13 #include "SingleModel.h"
14 #include "SingleQModel.h"
15 #include "PairedEndModel.h"
16 #include "PairedEndQModel.h"
19 #include "GroupInfo.h"
27 Item(int sid, double conprb) {
29 this->conprb = conprb;
34 int m, M, N0, N1, nHits;
36 int BURNIN, CHAINLEN, GAP;
37 char imdName[STRLEN], statName[STRLEN];
38 char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
44 vector<double> theta, pme_theta, pme_c, eel;
54 void load_data(char* reference_name, char* statName, char* imdName) {
60 sprintf(refF, "%s.seq", reference_name);
61 refs.loadRefs(refF, 1);
65 sprintf(groupF, "%s.grp", reference_name);
70 sprintf(thetaF, "%s.theta",statName);
73 fprintf(stderr, "Cannot open %s!\n", thetaF);
77 if (tmpVal != M + 1) {
78 fprintf(stderr, "Number of transcripts is not consistent in %s and %s!\n", refF, thetaF);
81 theta.clear(); theta.resize(M + 1);
82 for (int i = 0; i <= M; i++) fin>>theta[i];
86 sprintf(ofgF, "%s.ofg", imdName);
89 fprintf(stderr, "Cannot open %s!\n", ofgF);
94 fprintf(stderr, "M in %s is not consistent with %s!\n", ofgF, refF);
99 s.clear(); hits.clear();
101 while (getline(fin, line)) {
102 istringstream strin(line);
106 while (strin>>sid>>conprb) {
107 hits.push_back(Item(sid, conprb));
109 s.push_back(hits.size());
116 if (verbose) { printf("Loading Data is finished!\n"); }
127 counts.resize(M + 1, 1); // 1 pseudo count
130 for (int i = 0; i < N1; i++) {
131 fr = s[i]; to = s[i + 1];
134 for (int j = fr; j < to; j++) {
135 arr[j - fr] = theta[hits[j].sid] * hits[j].conprb;
136 if (j > fr) arr[j - fr] += arr[j - fr - 1]; // cumulative
138 z[i] = hits[fr + sample(arr, len)].sid;
142 totc = N0 + N1 + (M + 1);
144 if (verbose) { printf("Initialization is finished!\n"); }
147 void writeCountVector(FILE* fo) {
148 for (int i = 0; i < M; i++) {
149 fprintf(fo, "%d ", counts[i]);
151 fprintf(fo, "%d\n", counts[M]);
154 void Gibbs(char* imdName) {
158 sprintf(cvsF, "%s.countvectors", imdName);
159 fo = fopen(cvsF, "w");
160 assert(CHAINLEN % GAP == 0);
161 fprintf(fo, "%d %d\n", CHAINLEN / GAP, M + 1);
162 //fprintf(fo, "%d %d\n", CHAINLEN, M + 1);
164 pme_c.clear(); pme_c.resize(M + 1, 0.0);
165 pme_theta.clear(); pme_theta.resize(M + 1, 0.0);
166 for (int ROUND = 1; ROUND <= BURNIN + CHAINLEN; ROUND++) {
168 for (int i = 0; i < N1; i++) {
170 fr = s[i]; to = s[i + 1]; len = to - fr;
172 for (int j = fr; j < to; j++) {
173 arr[j - fr] = counts[hits[j].sid] * hits[j].conprb;
174 if (j > fr) arr[j - fr] += arr[j - fr - 1]; //cumulative
176 z[i] = hits[fr + sample(arr, len)].sid;
180 if (ROUND > BURNIN) {
181 if ((ROUND - BURNIN - 1) % GAP == 0) writeCountVector(fo);
182 for (int i = 0; i <= M; i++) {
183 pme_c[i] += counts[i] - 1;
184 pme_theta[i] += counts[i] / totc;
188 if (verbose) { printf("ROUND %d is finished!\n", ROUND); }
192 for (int i = 0; i <= M; i++) {
193 pme_c[i] /= CHAINLEN;
194 pme_theta[i] /= CHAINLEN;
197 if (verbose) { printf("Gibbs is finished!\n"); }
200 template<class ModelType>
201 void calcExpectedEffectiveLengths(ModelType& model) {
203 double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = sigma_{j=1}^{i}pdf[i]*(lb+i)
205 model.getGLD().copyTo(pdf, cdf, lb, ub, span);
206 clen = new double[span + 1];
208 for (int i = 1; i <= span; i++) {
209 clen[i] = clen[i - 1] + pdf[i] * (lb + i);
213 eel.resize(M + 1, 0.0);
214 for (int i = 1; i <= M; i++) {
215 int totLen = refs.getRef(i).getTotLen();
216 int fullLen = refs.getRef(i).getFullLen();
217 int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
218 int pos2 = max(min(totLen, ub) - lb, 0);
220 if (pos2 == 0) { eel[i] = 0.0; continue; }
222 eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
224 if (eel[i] < MINEEL) { eel[i] = 0.0; }
232 template<class ModelType>
233 void writeEstimatedParameters(char* modelF, char* imdName) {
241 calcExpectedEffectiveLengths<ModelType>(model);
243 denom = pme_theta[0];
244 for (int i = 1; i <= M; i++)
245 if (eel[i] < EPSILON) pme_theta[i] = 0.0;
246 else denom += pme_theta[i];
247 if (denom <= 0) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
248 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
251 double *mw = model.getMW();
252 for (int i = 0; i <= M; i++) {
253 pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
254 denom += pme_theta[i];
256 assert(denom >= EPSILON);
257 for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
259 //calculate tau values
260 double *tau = new double[M + 1];
261 memset(tau, 0, sizeof(double) * (M + 1));
264 for (int i = 1; i <= M; i++)
265 if (eel[i] > EPSILON) {
266 tau[i] = pme_theta[i] / eel[i];
269 if (denom <= 0) { fprintf(stderr, "No alignable reads?!\n"); exit(-1); }
271 for (int i = 1; i <= M; i++) {
275 //isoform level results
276 sprintf(outF, "%s.iso_res", imdName);
277 fo = fopen(outF, "a");
278 if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
279 for (int i = 1; i <= M; i++)
280 fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
281 for (int i = 1; i <= M; i++)
282 fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
286 sprintf(outF, "%s.gene_res", imdName);
287 fo = fopen(outF, "a");
288 if (fo == NULL) { fprintf(stderr, "Cannot open %s!\n", outF); exit(-1); }
289 for (int i = 0; i < m; i++) {
290 double sumC = 0.0; // sum of pme counts
291 int b = gi.spAt(i), e = gi.spAt(i + 1);
292 for (int j = b; j < e; j++) {
295 fprintf(fo, "%.15g%c", sumC, (i < m - 1 ? '\t' : '\n'));
297 for (int i = 0; i < m; i++) {
298 double sumT = 0.0; // sum of tau values
299 int b = gi.spAt(i), e = gi.spAt(i + 1);
300 for (int j = b; j < e; j++) {
303 fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
309 if (verbose) { printf("Gibbs based expression values are written!\n"); }
313 int main(int argc, char* argv[]) {
315 printf("Usage: rsem-run-gibbs reference_name sample_name sampleToken BURNIN CHAINLEN GAP [-q]\n");
319 BURNIN = atoi(argv[4]);
320 CHAINLEN = atoi(argv[5]);
322 sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
323 sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
324 load_data(argv[1], statName, imdName);
327 if (argc > 7 && !strcmp(argv[7], "-q")) {
335 sprintf(modelF, "%s.model", statName);
336 FILE *fi = fopen(modelF, "r");
337 if (fi == NULL) { fprintf(stderr, "Cannot open %s!\n", modelF); exit(-1); }
338 fscanf(fi, "%d", &model_type);
342 case 0 : writeEstimatedParameters<SingleModel>(modelF, imdName); break;
343 case 1 : writeEstimatedParameters<SingleQModel>(modelF, imdName); break;
344 case 2 : writeEstimatedParameters<PairedEndModel>(modelF, imdName); break;
345 case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;