Gibbs.cpp

   1 #include<cstdio>
   2 #include<cstring>
   3 #include<cstdlib>
   4 #include<cassert>
   5 #include<fstream>
   6 #include<sstream>
   7 #include<vector>
   8 #include<pthread.h>
   9
  10 #include "utils.h"
  11 #include "my_assert.h"
  12 #include "sampling.h"
  13
  14 #include "Model.h"
  15 #include "SingleModel.h"
  16 #include "SingleQModel.h"
  17 #include "PairedEndModel.h"
  18 #include "PairedEndQModel.h"
  19
  20 #include "Refs.h"
  21
  22 #include "GroupInfo.h"
  23 #include "WriteResults.h"
  24
  25 using namespace std;
  26
  27 struct Params {
  28         int no, nsamples;
  29         FILE *fo;
  30         engine_type *engine;
  31         double *pme_c, *pve_c; //posterior mean and variance vectors on counts
  32   double *pme_tpm, *pme_fpkm;
  33 };
  34
  35
  36 struct Item {
  37         int sid;
  38         double conprb;
  39
  40         Item(int sid, double conprb) {
  41                 this->sid = sid;
  42                 this->conprb = conprb;
  43         }
  44 };
  45
  46 int nThreads;
  47
  48 int model_type;
  49 int M;
  50 READ_INT_TYPE N0, N1;
  51 HIT_INT_TYPE nHits;
  52 double totc;
  53 int BURNIN, NSAMPLES, GAP;
  54 char refName[STRLEN], imdName[STRLEN], statName[STRLEN];
  55 char thetaF[STRLEN], ofgF[STRLEN], refF[STRLEN], modelF[STRLEN];
  56 char cvsF[STRLEN];
  57
  58 Refs refs;
  59
  60 vector<HIT_INT_TYPE> s;
  61 vector<Item> hits;
  62
  63 vector<double> eel;
  64 double *mw;
  65
  66 vector<double> pme_c, pve_c; //global posterior mean and variance vectors on counts
  67 vector<double> pme_tpm, pme_fpkm;
  68
  69 bool var_opt;
  70 bool quiet;
  71
  72 Params *paramsArray;
  73 pthread_t *threads;
  74 pthread_attr_t attr;
  75 int rc;
  76
  77 void load_data(char* refName, char* statName, char* imdName) {
  78         ifstream fin;
  79         string line;
  80         int tmpVal;
  81
  82         //load reference file
  83         sprintf(refF, "%s.seq", refName);
  84         refs.loadRefs(refF, 1);
  85         M = refs.getM();
  86
  87         //load ofgF;
  88         sprintf(ofgF, "%s.ofg", imdName);
  89         fin.open(ofgF);
  90         general_assert(fin.is_open(), "Cannot open " + cstrtos(ofgF) + "!");
  91         fin>>tmpVal>>N0;
  92         general_assert(tmpVal == M, "M in " + cstrtos(ofgF) + " is not consistent with " + cstrtos(refF) + "!");
  93         getline(fin, line);
  94
  95         s.clear(); hits.clear();
  96         s.push_back(0);
  97         while (getline(fin, line)) {
  98                 istringstream strin(line);
  99                 int sid;
 100                 double conprb;
 101
 102                 while (strin>>sid>>conprb) {
 103                         hits.push_back(Item(sid, conprb));
 104                 }
 105                 s.push_back(hits.size());
 106         }
 107         fin.close();
 108
 109         N1 = s.size() - 1;
 110         nHits = hits.size();
 111
 112         totc = N0 + N1 + (M + 1);
 113
 114         if (verbose) { printf("Loading Data is finished!\n"); }
 115 }
 116
 117 template<class ModelType>
 118 void init_model_related(char* modelF) {
 119         ModelType model;
 120         model.read(modelF);
 121
 122         calcExpectedEffectiveLengths<ModelType>(M, refs, model, eel);
 123         memcpy(mw, model.getMW(), sizeof(double) * (M + 1)); // otherwise, after exiting this procedure, mw becomes undefined
 124 }
 125
 126 // assign threads
 127 void init() {
 128         int quotient, left;
 129         char outF[STRLEN];
 130
 131         quotient = NSAMPLES / nThreads;
 132         left = NSAMPLES % nThreads;
 133
 134         sprintf(cvsF, "%s.countvectors", imdName);
 135         paramsArray = new Params[nThreads];
 136         threads = new pthread_t[nThreads];
 137
 138         for (int i = 0; i < nThreads; i++) {
 139                 paramsArray[i].no = i;
 140
 141                 paramsArray[i].nsamples = quotient;
 142                 if (i < left) paramsArray[i].nsamples++;
 143
 144                 sprintf(outF, "%s%d", cvsF, i);
 145                 paramsArray[i].fo = fopen(outF, "w");
 146
 147                 paramsArray[i].engine = engineFactory::new_engine();
 148                 paramsArray[i].pme_c = new double[M + 1];
 149                 memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
 150                 paramsArray[i].pve_c = new double[M + 1];
 151                 memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
 152                 paramsArray[i].pme_tpm = new double[M + 1];
 153                 memset(paramsArray[i].pme_tpm, 0, sizeof(double) * (M + 1));
 154                 paramsArray[i].pme_fpkm = new double[M + 1];
 155                 memset(paramsArray[i].pme_fpkm, 0, sizeof(double) * (M + 1));
 156         }
 157
 158         /* set thread attribute to be joinable */
 159         pthread_attr_init(&attr);
 160         pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
 161
 162         if (verbose) { printf("Initialization finished!\n"); }
 163 }
 164
 165 //sample theta from Dir(1)
 166 void sampleTheta(engine_type& engine, vector<double>& theta) {
 167         gamma_dist gm(1);
 168         gamma_generator gmg(engine, gm);
 169         double denom;
 170
 171         theta.assign(M + 1, 0);
 172         denom = 0.0;
 173         for (int i = 0; i <= M; i++) {
 174                 theta[i] = gmg();
 175                 denom += theta[i];
 176         }
 177         assert(denom > EPSILON);
 178         for (int i = 0; i <= M; i++) theta[i] /= denom;
 179 }
 180
 181 void writeCountVector(FILE* fo, vector<int>& counts) {
 182         for (int i = 0; i < M; i++) {
 183                 fprintf(fo, "%d ", counts[i]);
 184         }
 185         fprintf(fo, "%d\n", counts[M]);
 186 }
 187
 188 void* Gibbs(void* arg) {
 189         int CHAINLEN;
 190         HIT_INT_TYPE len, fr, to;
 191         Params *params = (Params*)arg;
 192
 193         vector<double> theta, tpm, fpkm;
 194         vector<int> z, counts;
 195         vector<double> arr;
 196
 197         uniform01 rg(*params->engine);
 198
 199         // generate initial state
 200         sampleTheta(*params->engine, theta);
 201
 202         z.assign(N1, 0);
 203
 204         counts.assign(M + 1, 1); // 1 pseudo count
 205         counts[0] += N0;
 206
 207         for (READ_INT_TYPE i = 0; i < N1; i++) {
 208                 fr = s[i]; to = s[i + 1];
 209                 len = to - fr;
 210                 arr.assign(len, 0);
 211                 for (HIT_INT_TYPE j = fr; j < to; j++) {
 212                         arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
 213                         if (j > fr) arr[j - fr] += arr[j - fr - 1];  // cumulative
 214                 }
 215                 z[i] = hits[fr + sample(rg, arr, len)].sid;
 216                 ++counts[z[i]];
 217         }
 218
 219         // Gibbs sampling
 220         CHAINLEN = 1 + (params->nsamples - 1) * GAP;
 221         for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
 222
 223                 for (READ_INT_TYPE i = 0; i < N1; i++) {
 224                         --counts[z[i]];
 225                         fr = s[i]; to = s[i + 1]; len = to - fr;
 226                         arr.assign(len, 0);
 227                         for (HIT_INT_TYPE j = fr; j < to; j++) {
 228                                 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
 229                                 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
 230                         }
 231                         z[i] = hits[fr + sample(rg, arr, len)].sid;
 232                         ++counts[z[i]];
 233                 }
 234
 235                 if (ROUND > BURNIN) {
 236                         if ((ROUND - BURNIN - 1) % GAP == 0) {
 237                                 writeCountVector(params->fo, counts);
 238                                 for (int i = 0; i <= M; i++) theta[i] = counts[i] / totc;
 239                                 polishTheta(M, theta, eel, mw);
 240                                 calcExpressionValues(M, theta, eel, tpm, fpkm);
 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_tpm[i] += tpm[i];
 245                                         params->pme_fpkm[i] += fpkm[i];
 246                                 }
 247                         }
 248                 }
 249
 250                 if (verbose && ROUND % 100 == 0) { printf("Thread %d, ROUND %d is finished!\n", params->no, ROUND); }
 251         }
 252
 253         return NULL;
 254 }
 255
 256 void release() {
 257 //      char inpF[STRLEN], command[STRLEN];
 258         string line;
 259
 260         /* destroy attribute */
 261         pthread_attr_destroy(&attr);
 262         delete[] threads;
 263
 264         pme_c.assign(M + 1, 0);
 265         pve_c.assign(M + 1, 0);
 266         pme_tpm.assign(M + 1, 0);
 267         pme_fpkm.assign(M + 1, 0);
 268         for (int i = 0; i < nThreads; i++) {
 269                 fclose(paramsArray[i].fo);
 270                 delete paramsArray[i].engine;
 271                 for (int j = 0; j <= M; j++) {
 272                         pme_c[j] += paramsArray[i].pme_c[j];
 273                         pve_c[j] += paramsArray[i].pve_c[j];
 274                         pme_tpm[j] += paramsArray[i].pme_tpm[j];
 275                         pme_fpkm[j] += paramsArray[i].pme_fpkm[j];
 276                 }
 277                 delete[] paramsArray[i].pme_c;
 278                 delete[] paramsArray[i].pve_c;
 279                 delete[] paramsArray[i].pme_tpm;
 280                 delete[] paramsArray[i].pme_fpkm;
 281         }
 282         delete[] paramsArray;
 283
 284
 285         for (int i = 0; i <= M; i++) {
 286                 pme_c[i] /= NSAMPLES;
 287                 pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
 288                 pme_tpm[i] /= NSAMPLES;
 289                 pme_fpkm[i] /= NSAMPLES;
 290         }
 291 }
 292
 293 int main(int argc, char* argv[]) {
 294         if (argc < 7) {
 295                 printf("Usage: rsem-run-gibbs reference_name imdName statName BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
 296                 exit(-1);
 297         }
 298
 299         strcpy(refName, argv[1]);
 300         strcpy(imdName, argv[2]);
 301         strcpy(statName, argv[3]);
 302
 303         BURNIN = atoi(argv[4]);
 304         NSAMPLES = atoi(argv[5]);
 305         GAP = atoi(argv[6]);
 306
 307         nThreads = 1;
 308         var_opt = false;
 309         quiet = false;
 310
 311         for (int i = 7; i < argc; i++) {
 312                 if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
 313                 if (!strcmp(argv[i], "--var")) var_opt = true;
 314                 if (!strcmp(argv[i], "-q")) quiet = true;
 315         }
 316         verbose = !quiet;
 317
 318         assert(NSAMPLES > 1); // Otherwise, we cannot calculate posterior variance
 319
 320         if (nThreads > NSAMPLES) {
 321                 nThreads = NSAMPLES;
 322                 printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
 323         }
 324
 325         load_data(refName, statName, imdName);
 326
 327         sprintf(modelF, "%s.model", statName);
 328         FILE *fi = fopen(modelF, "r");
 329         general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
 330         assert(fscanf(fi, "%d", &model_type) == 1);
 331         fclose(fi);
 332
 333         mw = new double[M + 1]; // make an extra copy
 334
 335         switch(model_type) {
 336         case 0 : init_model_related<SingleModel>(modelF); break;
 337         case 1 : init_model_related<SingleQModel>(modelF); break;
 338         case 2 : init_model_related<PairedEndModel>(modelF); break;
 339         case 3 : init_model_related<PairedEndQModel>(modelF); break;
 340         }
 341
 342         if (verbose) printf("Gibbs started!\n");
 343
 344         init();
 345         for (int i = 0; i < nThreads; i++) {
 346                 rc = pthread_create(&threads[i], &attr, Gibbs, (void*)(&paramsArray[i]));
 347                 pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0)!");
 348         }
 349         for (int i = 0; i < nThreads; i++) {
 350                 rc = pthread_join(threads[i], NULL);
 351                 pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0)!");
 352         }
 353         release();
 354
 355         if (verbose) printf("Gibbs finished!\n");
 356
 357         writeResultsGibbs(M, refName, imdName, pme_c, pme_fpkm, pme_tpm);
 358
 359         if (var_opt) {
 360                 char varF[STRLEN];
 361
 362                 // Load group info
 363                 int m;
 364                 GroupInfo gi;
 365                 char groupF[STRLEN];
 366                 sprintf(groupF, "%s.grp", refName);
 367                 gi.load(groupF);
 368                 m = gi.getm();
 369
 370                 sprintf(varF, "%s.var", statName);
 371                 FILE *fo = fopen(varF, "w");
 372                 general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
 373                 for (int i = 0; i < m; i++) {
 374                         int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
 375                         for (int j = b; j < e; j++) {
 376                                 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]);
 377                         }
 378                 }
 379                 fclose(fo);
 380         }
 381
 382         delete mw; // delete the copy
 383
 384         return 0;
 385 }