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;
76 void load_data(char* reference_name, char* statName, char* imdName) {
82 sprintf(refF, "%s.seq", reference_name);
83 refs.loadRefs(refF, 1);
87 sprintf(groupF, "%s.grp", reference_name);
92 sprintf(thetaF, "%s.theta",statName);
94 general_assert(fin.is_open(), "Cannot open " + cstrtos(thetaF) + "!");
96 general_assert(tmpVal == M + 1, "Number of transcripts is not consistent in " + cstrtos(refF) + " and " + cstrtos(thetaF) + "!");
97 theta.assign(M + 1, 0);
98 for (int i = 0; i <= M; i++) fin>>theta[i];
102 sprintf(ofgF, "%s.ofg", imdName);
104 general_assert(fin.is_open(), "Cannot open " + cstrtos(ofgF) + "!");
106 general_assert(tmpVal == M, "M in " + cstrtos(ofgF) + " is not consistent with " + cstrtos(refF) + "!");
109 s.clear(); hits.clear();
111 while (getline(fin, line)) {
112 istringstream strin(line);
116 while (strin>>sid>>conprb) {
117 hits.push_back(Item(sid, conprb));
119 s.push_back(hits.size());
126 totc = N0 + N1 + (M + 1);
128 if (verbose) { printf("Loading Data is finished!\n"); }
136 quotient = NSAMPLES / nThreads;
137 left = NSAMPLES % nThreads;
139 sprintf(cvsF, "%s.countvectors", imdName);
140 paramsArray = new Params[nThreads];
141 threads = new pthread_t[nThreads];
143 for (int i = 0; i < nThreads; i++) {
144 paramsArray[i].no = i;
146 paramsArray[i].nsamples = quotient;
147 if (i < left) paramsArray[i].nsamples++;
149 sprintf(outF, "%s%d", cvsF, i);
150 paramsArray[i].fo = fopen(outF, "w");
152 paramsArray[i].engine = engineFactory::new_engine();
153 paramsArray[i].pme_c = new double[M + 1];
154 memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
155 paramsArray[i].pve_c = new double[M + 1];
156 memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
157 paramsArray[i].pme_theta = new double[M + 1];
158 memset(paramsArray[i].pme_theta, 0, sizeof(double) * (M + 1));
161 /* set thread attribute to be joinable */
162 pthread_attr_init(&attr);
163 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
165 if (verbose) { printf("Initialization finished!\n"); }
168 //sample theta from Dir(1)
169 void sampleTheta(engine_type& engine, vector<double>& theta) {
171 gamma_generator gmg(engine, gm);
174 theta.assign(M + 1, 0);
176 for (int i = 0; i <= M; i++) {
180 assert(denom > EPSILON);
181 for (int i = 0; i <= M; i++) theta[i] /= denom;
184 void writeCountVector(FILE* fo, vector<int>& counts) {
185 for (int i = 0; i < M; i++) {
186 fprintf(fo, "%d ", counts[i]);
188 fprintf(fo, "%d\n", counts[M]);
191 void* Gibbs(void* arg) {
193 HIT_INT_TYPE len, fr, to;
194 Params *params = (Params*)arg;
196 vector<double> theta;
197 vector<int> z, counts;
200 uniform01 rg(*params->engine);
202 // generate initial state
203 sampleTheta(*params->engine, theta);
207 counts.assign(M + 1, 1); // 1 pseudo count
210 for (READ_INT_TYPE i = 0; i < N1; i++) {
211 fr = s[i]; to = s[i + 1];
214 for (HIT_INT_TYPE j = fr; j < to; j++) {
215 arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
216 if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
218 z[i] = hits[fr + sample(rg, arr, len)].sid;
223 CHAINLEN = 1 + (params->nsamples - 1) * GAP;
224 for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
226 for (READ_INT_TYPE i = 0; i < N1; i++) {
228 fr = s[i]; to = s[i + 1]; len = to - fr;
230 for (HIT_INT_TYPE j = fr; j < to; j++) {
231 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
232 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
234 z[i] = hits[fr + sample(rg, arr, len)].sid;
238 if (ROUND > BURNIN) {
239 if ((ROUND - BURNIN - 1) % GAP == 0) {
240 writeCountVector(params->fo, counts);
241 for (int i = 0; i <= M; i++) {
242 params->pme_c[i] += counts[i] - 1;
243 params->pve_c[i] += (counts[i] - 1) * (counts[i] - 1);
244 params->pme_theta[i] += counts[i] / totc;
249 if (verbose && ROUND % 100 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
256 // char inpF[STRLEN], command[STRLEN];
259 /* destroy attribute */
260 pthread_attr_destroy(&attr);
263 pme_c.assign(M + 1, 0);
264 pve_c.assign(M + 1, 0);
265 pme_theta.assign(M + 1, 0);
266 for (int i = 0; i < nThreads; i++) {
267 fclose(paramsArray[i].fo);
268 delete paramsArray[i].engine;
269 for (int j = 0; j <= M; j++) {
270 pme_c[j] += paramsArray[i].pme_c[j];
271 pve_c[j] += paramsArray[i].pve_c[j];
272 pme_theta[j] += paramsArray[i].pme_theta[j];
274 delete[] paramsArray[i].pme_c;
275 delete[] paramsArray[i].pve_c;
276 delete[] paramsArray[i].pme_theta;
278 delete[] paramsArray;
281 for (int i = 0; i <= M; i++) {
282 pme_c[i] /= NSAMPLES;
283 pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
284 pme_theta[i] /= NSAMPLES;
288 template<class ModelType>
289 void calcExpectedEffectiveLengths(ModelType& model) {
291 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = \sigma_{j=1}^{i}pdf[i]*(lb+i)
293 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
294 clen = new double[span + 1];
296 for (int i = 1; i <= span; i++) {
297 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
300 eel.assign(M + 1, 0.0);
301 for (int i = 1; i <= M; i++) {
302 int totLen = refs.getRef(i).getTotLen();
303 int fullLen = refs.getRef(i).getFullLen();
304 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
305 int pos2 = max(min(totLen, ub) - lb, 0);
307 if (pos2 == 0) { eel[i] = 0.0; continue; }
309 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
311 if (eel[i] < MINEEL) { eel[i] = 0.0; }
319 template<class ModelType>
320 void writeEstimatedParameters(char* modelF, char* imdName) {
328 calcExpectedEffectiveLengths<ModelType>(model);
330 denom = pme_theta[0];
331 for (int i = 1; i <= M; i++)
332 if (eel[i] < EPSILON) pme_theta[i] = 0.0;
333 else denom += pme_theta[i];
335 general_assert(denom >= EPSILON, "No Expected Effective Length is no less than " + ftos(MINEEL, 6) + "?!");
337 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
340 double *mw = model.getMW();
341 for (int i = 0; i <= M; i++) {
342 pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
343 denom += pme_theta[i];
345 assert(denom >= EPSILON);
346 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
348 //calculate tau values
349 double *tau = new double[M + 1];
350 memset(tau, 0, sizeof(double) * (M + 1));
353 for (int i = 1; i <= M; i++)
354 if (eel[i] > EPSILON) {
355 tau[i] = pme_theta[i] / eel[i];
359 general_assert(denom >= EPSILON, "No alignable reads?!");
361 for (int i = 1; i <= M; i++) {
365 //isoform level results
366 sprintf(outF, "%s.iso_res", imdName);
367 fo = fopen(outF, "a");
368 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
370 for (int i = 1; i <= M; i++)
371 fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
372 for (int i = 1; i <= M; i++)
373 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
378 sprintf(outF, "%s.gene_res", imdName);
379 fo = fopen(outF, "a");
380 general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
382 for (int i = 0; i < m; i++) {
383 double sumC = 0.0; // sum of pme counts
384 int b = gi.spAt(i), e = gi.spAt(i + 1);
385 for (int j = b; j < e; j++) {
388 fprintf(fo, "%.15g%c", sumC, (i < m - 1 ? '\t' : '\n'));
390 for (int i = 0; i < m; i++) {
391 double sumT = 0.0; // sum of tau values
392 int b = gi.spAt(i), e = gi.spAt(i + 1);
393 for (int j = b; j < e; j++) {
396 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
402 if (verbose) { printf("Gibbs based expression values are written!\n"); }
405 int main(int argc, char* argv[]) {
407 printf("Usage: rsem-run-gibbs reference_name imdName statName BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
411 strcpy(imdName, argv[2]);
412 strcpy(statName, argv[3]);
414 BURNIN = atoi(argv[4]);
415 NSAMPLES = atoi(argv[5]);
418 load_data(argv[1], statName, imdName);
424 for (int i = 7; i < argc; i++) {
425 if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
426 if (!strcmp(argv[i], "--var")) var_opt = true;
427 if (!strcmp(argv[i], "-q")) quiet = true;
431 assert(NSAMPLES > 1); // Otherwise, we cannot calculate posterior variance
433 if (nThreads > NSAMPLES) {
435 printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
438 if (verbose) printf("Gibbs started!\n");
441 for (int i = 0; i < nThreads; i++) {
442 rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(¶msArray[i]));
443 pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0)!");
445 for (int i = 0; i < nThreads; i++) {
446 rc = pthread_join(threads[i], &status);
447 pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0)!");
451 if (verbose) printf("Gibbs finished!\n");
453 sprintf(modelF, "%s.model", statName);
454 FILE *fi = fopen(modelF, "r");
455 general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
456 assert(fscanf(fi, "%d", &model_type) == 1);
460 case 0 : writeEstimatedParameters<SingleModel>(modelF, imdName); break;
461 case 1 : writeEstimatedParameters<SingleQModel>(modelF, imdName); break;
462 case 2 : writeEstimatedParameters<PairedEndModel>(modelF, imdName); break;
463 case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;
469 sprintf(varF, "%s.var", statName);
470 FILE *fo = fopen(varF, "w");
471 general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
472 for (int i = 0; i < m; i++) {
473 int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
474 for (int j = b; j < e; j++) {
475 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]);