleTheta(engine_type& engine, vector<double>& theta) {
169 gamma_generator gmg(engine, gm);
172 theta.assign(M + 1, 0);
174 for (int i = 0; i <= M; i++) {
178 assert(denom > EPSILON);
179 for (int i = 0; i <= M; i++) theta[i] /= denom;
182 void writeCountVector(FILE* fo, vector<int>& counts) {
183 for (int i = 0; i < M; i++) {
184 fprintf(fo, "%d ", counts[i]);
186 fprintf(fo, "%d\n", counts[M]);
189 void* Gibbs(void* arg) {
192 Params *params = (Params*)arg;
194 vector<double> theta;
195 vector<int> z, counts;
198 uniform01 rg(*params->engine);
200 // generate initial state
201 sampleTheta(*params->engine, theta);
205 counts.assign(M + 1, 1); // 1 pseudo count
208 for (int i = 0; i < N1; i++) {
209 fr = s[i]; to = s[i + 1];
212 for (int j = fr; j < to; j++) {
213 arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
214 if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
216 z[i] = hits[fr + sample(rg, arr, len)].sid;
221 CHAINLEN = 1 + (params->nsamples - 1) * GAP;
222 for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
224 for (int i = 0; i < N1; i++) {
226 fr = s[i]; to = s[i + 1]; len = to - fr;
228 for (int j = fr; j < to; j++) {
229 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
230 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
232 z[i] = hits[fr + sample(rg, arr, len)].sid;
236 if (ROUND > BURNIN) {
237 if ((ROUND - BURNIN - 1) % GAP == 0) {
238 writeCountVector(params->fo, counts);
239 for (int i = 0; i <= M; i++) {
240 params->pme_c[i] += counts[i] - 1;
241 params->pve_c[i] += (counts[i] - 1) * (counts[i] - 1);
242 params->pme_theta[i] += counts[i] / totc;
247 if (verbose && ROUND % 100 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
254 // char inpF[STRLEN], command[STRLEN];
257 /* destroy attribute */
258 pthread_attr_destroy(&attr);
261 pme_c.assign(M + 1, 0);
262 pve_c.assign(M + 1, 0);
263 pme_theta.assign(M + 1, 0);
264 for (int i = 0; i < nThreads; i++) {
265 fclose(paramsArray[i].fo);
266 delete paramsArray[i].engine;
267 for (int j = 0; j <= M; j++) {
268 pme_c[j] += paramsArray[i].pme_c[j];
269 pve_c[j] += paramsArray[i].pve_c[j];
270 pme_theta[j] += paramsArray[i].pme_theta[j];
272 delete[] paramsArray[i].pme_c;
273 delete[] paramsArray[i].pve_c;
274 delete[] paramsArray[i].pme_theta;
276 delete[] paramsArray;
279 for (int i = 0; i <= M; i++) {
280 pme_c[i] /= NSAMPLES;
281 pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
282 pme_theta[i] /= NSAMPLES;
287 FILE *fo = fopen(cvsF, "a");
288 for (int i = 1; i < nThreads; i++) {
289 sprintf(inpF, "%s%d", cvsF, i);
291 while (getline(fin, line)) {
292 fprintf(fo, "%s\n", line.c_str());
295 sprintf(command, "rm -f %s", inpF);
296 int status = system(command);
297 general_assert(status == 0, "Fail to delete file " + cstrtos(inpF) + "!");
303 template<class ModelType>
304 void calcExpectedEffectiveLengths(ModelType& model) {
306 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = \sigma_{j=1}^{i}pdf[i]*(lb+i)
308 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
309 clen = new double[span + 1];
311 for (int i = 1; i <= span; i++) {
312 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
315 eel.assign(M + 1, 0.0);
316 for (int i = 1; i <= M; i++) {
317 int totLen = refs.getRef(i).getTotLen();
318 int fullLen = refs.getRef(i).getFullLen();
319 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
320 int pos2 = max(min(totLen, ub) - lb, 0);
322 if (pos2 == 0) { eel[i] = 0.0; continue; }
324 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
326 if (eel[i] < MINEEL) { eel[i] = 0.0; }
334 template<class ModelType>
335 void writeEstimatedParameters(char* modelF, char* imdName) {
343 calcExpectedEffectiveLengths<ModelType>(model);
345 denom = pme_theta[0];
346 for (int i = 1; i <= M; i++)
347 if (eel[i] < EPSILON) pme_theta[i] = 0.0;
348 else denom += pme_theta[i];
350 general_assert(denom >= EPSILON, "No Expected Effective Length is no less than " + ftos(MINEEL, 6) + "?!");
352 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
355 double *mw = model.getMW();
356 for (int i = 0; i <= M; i++) {
357 pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
358 denom += pme_theta[i];
360 assert(denom >= EPSILON);
361 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
363 //calculate tau values
364 double *tau = new double[M + 1];
365 memset(tau, 0, sizeof(double) * (M + 1));
368 for (int i = 1; i <= M; i++)
369 if (eel[i] > EPSILON) {
370 tau[i] = pme_theta[i] / eel[i];
374 general_assert(denom >= EPSILON, "No alignable reads?!");
376 for (int i = 1; i <= M; i++) {
380 //isoform level results
381 sprintf(outF, "%s.iso_res", imdName);
382 fo = fopen(outF, "a");
383 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
385 for (int i = 1; i <= M; i++)
386 fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
387 for (int i = 1; i <= M; i++)
388 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
393 sprintf(outF, "%s.gene_res", imdName);
394 fo = fopen(outF, "a");
395 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
397 for (int i = 0; i < m; i++) {
398 double sumC = 0.0; // sum of pme counts
399 int b = gi.spAt(i), e = gi.spAt(i + 1);
400 for (int j = b; j < e; j++) {
403 fprintf(fo, "%.15g%c", sumC, (i < m - 1 ? '\t' : '\n'));
405 for (int i = 0; i < m; i++) {
406 double sumT = 0.0; // sum of tau values
407 int b = gi.spAt(i), e = gi.spAt(i + 1);
408 for (int j = b; j < e; j++) {
411 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
417 if (verbose) { printf("Gibbs based expression values are written!\n"); }
420 int main(int argc, char* argv[]) {
422 printf("Usage: rsem-run-gibbs-multi reference_name sample_name sampleToken BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
426 BURNIN = atoi(argv[4]);
427 NSAMPLES = atoi(argv[5]);
429 sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
430 sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
431 load_data(argv[1], statName, imdName);
437 for (int i = 7; i < argc; i++) {
438 if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
439 if (!strcmp(argv[i], "--var")) var_opt = true;
440 if (!strcmp(argv[i], "-q")) quiet = true;
444 assert(NSAMPLES > 1); // Otherwise, we cannot calculate posterior variance
446 if (nThreads > NSAMPLES) {
448 printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
451 if (verbose) printf("Gibbs started!\n");
454 for (int i = 0; i < nThreads; i++) {
455 rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(¶msArray[i]));
456 pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0)!");
458 for (int i = 0; i < nThreads; i++) {
459 rc = pthread_join(threads[i], &status);
460 pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0)!");
464 if (verbose) printf("Gibbs finished!\n");
466 sprintf(modelF, "%s.model", statName);
467 FILE *fi = fopen(modelF, "r");
468 general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
469 assert(fscanf(fi, "%d", &model_type) == 1);
473 case 0 : writeEstimatedParameters<SingleModel>(modelF, imdName); break;
474 case 1 : writeEstimatedParameters<SingleQModel>(modelF, imdName); break;
475 case 2 : writeEstimatedParameters<PairedEndModel>(modelF, imdName); break;
476 case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;
482 sprintf(varF, "%s.var", statName);
483 FILE *fo = fopen(varF, "w");
484 general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
485 for (int i = 0; i < m; i++) {
486 int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
487 for (int j = b; j < e; j++) {
488 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]);