#include "PairedEndQModel.h"
#include "Refs.h"
+
#include "GroupInfo.h"
+#include "WriteResults.h"
using namespace std;
struct Params {
- int no, nsamples;
- FILE *fo;
- engine_type *engine;
- double *pme_c, *pve_c; //posterior mean and variance vectors on counts
- double *pme_theta;
+ int no, nsamples;
+ FILE *fo;
+ engine_type *engine;
+ double *pme_c, *pve_c; //posterior mean and variance vectors on counts
+ double *pme_tpm, *pme_fpkm;
+
+ double *pve_c_genes, *pve_c_trans;
};
-
struct Item {
int sid;
double conprb;
int nThreads;
int model_type;
-int m, M;
+int M;
READ_INT_TYPE N0, N1;
HIT_INT_TYPE nHits;
double totc;
int BURNIN, NSAMPLES, GAP;
-char imdName[STRLEN], statName[STRLEN];
-char thetaF[STRLEN], ofgF[STRLEN], groupF[STRLEN], refF[STRLEN], modelF[STRLEN];
+char refName[STRLEN], imdName[STRLEN], statName[STRLEN];
+char thetaF[STRLEN], ofgF[STRLEN], refF[STRLEN], modelF[STRLEN];
char cvsF[STRLEN];
Refs refs;
-GroupInfo gi;
vector<HIT_INT_TYPE> s;
vector<Item> hits;
-vector<double> theta;
+vector<double> eel;
+double *mw;
+vector<int> pseudo_counts;
vector<double> pme_c, pve_c; //global posterior mean and variance vectors on counts
-vector<double> pme_theta, eel;
+vector<double> pme_tpm, pme_fpkm;
-bool var_opt;
bool quiet;
Params *paramsArray;
pthread_attr_t attr;
int rc;
-void load_data(char* reference_name, char* statName, char* imdName) {
+bool hasSeed;
+seedType seed;
+
+int m;
+char groupF[STRLEN];
+GroupInfo gi;
+
+bool alleleS;
+int m_trans;
+GroupInfo gt, ta;
+vector<double> pve_c_genes, pve_c_trans;
+
+void load_data(char* refName, char* statName, char* imdName) {
ifstream fin;
string line;
int tmpVal;
//load reference file
- sprintf(refF, "%s.seq", reference_name);
+ sprintf(refF, "%s.seq", refName);
refs.loadRefs(refF, 1);
M = refs.getM();
- //load groupF
- sprintf(groupF, "%s.grp", reference_name);
- gi.load(groupF);
- m = gi.getm();
-
- //load thetaF
- sprintf(thetaF, "%s.theta",statName);
- fin.open(thetaF);
- general_assert(fin.is_open(), "Cannot open " + cstrtos(thetaF) + "!");
- fin>>tmpVal;
- general_assert(tmpVal == M + 1, "Number of transcripts is not consistent in " + cstrtos(refF) + " and " + cstrtos(thetaF) + "!");
- theta.assign(M + 1, 0);
- for (int i = 0; i <= M; i++) fin>>theta[i];
- fin.close();
-
//load ofgF;
sprintf(ofgF, "%s.ofg", imdName);
fin.open(ofgF);
totc = N0 + N1 + (M + 1);
- if (verbose) { printf("Loading Data is finished!\n"); }
+ if (verbose) { printf("Loading data is finished!\n"); }
+}
+
+void load_group_info(char* refName) {
+ // Load group info
+ sprintf(groupF, "%s.grp", refName);
+ gi.load(groupF);
+ m = gi.getm();
+
+ alleleS = isAlleleSpecific(refName, >, &ta); // if allele-specific
+ m_trans = (alleleS ? ta.getm() : 0);
+
+ if (verbose) { printf("Loading group information is finished!\n"); }
+}
+
+// Load imdName.omit and initialize the pseudo count vector.
+void load_omit_info(const char* imdName) {
+ char omitF[STRLEN];
+ sprintf(omitF, "%s.omit", imdName);
+ FILE *fi = fopen(omitF, "r");
+ pseudo_counts.assign(M + 1, 1);
+ int tid;
+ while (fscanf(fi, "%d", &tid) == 1) pseudo_counts[tid] = 0;
+ fclose(fi);
+}
+
+template<class ModelType>
+void init_model_related(char* modelF) {
+ ModelType model;
+ model.read(modelF);
+
+ calcExpectedEffectiveLengths<ModelType>(M, refs, model, eel);
+ memcpy(mw, model.getMW(), sizeof(double) * (M + 1)); // otherwise, after exiting this procedure, mw becomes undefined
}
// assign threads
paramsArray = new Params[nThreads];
threads = new pthread_t[nThreads];
+ hasSeed ? engineFactory::init(seed) : engineFactory::init();
for (int i = 0; i < nThreads; i++) {
paramsArray[i].no = i;
memset(paramsArray[i].pme_c, 0, sizeof(double) * (M + 1));
paramsArray[i].pve_c = new double[M + 1];
memset(paramsArray[i].pve_c, 0, sizeof(double) * (M + 1));
- paramsArray[i].pme_theta = new double[M + 1];
- memset(paramsArray[i].pme_theta, 0, sizeof(double) * (M + 1));
+ paramsArray[i].pme_tpm = new double[M + 1];
+ memset(paramsArray[i].pme_tpm, 0, sizeof(double) * (M + 1));
+ paramsArray[i].pme_fpkm = new double[M + 1];
+ memset(paramsArray[i].pme_fpkm, 0, sizeof(double) * (M + 1));
+
+ paramsArray[i].pve_c_genes = new double[m];
+ memset(paramsArray[i].pve_c_genes, 0, sizeof(double) * m);
+
+ paramsArray[i].pve_c_trans = NULL;
+ if (alleleS) {
+ paramsArray[i].pve_c_trans = new double[m_trans];
+ memset(paramsArray[i].pve_c_trans, 0, sizeof(double) * m_trans);
+ }
}
+ engineFactory::finish();
/* set thread attribute to be joinable */
pthread_attr_init(&attr);
theta.assign(M + 1, 0);
denom = 0.0;
for (int i = 0; i <= M; i++) {
- theta[i] = gmg();
+ theta[i] = (pseudo_counts[i] > 0 ? gmg() : 0.0);
denom += theta[i];
}
assert(denom > EPSILON);
HIT_INT_TYPE len, fr, to;
Params *params = (Params*)arg;
- vector<double> theta;
- vector<int> z, counts;
+ vector<double> theta, tpm, fpkm;
+ vector<int> z, counts(pseudo_counts);
vector<double> arr;
- uniform01 rg(*params->engine);
+ uniform_01_generator rg(*params->engine, uniform_01_dist());
// generate initial state
sampleTheta(*params->engine, theta);
z.assign(N1, 0);
-
- counts.assign(M + 1, 1); // 1 pseudo count
counts[0] += N0;
for (READ_INT_TYPE i = 0; i < N1; i++) {
if (ROUND > BURNIN) {
if ((ROUND - BURNIN - 1) % GAP == 0) {
writeCountVector(params->fo, counts);
+ for (int i = 0; i <= M; i++) theta[i] = counts[i] / totc;
+ polishTheta(M, theta, eel, mw);
+ calcExpressionValues(M, theta, eel, tpm, fpkm);
for (int i = 0; i <= M; i++) {
- params->pme_c[i] += counts[i] - 1;
- params->pve_c[i] += (counts[i] - 1) * (counts[i] - 1);
- params->pme_theta[i] += counts[i] / totc;
+ params->pme_c[i] += counts[i] - pseudo_counts[i];
+ params->pve_c[i] += double(counts[i] - pseudo_counts[i]) * (counts[i] - pseudo_counts[i]);
+ params->pme_tpm[i] += tpm[i];
+ params->pme_fpkm[i] += fpkm[i];
}
+
+ for (int i = 0; i < m; i++) {
+ int b = gi.spAt(i), e = gi.spAt(i + 1);
+ double count = 0.0;
+ for (int j = b; j < e; j++) count += counts[j] - pseudo_counts[j];
+ params->pve_c_genes[i] += count * count;
+ }
+
+ if (alleleS)
+ for (int i = 0; i < m_trans; i++) {
+ int b = ta.spAt(i), e = ta.spAt(i + 1);
+ double count = 0.0;
+ for (int j = b; j < e; j++) count += counts[j] - pseudo_counts[j];
+ params->pve_c_trans[i] += count * count;
+ }
}
}
pme_c.assign(M + 1, 0);
pve_c.assign(M + 1, 0);
- pme_theta.assign(M + 1, 0);
+ pme_tpm.assign(M + 1, 0);
+ pme_fpkm.assign(M + 1, 0);
+
+ pve_c_genes.assign(m, 0);
+ pve_c_trans.clear();
+ if (alleleS) pve_c_trans.assign(m_trans, 0);
+
for (int i = 0; i < nThreads; i++) {
fclose(paramsArray[i].fo);
delete paramsArray[i].engine;
for (int j = 0; j <= M; j++) {
pme_c[j] += paramsArray[i].pme_c[j];
pve_c[j] += paramsArray[i].pve_c[j];
- pme_theta[j] += paramsArray[i].pme_theta[j];
+ pme_tpm[j] += paramsArray[i].pme_tpm[j];
+ pme_fpkm[j] += paramsArray[i].pme_fpkm[j];
}
+
+ for (int j = 0; j < m; j++)
+ pve_c_genes[j] += paramsArray[i].pve_c_genes[j];
+
+ if (alleleS)
+ for (int j = 0; j < m_trans; j++)
+ pve_c_trans[j] += paramsArray[i].pve_c_trans[j];
+
delete[] paramsArray[i].pme_c;
delete[] paramsArray[i].pve_c;
- delete[] paramsArray[i].pme_theta;
+ delete[] paramsArray[i].pme_tpm;
+ delete[] paramsArray[i].pme_fpkm;
+
+ delete[] paramsArray[i].pve_c_genes;
+ if (alleleS) delete[] paramsArray[i].pve_c_trans;
}
delete[] paramsArray;
-
for (int i = 0; i <= M; i++) {
pme_c[i] /= NSAMPLES;
- pve_c[i] = (pve_c[i] - NSAMPLES * pme_c[i] * pme_c[i]) / (NSAMPLES - 1);
- pme_theta[i] /= NSAMPLES;
- }
-}
-
-template<class ModelType>
-void calcExpectedEffectiveLengths(ModelType& model) {
- int lb, ub, span;
- double *pdf = NULL, *cdf = NULL, *clen = NULL; // clen[i] = \sigma_{j=1}^{i}pdf[i]*(lb+i)
-
- model.getGLD().copyTo(pdf, cdf, lb, ub, span);
- clen = new double[span + 1];
- clen[0] = 0.0;
- for (int i = 1; i <= span; i++) {
- clen[i] = clen[i - 1] + pdf[i] * (lb + i);
+ pve_c[i] = (pve_c[i] - double(NSAMPLES) * pme_c[i] * pme_c[i]) / double(NSAMPLES - 1);
+ if (pve_c[i] < 0.0) pve_c[i] = 0.0;
+ pme_tpm[i] /= NSAMPLES;
+ pme_fpkm[i] /= NSAMPLES;
}
- eel.assign(M + 1, 0.0);
- for (int i = 1; i <= M; i++) {
- int totLen = refs.getRef(i).getTotLen();
- int fullLen = refs.getRef(i).getFullLen();
- int pos1 = max(min(totLen - fullLen + 1, ub) - lb, 0);
- int pos2 = max(min(totLen, ub) - lb, 0);
-
- if (pos2 == 0) { eel[i] = 0.0; continue; }
-
- eel[i] = fullLen * cdf[pos1] + ((cdf[pos2] - cdf[pos1]) * (totLen + 1) - (clen[pos2] - clen[pos1]));
- assert(eel[i] >= 0);
- if (eel[i] < MINEEL) { eel[i] = 0.0; }
- }
-
- delete[] pdf;
- delete[] cdf;
- delete[] clen;
-}
-
-template<class ModelType>
-void writeEstimatedParameters(char* modelF, char* imdName) {
- ModelType model;
- double denom;
- char outF[STRLEN];
- FILE *fo;
-
- model.read(modelF);
-
- calcExpectedEffectiveLengths<ModelType>(model);
-
- denom = pme_theta[0];
- for (int i = 1; i <= M; i++)
- if (eel[i] < EPSILON) pme_theta[i] = 0.0;
- else denom += pme_theta[i];
-
- general_assert(denom >= EPSILON, "No Expected Effective Length is no less than " + ftos(MINEEL, 6) + "?!");
-
- for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
-
- denom = 0.0;
- double *mw = model.getMW();
- for (int i = 0; i <= M; i++) {
- pme_theta[i] = (mw[i] < EPSILON ? 0.0 : pme_theta[i] / mw[i]);
- denom += pme_theta[i];
- }
- assert(denom >= EPSILON);
- for (int i = 0; i <= M; i++) pme_theta[i] /= denom;
-
- //calculate tau values
- double *tau = new double[M + 1];
- memset(tau, 0, sizeof(double) * (M + 1));
-
- denom = 0.0;
- for (int i = 1; i <= M; i++)
- if (eel[i] > EPSILON) {
- tau[i] = pme_theta[i] / eel[i];
- denom += tau[i];
- }
-
- general_assert(denom >= EPSILON, "No alignable reads?!");
-
- for (int i = 1; i <= M; i++) {
- tau[i] /= denom;
- }
-
- //isoform level results
- sprintf(outF, "%s.iso_res", imdName);
- fo = fopen(outF, "a");
- general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
-
- for (int i = 1; i <= M; i++)
- fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
- for (int i = 1; i <= M; i++)
- fprintf(fo, "%.15g%c", tau[i], (i < M ? '\t' : '\n'));
-
- fclose(fo);
-
- //gene level results
- sprintf(outF, "%s.gene_res", imdName);
- fo = fopen(outF, "a");
- general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
-
- for (int i = 0; i < m; i++) {
- double sumC = 0.0; // sum of pme counts
- int b = gi.spAt(i), e = gi.spAt(i + 1);
- for (int j = b; j < e; j++) {
- sumC += pme_c[j];
- }
- fprintf(fo, "%.15g%c", sumC, (i < m - 1 ? '\t' : '\n'));
- }
for (int i = 0; i < m; i++) {
- double sumT = 0.0; // sum of tau values
- int b = gi.spAt(i), e = gi.spAt(i + 1);
- for (int j = b; j < e; j++) {
- sumT += tau[j];
- }
- fprintf(fo, "%.15g%c", sumT, (i < m - 1 ? '\t' : '\n'));
+ int b = gi.spAt(i), e = gi.spAt(i + 1);
+ double pme_c_gene = 0.0;
+ for (int j = b; j < e; j++) pme_c_gene += pme_c[j];
+ pve_c_genes[i] = (pve_c_genes[i] - double(NSAMPLES) * pme_c_gene * pme_c_gene) / double(NSAMPLES - 1);
+ if (pve_c_genes[i] < 0.0) pve_c_genes[i] = 0.0;
}
- fclose(fo);
- delete[] tau;
-
- if (verbose) { printf("Gibbs based expression values are written!\n"); }
+ if (alleleS)
+ for (int i = 0; i < m_trans; i++) {
+ int b = ta.spAt(i), e = ta.spAt(i + 1);
+ double pme_c_tran = 0.0;
+ for (int j = b; j < e; j++) pme_c_tran += pme_c[j];
+ pve_c_trans[i] = (pve_c_trans[i] - double(NSAMPLES) * pme_c_tran * pme_c_tran) / double(NSAMPLES - 1);
+ if (pve_c_trans[i] < 0.0) pve_c_trans[i] = 0.0;
+ }
}
int main(int argc, char* argv[]) {
if (argc < 7) {
- printf("Usage: rsem-run-gibbs reference_name imdName statName BURNIN NSAMPLES GAP [-p #Threads] [--var] [-q]\n");
+ printf("Usage: rsem-run-gibbs reference_name imdName statName BURNIN NSAMPLES GAP [-p #Threads] [--seed seed] [-q]\n");
exit(-1);
}
+ strcpy(refName, argv[1]);
strcpy(imdName, argv[2]);
strcpy(statName, argv[3]);
NSAMPLES = atoi(argv[5]);
GAP = atoi(argv[6]);
- load_data(argv[1], statName, imdName);
-
nThreads = 1;
- var_opt = false;
+ hasSeed = false;
quiet = false;
for (int i = 7; i < argc; i++) {
if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
- if (!strcmp(argv[i], "--var")) var_opt = true;
+ if (!strcmp(argv[i], "--seed")) {
+ hasSeed = true;
+ int len = strlen(argv[i + 1]);
+ seed = 0;
+ for (int k = 0; k < len; k++) seed = seed * 10 + (argv[i + 1][k] - '0');
+ }
if (!strcmp(argv[i], "-q")) quiet = true;
}
verbose = !quiet;
printf("Warning: Number of samples is less than number of threads! Change the number of threads to %d!\n", nThreads);
}
+ load_data(refName, statName, imdName);
+ load_group_info(refName);
+ load_omit_info(imdName);
+
+ sprintf(modelF, "%s.model", statName);
+ FILE *fi = fopen(modelF, "r");
+ general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
+ assert(fscanf(fi, "%d", &model_type) == 1);
+ fclose(fi);
+
+ mw = new double[M + 1]; // make an extra copy
+
+ switch(model_type) {
+ case 0 : init_model_related<SingleModel>(modelF); break;
+ case 1 : init_model_related<SingleQModel>(modelF); break;
+ case 2 : init_model_related<PairedEndModel>(modelF); break;
+ case 3 : init_model_related<PairedEndQModel>(modelF); break;
+ }
+
if (verbose) printf("Gibbs started!\n");
init();
release();
if (verbose) printf("Gibbs finished!\n");
+
+ writeResultsGibbs(M, m, m_trans, gi, gt, ta, alleleS, imdName, pme_c, pme_fpkm, pme_tpm, pve_c, pve_c_genes, pve_c_trans);
- sprintf(modelF, "%s.model", statName);
- FILE *fi = fopen(modelF, "r");
- general_assert(fi != NULL, "Cannot open " + cstrtos(modelF) + "!");
- assert(fscanf(fi, "%d", &model_type) == 1);
- fclose(fi);
-
- switch(model_type) {
- case 0 : writeEstimatedParameters<SingleModel>(modelF, imdName); break;
- case 1 : writeEstimatedParameters<SingleQModel>(modelF, imdName); break;
- case 2 : writeEstimatedParameters<PairedEndModel>(modelF, imdName); break;
- case 3 : writeEstimatedParameters<PairedEndQModel>(modelF, imdName); break;
- }
-
- if (var_opt) {
- char varF[STRLEN];
-
- sprintf(varF, "%s.var", statName);
- FILE *fo = fopen(varF, "w");
- general_assert(fo != NULL, "Cannot open " + cstrtos(varF) + "!");
- for (int i = 0; i < m; i++) {
- int b = gi.spAt(i), e = gi.spAt(i + 1), number_of_isoforms = e - b;
- for (int j = b; j < e; j++) {
- 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]);
- }
- }
- fclose(fo);
- }
+ delete mw; // delete the copy
return 0;
}
projects / rsem.git / blobdiff