14 #include "SingleModel.h"
15 #include "SingleQModel.h"
16 #include "PairedEndModel.h"
17 #include "PairedEndQModel.h"
20 #include "GroupInfo.h"
28 Item(int sid, double conprb) {
30 this->conprb = conprb;
35 int m, M, N0, N1, nHits;
37 int BURNIN, CHAINLEN, GAP;
38 char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
44 vector<double> theta, pme_theta, eel;
53 CRandomMersenne rg(time(NULL));
55 void load_data(char* reference_name, char* sample_name, char* imdName) {
61 sprintf(refF, "%s.seq", reference_name);
62 refs.loadRefs(refF, 1);
66 sprintf(groupF, "%s.grp", reference_name);
71 sprintf(thetaF, "%s.theta",sample_name);
74 fprintf(stderr, "Cannot open %s!\n", thetaF);
78 if (tmpVal != M + 1) {
79 fprintf(stderr, "Number of transcripts is not consistent in %s and %s!\n", refF, thetaF);
82 theta.clear(); theta.resize(M + 1);
83 for (int i = 0; i <= M; i++) fin>>theta[i];
87 sprintf(ofgF, "%s.ofg", imdName);
90 fprintf(stderr, "Cannot open %s!\n", ofgF);
95 fprintf(stderr, "M in %s is not consistent with %s!\n", ofgF, refF);
100 s.clear(); hits.clear();
102 while (getline(fin, line)) {
103 istringstream strin(line);
107 while (strin>>sid>>conprb) {
108 hits.push_back(Item(sid, conprb));
110 s.push_back(hits.size());
117 if (verbose) { printf("Loading Data is finished!\n"); }
120 // arr should be cumulative!
122 // random number should be in [0, arr[len - 1])
123 // If by chance arr[len - 1] == 0.0, one possibility is to sample uniformly from 0...len-1
124 int sample(vector<double>& arr, int len) {
126 double prb = rg.Random() * arr[len - 1];
131 if (arr[mid] <= prb) l = mid + 1;
135 if (l >= len) { printf("%d %lf %lf\n", len, arr[len - 1], prb); }
149 counts.resize(M + 1, 1); // 1 pseudo count
152 for (int i = 0; i < N1; i++) {
153 fr = s[i]; to = s[i + 1];
156 for (int j = fr; j < to; j++) {
157 arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
158 if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
160 z[i] = hits[fr + sample(arr, len)].sid;
164 totc = N0 + N1 + (M + 1);
166 if (verbose) { printf("Initialization is finished!\n"); }
169 void writeCountVector(FILE* fo) {
170 for (int i = 0; i < M; i++) {
171 fprintf(fo, "%d ", counts[i]);
173 fprintf(fo, "%d\n", counts[M]);
176 void Gibbs(char* imdName) {
180 sprintf(cvsF, "%s.countvectors", imdName);
181 fo = fopen(cvsF, "w");
182 assert(CHAINLEN % GAP == 0);
183 fprintf(fo, "%d %d\n", CHAINLEN / GAP, M + 1);
184 //fprintf(fo, "%d %d\n", CHAINLEN, M + 1);
186 pme_theta.clear(); pme_theta.resize(M + 1, 0.0);
187 for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
189 for (int i = 0; i < N1; i++) {
191 fr = s[i]; to = s[i + 1]; len = to - fr;
193 for (int j = fr; j < to; j++) {
194 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
195 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
197 z[i] = hits[fr + sample(arr, len)].sid;
201 if (ROUND > BURNIN) {
202 if ((ROUND - BURNIN -1) % GAP == 0) writeCountVector(fo);
203 writeCountVector(fo);
204 for (int i = 0; i <= M; i++) pme_theta[i] += counts[i] / totc;
207 if (verbose) { printf("ROUND %d is finished!\n", ROUND); }
211 for (int i = 0; i <= M; i++) pme_theta[i] /= CHAINLEN;
213 if (verbose) { printf("Gibbs is finished!\n"); }
216 template<class ModelType>
217 void calcExpectedEffectiveLengths(ModelType& model) {
219 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = sigma_{j=1}^{i}pdf[i]*(lb+i)
221 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
222 clen = new double[span + 1];
224 for (int i = 1; i <= span; i++) {
225 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
229 eel.resize(M + 1, 0.0);
230 for (int i = 1; i <= M; i++) {
231 int totLen = refs.getRef(i).getTotLen();
232 int fullLen = refs.getRef(i).getFullLen();
233 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
234 int pos2 = max(min(totLen, ub) - lb, 0);
236 if (pos2 == 0) { eel[i] = 0.0; continue; }
238 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
240 if (eel[i] < MINEEL) { eel[i] = 0.0; }
248 template<class ModelType>
249 void writeEstimatedParameters(char* modelF, char* imdName) {
257 calcExpectedEffectiveLengths<ModelType>(model);
259 denom = pme_theta[0];
260 for (int i = 1; i <= M; i++)
261 if (eel[i] < EPSILON) pme_theta[i] = 0.0;
262 else denom += pme_theta[i];
263 if (denom <= 0) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
264 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
267 double *mw = model.getMW();
268 for (int i = 0; i <= M; i++) {
269 pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
270 denom += pme_theta[i];
272 assert(denom >= EPSILON);
273 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
275 //calculate normalized read fraction
276 double *nrf = new double[M + 1];
277 memset(nrf, 0, sizeof(double) * (M + 1));
279 denom = 1.0 - pme_theta[0];
280 if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
281 for (int i = 1; i <= M; i++) nrf[i] = pme_theta[i] / denom;
283 //calculate tau values
284 double *tau = new double[M + 1];
285 memset(tau, 0, sizeof(double) * (M + 1));
288 for (int i = 1; i <= M; i++)
289 if (eel[i] > EPSILON) {
290 tau[i] = pme_theta[i] / eel[i];
293 if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
295 for (int i = 1; i <= M; i++) {
299 //isoform level results
300 sprintf(outF, "%s.iso_res", imdName);
301 fo = fopen(outF, "a");
302 if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
303 for (int i = 1; i <= M; i++)
304 fprintf(fo, "%.15g%c", nrf[i], (i < M ? '\t' : '\n'));
305 for (int i = 1; i <= M; i++)
306 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
310 sprintf(outF, "%s.gene_res", imdName);
311 fo = fopen(outF, "a");
312 if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
313 for (int i = 0; i < m; i++) {
314 double sumN = 0.0; // sum of normalized read fraction
315 int b = gi.spAt(i), e = gi.spAt(i + 1);
316 for (int j = b; j < e; j++) {
319 fprintf(fo, "%.15g%c", sumN, (i < m - 1 ? '\t' : '\n'));
321 for (int i = 0; i < m; i++) {
322 double sumT = 0.0; // sum of tau values
323 int b = gi.spAt(i), e = gi.spAt(i + 1);
324 for (int j = b; j < e; j++) {
327 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
334 if (verbose) { printf("Gibbs based expression values are written!\n"); }
338 int main(int argc, char* argv[]) {
340 printf("Usage: rsem-run-gibbs reference_name sample_name imdName BURNIN CHAINLEN GAP [-q]\n");
344 BURNIN = atoi(argv[4]);
345 CHAINLEN = atoi(argv[5]);
347 load_data(argv[1], argv[2], argv[3]);
350 if (argc > 7 && !strcmp(argv[7], "-q")) {
358 sprintf(modelF, "%s.model", argv[2]);
359 FILE *fi = fopen(modelF, "r");
360 if (fi == NULL) { fprintf(stderr, "Cannot open %s!\n", modelF); exit(-1); }
361 fscanf(fi, "%d", &model_type);
365 case 0 : writeEstimatedParameters<SingleModel>(modelF, argv[3]); break;
366 case 1 : writeEstimatedParameters<SingleQModel>(modelF, argv[3]); break;
367 case 2 : writeEstimatedParameters<PairedEndModel>(modelF, argv[3]); break;
368 case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, argv[3]); break;