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;
51 int BURNIN, NSAMPLES, GAP;
52 char imdName[STRLEN], statName[STRLEN];
53 char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
59 vector<HIT_INT_TYPE> s;
64 vector<double> pme_c, pve_c; //global posterior mean and variance vectors on counts
65 vector<double> pme_theta, eel;
75 void load_data(char* reference_name, char* statName, char* imdName) {
81 sprintf(refF, "%s.seq", reference_name);
82 refs.loadRefs(refF, 1);
86 sprintf(groupF, "%s.grp", reference_name);
91 sprintf(thetaF, "%s.theta",statName);
93 general_assert(fin.is_open(), "Cannot open " + cstrtos(thetaF) + "!");
95 general_assert(tmpVal == M + 1, "Number of transcripts is not consistent in " + cstrtos(refF) + " and " + cstrtos(thetaF) + "!");
96 theta.assign(M + 1, 0);
97 for (int i = 0; i <= M; i++) fin>>theta[i];
101 sprintf(ofgF, "%s.ofg", imdName);
103 general_assert(fin.is_open(), "Cannot open " + cstrtos(ofgF) + "!");
105 general_assert(tmpVal == M, "M in " + cstrtos(ofgF) + " is not consistent with " + cstrtos(refF) + "!");
108 s.clear(); hits.clear();
110 while (getline(fin, line)) {
111 istringstream strin(line);
115 while (strin>>sid>>conprb) {
116 hits.push_back(Item(sid, conprb));
118 s.push_back(hits.size());
125 totc = N0 + N1 + (M + 1);
127 if (verbose) { printf("Loading Data is finished!\n"); }
135 quotient = NSAMPLES / nThreads;
136 left = NSAMPLES % nThreads;
138 sprintf(cvsF, "%s.countvectors", imdName);
139 paramsArray = new Params[nThreads];
140 threads = new pthread_t[nThreads];
142 for (int i = 0; i < nThreads; i++) {
143 paramsArray[i].no = i;
145 paramsArray[i].nsamples = quotient;
146 if (i < left) paramsArray[i].nsamples++;
148 sprintf(outF, "%s%d", cvsF, i);
149 paramsArray[i].fo = fopen(outF, "w");
151 paramsArray[i].engine = engineFactory::new_engine();
152 paramsArray[i].pme_c = new double[M + 1];
153 memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
154 paramsArray[i].pve_c = new double[M + 1];
155 memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
156 paramsArray[i].pme_theta = new double[M + 1];
157 memset(paramsArray[i].pme_theta, 0, sizeof(double) * (M + 1));
160 /* set thread attribute to be joinable */
161 pthread_attr_init(&attr);
162 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
164 if (verbose) { printf("Initialization finished!\n"); }
167 //sample theta from Dir(1)
168 void sampleTheta(engine_type& engine, vector<double>& theta) {
170 gamma_generator gmg(engine, gm);
173 theta.assign(M + 1, 0);
175 for (int i = 0; i <= M; i++) {
179 assert(denom > EPSILON);
180 for (int i = 0; i <= M; i++) theta[i] /= denom;
183 void writeCountVector(FILE* fo, vector<int>& counts) {
184 for (int i = 0; i < M; i++) {
185 fprintf(fo, "%d ", counts[i]);
187 fprintf(fo, "%d\n", counts[M]);
190 void* Gibbs(void* arg) {
192 HIT_INT_TYPE len, fr, to;
193 Params *params = (Params*)arg;
195 vector<double> theta;
196 vector<int> z, counts;
199 uniform01 rg(*params->engine);
201 // generate initial state
202 sampleTheta(*params->engine, theta);
206 counts.assign(M + 1, 1); // 1 pseudo count
209 for (READ_INT_TYPE i = 0; i < N1; i++) {
210 fr = s[i]; to = s[i + 1];
213 for (HIT_INT_TYPE j = fr; j < to; j++) {
214 arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
215 if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
217 z[i] = hits[fr + sample(rg, arr, len)].sid;
222 CHAINLEN = 1 + (params->nsamples - 1) * GAP;
223 for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
225 for (READ_INT_TYPE i = 0; i < N1; i++) {
227 fr = s[i]; to = s[i + 1]; len = to - fr;
229 for (HIT_INT_TYPE j = fr; j < to; j++) {
230 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
231 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
233 z[i] = hits[fr + sample(rg, arr, len)].sid;
237 if (ROUND > BURNIN) {
238 if ((ROUND - BURNIN - 1) % GAP == 0) {
239 writeCountVector(params->fo, counts);
240 for (int i = 0; i <= M; i++) {
241 params->pme_c[i] += counts[i] - 1;
242 params->pve_c[i] += (counts[i] - 1) * (counts[i] - 1);
243 params->pme_theta[i] += counts[i] / totc;
248 if (verbose && ROUND % 100 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
255 // char inpF[STRLEN], command[STRLEN];
258 /* destroy attribute */
259 pthread_attr_destroy(&attr);
262 pme_c.assign(M + 1, 0);
263 pve_c.assign(M + 1, 0);
264 pme_theta.assign(M + 1, 0);
265 for (int i = 0; i < nThreads; i++) {
266 fclose(paramsArray[i].fo);
267 delete paramsArray[i].engine;
268 for (int j = 0; j <= M; j++) {
269 pme_c[j] += paramsArray[i].pme_c[j];
270 pve_c[j] += paramsArray[i].pve_c[j];
271 pme_theta[j] += paramsArray[i].pme_theta[j];
273 delete[] paramsArray[i].pme_c;
274 delete[] paramsArray[i].pve_c;
275 delete[] paramsArray[i].pme_theta;
277 delete[] paramsArray;
280 for (int i = 0; i <= M; i++) {
281 pme_c[i] /= NSAMPLES;
282 pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
283 pme_theta[i] /= NSAMPLES;
287 template<class ModelType>
288 void calcExpectedEffectiveLengths(ModelType& model) {
290 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = \sigma_{j=1}^{i}pdf[i]*(lb+i)
292 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
293 clen = new double[span + 1];
295 for (int i = 1; i <= span; i++) {
296 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
299 eel.assign(M + 1, 0.0);
300 for (int i = 1; i <= M; i++) {
301 int totLen = refs.getRef(i).getTotLen();
302 int fullLen = refs.getRef(i).getFullLen();
303 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
304 int pos2 = max(min(totLen, ub) - lb, 0);
306 if (pos2 == 0) { eel[i] = 0.0; continue; }
308 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
310 if (eel[i] < MINEEL) { eel[i] = 0.0; }
318 template<class ModelType>
319 void writeEstimatedParameters(char* modelF, char* imdName) {
327 calcExpectedEffectiveLengths<ModelType>(model);
329 denom = pme_theta[0];
330 for (int i = 1; i <= M; i++)
331 if (eel[i] < EPSILON) pme_theta[i] = 0.0;
332 else denom += pme_theta[i];
334 general_assert(denom >= EPSILON, "No Expected Effective Length is no less than " + ftos(MINEEL, 6) + "?!");
336 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
339 double *mw = model.getMW();
340 for (int i = 0; i <= M; i++) {
341 pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
342 denom += pme_theta[i];
344 assert(denom >= EPSILON);
345 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
347 //calculate tau values
348 double *tau = new double[M + 1];
349 memset(tau, 0, sizeof(double) * (M + 1));
352 for (int i = 1; i <= M; i++)
353 if (eel[i] > EPSILON) {
354 tau[i] = pme_theta[i] / eel[i];
358 general_assert(denom >= EPSILON, "No alignable reads?!");
360 for (int i = 1; i <= M; i++) {
364 //isoform level results
365 sprintf(outF, "%s.iso_res", imdName);
366 fo = fopen(outF, "a");
367 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
369 for (int i = 1; i <= M; i++)
370 fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
371 for (int i = 1; i <= M; i++)
372 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
377 sprintf(outF, "%s.gene_res", imdName);
378 fo = fopen(outF, "a");
379 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
381 for (int i = 0; i < m; i++) {
382 double sumC = 0.0; // sum of pme counts
383 int b = gi.spAt(i), e = gi.spAt(i + 1);
384 for (int j = b; j < e; j++) {
387 fprintf(fo, "%.15g%c", sumC, (i < m - 1 ? '\t' : '\n'));
389 for (int i = 0; i < m; i++) {
390 double sumT = 0.0; // sum of tau values
391 int b = gi.spAt(i), e = gi.spAt(i + 1);
392 for (int j = b; j < e; j++) {
395 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
401 if (verbose) { printf("Gibbs based expression values are written!\n"); }
404 int main(int argc, char* argv[]) {
406 printf("Usage: rsem-run-gibbs reference_name imdName statName BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
410 strcpy(imdName, argv[2]);
411 strcpy(statName, argv[3]);
413 BURNIN = atoi(argv[4]);
414 NSAMPLES = atoi(argv[5]);
417 load_data(argv[1], statName, imdName);
423 for (int i = 7; i < argc; i++) {
424 if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
425 if (!strcmp(argv[i], "--var")) var_opt = true;
426 if (!strcmp(argv[i], "-q")) quiet = true;
430 assert(NSAMPLES > 1); // Otherwise, we cannot calculate posterior variance
432 if (nThreads > NSAMPLES) {
434 printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
437 if (verbose) printf("Gibbs started!\n");
440 for (int i = 0; i < nThreads; i++) {
441 rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(¶msArray[i]));
442 pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0)!");
444 for (int i = 0; i < nThreads; i++) {
445 rc = pthread_join(threads[i], NULL);
446 pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0)!");
450 if (verbose) printf("Gibbs finished!\n");
452 sprintf(modelF, "%s.model", statName);
453 FILE *fi = fopen(modelF, "r");
454 general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
455 assert(fscanf(fi, "%d", &model_type) == 1);
459 case 0 : writeEstimatedParameters<SingleModel>(modelF, imdName); break;
460 case 1 : writeEstimatedParameters<SingleQModel>(modelF, imdName); break;
461 case 2 : writeEstimatedParameters<PairedEndModel>(modelF, imdName); break;
462 case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;
468 sprintf(varF, "%s.var", statName);
469 FILE *fo = fopen(varF, "w");
470 general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
471 for (int i = 0; i < m; i++) {
472 int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
473 for (int j = b; j < e; j++) {
474 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]);