bool updateModel, calcExpectedWeights;
bool genGibbsOut; // generate file for Gibbs sampler
-char refName[STRLEN], imdName[STRLEN], outName[STRLEN];
+char refName[STRLEN], outName[STRLEN];
+char imdName[STRLEN], statName[STRLEN];
char refF[STRLEN], groupF[STRLEN], cntF[STRLEN], tiF[STRLEN];
char mparamsF[STRLEN], bmparamsF[STRLEN];
+char modelF[STRLEN], thetaF[STRLEN];
char inpSamType;
char *pt_fn_list, *pt_chr_list;
if (!readers[i]->locate(curnr)) { fprintf(stderr, "Read indices files do not match!\n"); exit(-1); }
//assert(readers[i]->locate(curnr));
- while (nrLeft > ntLeft && hitvs[i]->getNHits() < nhT) {
+ while (nrLeft > ntLeft && (i == nThreads - 1 || hitvs[i]->getNHits() < nhT)) {
if (!hitvs[i]->read(fin)) { fprintf(stderr, "Cannot read alignments from .dat file!\n"); exit(-1); }
//assert(hitvs[i]->read(fin));
--nrLeft;
template<class ModelType>
void writeResults(ModelType& model, double* counts) {
double denom;
- char modelF[STRLEN], thetaF[STRLEN];
char outF[STRLEN];
FILE *fo;
- sprintf(modelF, "%s.model", outName);
+ sprintf(modelF, "%s.model", statName);
model.write(modelF);
- sprintf(thetaF, "%s.theta", outName);
- fo = fopen(thetaF, "w");
- fprintf(fo, "%d\n", M + 1);
- for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
- fprintf(fo, "%.15g\n", theta[M]);
- fclose(fo);
-
//calculate tau values
double *tau = new double[M + 1];
memset(tau, 0, sizeof(double) * (M + 1));
//Including initialize, algorithm and results saving
template<class ReadType, class HitType, class ModelType>
void EM() {
+ FILE *fo;
+
int ROUND;
double sum;
void *status;
int rc;
+
//initialize boolean variables
updateModel = calcExpectedWeights = false;
if (totNum > 0) fprintf(stderr, "Warning: RSEM reaches %d iterations before meeting the convergence criteria.\n", MAX_ROUND);
- //calculate expected effective lengths for each isoform
- calcExpectedEffectiveLengths<ModelType>(model);
-
- //correct theta vector
- sum = theta[0];
- for (int i = 1; i <= M; i++)
- if (eel[i] < EPSILON) { theta[i] = 0.0; }
- else sum += theta[i];
- if (sum < EPSILON) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
- for (int i = 0; i <= M; i++) theta[i] /= sum;
-
//generate output file used by Gibbs sampler
if (genGibbsOut) {
if (model.getNeedCalcConPrb()) {
model.setNeedCalcConPrb(false);
sprintf(out_for_gibbs_F, "%s.ofg", imdName);
- FILE *fo = fopen(out_for_gibbs_F, "w");
+ fo = fopen(out_for_gibbs_F, "w");
fprintf(fo, "%d %d\n", M, N0);
for (int i = 0; i < nThreads; i++) {
int numN = hitvs[i]->getN();
int to = hitvs[i]->getSAt(j + 1);
int totNum = 0;
- if (ncpvs[i][j] > 0.0) { ++totNum; fprintf(fo, "%d %.15g ", 0, ncpvs[i][j]); }
+ if (ncpvs[i][j] >= EPSILON) { ++totNum; fprintf(fo, "%d %.15g ", 0, ncpvs[i][j]); }
for (int k = fr; k < to; k++) {
HitType &hit = hitvs[i]->getHitAt(k);
if (hit.getConPrb() >= EPSILON) {
fclose(fo);
}
+ sprintf(thetaF, "%s.theta", statName);
+ fo = fopen(thetaF, "w");
+ fprintf(fo, "%d\n", M + 1);
+
+ // output theta'
+ for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
+ fprintf(fo, "%.15g\n", theta[M]);
+
+ //calculate expected effective lengths for each isoform
+ calcExpectedEffectiveLengths<ModelType>(model);
+
+ //correct theta vector
+ sum = theta[0];
+ for (int i = 1; i <= M; i++)
+ if (eel[i] < EPSILON) { theta[i] = 0.0; }
+ else sum += theta[i];
+ if (sum < EPSILON) { fprintf(stderr, "No Expected Effective Length is no less than %.6g?!\n", MINEEL); exit(-1); }
+ for (int i = 0; i <= M; i++) theta[i] /= sum;
+
//calculate expected weights and counts using learned parameters
updateModel = false; calcExpectedWeights = true;
for (int i = 0; i < nThreads; i++) {
/* destroy attribute */
pthread_attr_destroy(&attr);
-
- //for all
+ //convert theta' to theta
double *mw = model.getMW();
sum = 0.0;
for (int i = 0; i <= M; i++) {
assert(sum >= EPSILON);
for (int i = 0; i <= M; i++) theta[i] /= sum;
+ // output theta
+ for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]);
+ fprintf(fo, "%.15g\n", theta[M]);
+
+ fclose(fo);
+
writeResults<ModelType>(model, countvs[0]);
if (genBamF) {
bool quiet = false;
if (argc < 5) {
- printf("Usage : rsem-run-em refName read_type imdName outName [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out]\n\n");
+ printf("Usage : rsem-run-em refName read_type sampleName sampleToken [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out]\n\n");
printf(" refName: reference name\n");
printf(" read_type: 0 single read without quality score; 1 single read with quality score; 2 paired-end read without quality score; 3 paired-end read with quality score.\n");
- printf(" imdName: name for all upstream/downstream user-unseen files. (different files have different suffices)\n");
- printf(" outName: name for all output files. (different files have different suffices)\n");
+ printf(" sampleName: sample's name, including the path\n");
+ printf(" sampleToken: sampleName excludes the path\n");
printf(" -p: number of threads which user wants to use. (default: 1)\n");
printf(" -b: produce bam format output file. (default: off)\n");
printf(" -q: set it quiet\n");
strcpy(refName, argv[1]);
read_type = atoi(argv[2]);
- strcpy(imdName, argv[3]);
- strcpy(outName, argv[4]);
+ strcpy(outName, argv[3]);
+ sprintf(imdName, "%s.temp/%s", argv[3], argv[4]);
+ sprintf(statName, "%s.stat/%s", argv[3], argv[4]);
nThreads = 1;
sprintf(tiF, "%s.ti", refName);
transcripts.readFrom(tiF);
- sprintf(cntF, "%s.cnt", imdName);
+ sprintf(cntF, "%s.cnt", statName);
fin.open(cntF);
if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", cntF); exit(-1); }
fin>>N0>>N1>>N2>>N_tot;
projects / rsem.git / blobdiff