#include "Refs.h"
#include "GroupInfo.h"
+#include "WriteResults.h"
#include "Buffer.h"
+
using namespace std;
struct Params {
int no;
FILE *fi;
engine_type *engine;
- double *mw;
+ const double *mw;
+};
+
+struct CIParams {
+ int no;
+ int start_gene_id, end_gene_id;
};
struct CIType {
CIType() { lb = ub = 0.0; }
};
-struct CIParams {
- int no;
- int start_gene_id, end_gene_id;
-};
-
int model_type;
int nMB;
double confidence;
int nCV, nSpC, nSamples; // nCV: number of count vectors; nSpC: number of theta vectors sampled per count vector; nSamples: nCV * nSpC
int nThreads;
-int cvlen;
+
+float *l_bars;
char cvsF[STRLEN], tmpF[STRLEN], command[STRLEN];
-CIType *iso_tau, *gene_tau;
+CIType *tpm, *fpkm;
+CIType *iso_tpm = NULL, *iso_fpkm = NULL;
+CIType *gene_tpm, *gene_fpkm;
int M, m;
Refs refs;
GroupInfo gi;
-char imdName[STRLEN], statName[STRLEN];
+char refName[STRLEN], imdName[STRLEN], statName[STRLEN];
char modelF[STRLEN], groupF[STRLEN], refF[STRLEN];
+bool alleleS;
+int m_trans;
+GroupInfo ta;
+
vector<double> eel; //expected effective lengths
Buffer *buffer;
Params *paramsArray;
pthread_t *threads;
pthread_attr_t attr;
-void *status;
int rc;
-CIParams *ciParamsArray;
+bool hasSeed;
+seedType seed;
-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);
- }
-
- 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;
-}
+CIParams *ciParamsArray;
void* sample_theta_from_c(void* arg) {
-
int *cvec;
double *theta;
+ float *tpm;
gamma_dist **gammas;
gamma_generator **rgs;
Params *params = (Params*)arg;
FILE *fi = params->fi;
- double *mw = params->mw;
-
- cvec = new int[cvlen];
- theta = new double[cvlen];
- gammas = new gamma_dist*[cvlen];
- rgs = new gamma_generator*[cvlen];
+ const double *mw = params->mw;
- float **vecs = new float*[nSpC];
- for (int i = 0; i < nSpC; i++) vecs[i] = new float[cvlen];
+ cvec = new int[M + 1];
+ theta = new double[M + 1];
+ gammas = new gamma_dist*[M + 1];
+ rgs = new gamma_generator*[M + 1];
+ tpm = new float[M + 1];
+ float l_bar; // the mean transcript length over the sample
int cnt = 0;
while (fscanf(fi, "%d", &cvec[0]) == 1) {
- for (int j = 1; j < cvlen; j++) assert(fscanf(fi, "%d", &cvec[j]) == 1);
+ for (int j = 1; j <= M; j++) assert(fscanf(fi, "%d", &cvec[j]) == 1);
++cnt;
- for (int j = 0; j < cvlen; j++) {
+ for (int j = 0; j <= M; j++) {
gammas[j] = new gamma_dist(cvec[j]);
rgs[j] = new gamma_generator(*(params->engine), *gammas[j]);
}
for (int i = 0; i < nSpC; i++) {
double sum = 0.0;
- for (int j = 0; j < cvlen; j++) {
- theta[j] = ((j == 0 || eel[j] >= EPSILON) ? (*rgs[j])() : 0.0);
+ for (int j = 0; j <= M; j++) {
+ theta[j] = ((j == 0 || (eel[j] >= EPSILON && mw[j] >= EPSILON)) ? (*rgs[j])() / mw[j] : 0.0);
sum += theta[j];
}
assert(sum >= EPSILON);
- for (int j = 0; j < cvlen; j++) theta[j] /= sum;
+ for (int j = 0; j <= M; j++) theta[j] /= sum;
sum = 0.0;
- for (int j = 0; j < cvlen; j++) {
- theta[j] = (mw[j] < EPSILON ? 0.0 : theta[j] / mw[j]);
- sum += theta[j];
- }
- assert(sum >= EPSILON);
- for (int j = 0; j < cvlen; j++) theta[j] /= sum;
-
-
- sum = 0.0;
- vecs[i][0] = theta[0];
- for (int j = 1; j < cvlen; j++)
+ tpm[0] = 0.0;
+ for (int j = 1; j <= M; j++)
if (eel[j] >= EPSILON) {
- vecs[i][j] = theta[j] / eel[j];
- sum += vecs[i][j];
+ tpm[j] = theta[j] / eel[j];
+ sum += tpm[j];
}
else assert(theta[j] < EPSILON);
-
assert(sum >= EPSILON);
- for (int j = 1; j < cvlen; j++) vecs[i][j] /= sum;
+ l_bar = 0.0; // store mean effective length of the sample
+ for (int j = 1; j <= M; j++) { tpm[j] /= sum; l_bar += tpm[j] * eel[j]; tpm[j] *= 1e6; }
+ buffer->write(l_bar, tpm + 1); // ommit the first element in tpm
}
- buffer->write(nSpC, vecs);
-
- for (int j = 0; j < cvlen; j++) {
+ for (int j = 0; j <= M; j++) {
delete gammas[j];
delete rgs[j];
}
delete[] theta;
delete[] gammas;
delete[] rgs;
-
- for (int i = 0; i < nSpC; i++) delete[] vecs[i];
- delete[] vecs;
+ delete[] tpm;
return NULL;
}
void sample_theta_vectors_from_count_vectors() {
ModelType model;
model.read(modelF);
- calcExpectedEffectiveLengths<ModelType>(model);
-
+ calcExpectedEffectiveLengths<ModelType>(M, refs, model, eel);
int num_threads = min(nThreads, nCV);
- buffer = new Buffer(nMB, nSamples, cvlen, tmpF);
+ buffer = new Buffer(nMB, nSamples, M, l_bars, tmpF);
paramsArray = new Params[num_threads];
threads = new pthread_t[num_threads];
char inpF[STRLEN];
+ hasSeed ? engineFactory::init(seed) : engineFactory::init();
for (int i = 0; i < num_threads; i++) {
paramsArray[i].no = i;
sprintf(inpF, "%s%d", cvsF, i);
paramsArray[i].engine = engineFactory::new_engine();
paramsArray[i].mw = model.getMW();
}
+ engineFactory::finish();
/* set thread attribute to be joinable */
pthread_attr_init(&attr);
pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) in sample_theta_vectors_from_count_vectors!");
}
for (int i = 0; i < num_threads; i++) {
- rc = pthread_join(threads[i], &status);
+ rc = pthread_join(threads[i], NULL);
pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in sample_theta_vectors_from_count_vectors!");
}
}
void* calcCI_batch(void* arg) {
- float *itsamples, *gtsamples;
+ float *tsamples, *fsamples;
+ float *itsamples = NULL, *ifsamples = NULL, *gtsamples, *gfsamples;
ifstream fin;
CIParams *ciParams = (CIParams*)arg;
+ int curtid, curaid, tid;
- itsamples = new float[nSamples];
+ tsamples = new float[nSamples];
+ fsamples = new float[nSamples];
+ if (alleleS) {
+ itsamples = new float[nSamples];
+ ifsamples = new float[nSamples];
+ }
gtsamples = new float[nSamples];
+ gfsamples = new float[nSamples];
fin.open(tmpF, ios::binary);
- streampos pos = streampos(gi.spAt(ciParams->start_gene_id)) * nSamples * FLOATSIZE;
+ // minus 1 here for that theta0 is not written!
+ streampos pos = streampos(gi.spAt(ciParams->start_gene_id) - 1) * nSamples * FLOATSIZE;
fin.seekg(pos, ios::beg);
int cnt = 0;
+ if (alleleS) {
+ curtid = curaid = -1;
+ memset(itsamples, 0, FLOATSIZE * nSamples);
+ memset(ifsamples, 0, FLOATSIZE * nSamples);
+ }
for (int i = ciParams->start_gene_id; i < ciParams->end_gene_id; i++) {
int b = gi.spAt(i), e = gi.spAt(i + 1);
memset(gtsamples, 0, FLOATSIZE * nSamples);
+ memset(gfsamples, 0, FLOATSIZE * nSamples);
for (int j = b; j < e; j++) {
+ if (alleleS) {
+ tid = ta.gidAt(j);
+ if (curtid != tid) {
+ if (curtid >= 0) {
+ if (j - curaid > 1) {
+ calcCI(nSamples, itsamples, iso_tpm[curtid].lb, iso_tpm[curtid].ub);
+ calcCI(nSamples, ifsamples, iso_fpkm[curtid].lb, iso_fpkm[curtid].ub);
+ }
+ else {
+ iso_tpm[curtid] = tpm[curaid];
+ iso_fpkm[curtid] = fpkm[curaid];
+ }
+ }
+ curtid = tid;
+ curaid = j;
+ }
+ }
+
for (int k = 0; k < nSamples; k++) {
- fin.read((char*)(&itsamples[k]), FLOATSIZE);
- gtsamples[k] += itsamples[k];
+ fin.read((char*)(&tsamples[k]), FLOATSIZE);
+ fsamples[k] = 1e3 / l_bars[k] * tsamples[k];
+ if (alleleS) {
+ itsamples[k] += tsamples[k];
+ ifsamples[k] += fsamples[k];
+ }
+ gtsamples[k] += tsamples[k];
+ gfsamples[k] += fsamples[k];
}
- calcCI(nSamples, itsamples, iso_tau[j].lb, iso_tau[j].ub);
+ calcCI(nSamples, tsamples, tpm[j].lb, tpm[j].ub);
+ calcCI(nSamples, fsamples, fpkm[j].lb, fpkm[j].ub);
+ }
+
+ if (e - b > 1) {
+ calcCI(nSamples, gtsamples, gene_tpm[i].lb, gene_tpm[i].ub);
+ calcCI(nSamples, gfsamples, gene_fpkm[i].lb, gene_fpkm[i].ub);
+ }
+ else {
+ gene_tpm[i] = tpm[b];
+ gene_fpkm[i] = fpkm[b];
}
- calcCI(nSamples, gtsamples, gene_tau[i].lb, gene_tau[i].ub);
++cnt;
if (verbose && cnt % 1000 == 0) { printf("In thread %d, %d genes are processed for CI calculation!\n", ciParams->no, cnt); }
}
-
fin.close();
- delete[] itsamples;
+ if (alleleS && (curtid >= 0)) {
+ if (gi.spAt(ciParams->end_gene_id) - curaid > 1) {
+ calcCI(nSamples, itsamples, iso_tpm[curtid].lb, iso_tpm[curtid].ub);
+ calcCI(nSamples, ifsamples, iso_fpkm[curtid].lb, iso_fpkm[curtid].ub);
+ }
+ else {
+ iso_tpm[curtid] = tpm[curaid];
+ iso_fpkm[curtid] = fpkm[curaid];
+ }
+ }
+
+ delete[] tsamples;
+ delete[] fsamples;
+ if (alleleS) {
+ delete[] itsamples;
+ delete[] ifsamples;
+ }
delete[] gtsamples;
+ delete[] gfsamples;
return NULL;
}
char outF[STRLEN];
int num_threads = nThreads;
- iso_tau = new CIType[M + 1];
- gene_tau = new CIType[m];
+ tpm = new CIType[M + 1];
+ fpkm = new CIType[M + 1];
+ if (alleleS) {
+ iso_tpm = new CIType[m_trans];
+ iso_fpkm = new CIType[m_trans];
+ }
+ gene_tpm = new CIType[m];
+ gene_fpkm = new CIType[m];
assert(M > 0);
int quotient = M / num_threads;
pthread_assert(rc, "pthread_create", "Cannot create thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
}
for (int i = 0; i < num_threads; i++) {
- rc = pthread_join(threads[i], &status);
+ rc = pthread_join(threads[i], NULL);
pthread_assert(rc, "pthread_join", "Cannot join thread " + itos(i) + " (numbered from 0) in calculate_credibility_intervals!");
}
delete[] ciParamsArray;
- //isoform level results
- sprintf(outF, "%s.iso_res", imdName);
+ alleleS ? sprintf(outF, "%s.allele_res", imdName) : sprintf(outF, "%s.iso_res", imdName);
fo = fopen(outF, "a");
for (int i = 1; i <= M; i++)
- fprintf(fo, "%.6g%c", iso_tau[i].lb, (i < M ? '\t' : '\n'));
+ fprintf(fo, "%.6g%c", tpm[i].lb, (i < M ? '\t' : '\n'));
+ for (int i = 1; i <= M; i++)
+ fprintf(fo, "%.6g%c", tpm[i].ub, (i < M ? '\t' : '\n'));
for (int i = 1; i <= M; i++)
- fprintf(fo, "%.6g%c", iso_tau[i].ub, (i < M ? '\t' : '\n'));
+ fprintf(fo, "%.6g%c", fpkm[i].lb, (i < M ? '\t' : '\n'));
+ for (int i = 1; i <= M; i++)
+ fprintf(fo, "%.6g%c", fpkm[i].ub, (i < M ? '\t' : '\n'));
fclose(fo);
+ if (alleleS) {
+ //isoform level results
+ sprintf(outF, "%s.iso_res", imdName);
+ fo = fopen(outF, "a");
+ for (int i = 0; i < m_trans; i++)
+ fprintf(fo, "%.6g%c", iso_tpm[i].lb, (i < m_trans - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m_trans; i++)
+ fprintf(fo, "%.6g%c", iso_tpm[i].ub, (i < m_trans - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m_trans; i++)
+ fprintf(fo, "%.6g%c", iso_fpkm[i].lb, (i < m_trans - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m_trans; i++)
+ fprintf(fo, "%.6g%c", iso_fpkm[i].ub, (i < m_trans - 1 ? '\t' : '\n'));
+ fclose(fo);
+ }
+
//gene level results
sprintf(outF, "%s.gene_res", imdName);
fo = fopen(outF, "a");
for (int i = 0; i < m; i++)
- fprintf(fo, "%.6g%c", gene_tau[i].lb, (i < m - 1 ? '\t' : '\n'));
+ fprintf(fo, "%.6g%c", gene_tpm[i].lb, (i < m - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m; i++)
+ fprintf(fo, "%.6g%c", gene_tpm[i].ub, (i < m - 1 ? '\t' : '\n'));
+ for (int i = 0; i < m; i++)
+ fprintf(fo, "%.6g%c", gene_fpkm[i].lb, (i < m - 1 ? '\t' : '\n'));
for (int i = 0; i < m; i++)
- fprintf(fo, "%.6g%c", gene_tau[i].ub, (i < m - 1 ? '\t' : '\n'));
+ fprintf(fo, "%.6g%c", gene_fpkm[i].ub, (i < m - 1 ? '\t' : '\n'));
fclose(fo);
- delete[] iso_tau;
- delete[] gene_tau;
+ delete[] tpm;
+ delete[] fpkm;
+ if (alleleS) {
+ delete[] iso_tpm;
+ delete[] iso_fpkm;
+ }
+ delete[] gene_tpm;
+ delete[] gene_fpkm;
if (verbose) { printf("All credibility intervals are calculated!\n"); }
}
int main(int argc, char* argv[]) {
if (argc < 8) {
- printf("Usage: rsem-calculate-credibility-intervals reference_name sample_name sampleToken confidence nCV nSpC nMB [-p #Threads] [-q]\n");
+ printf("Usage: rsem-calculate-credibility-intervals reference_name imdName statName confidence nCV nSpC nMB [-p #Threads] [--seed seed] [-q]\n");
exit(-1);
}
+ strcpy(refName, argv[1]);
+ strcpy(imdName, argv[2]);
+ strcpy(statName, argv[3]);
+
confidence = atof(argv[4]);
nCV = atoi(argv[5]);
nSpC = atoi(argv[6]);
nThreads = 1;
quiet = false;
+ hasSeed = false;
for (int i = 8; i < argc; i++) {
if (!strcmp(argv[i], "-p")) nThreads = atoi(argv[i + 1]);
+ 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;
- sprintf(refF, "%s.seq", argv[1]);
+ sprintf(refF, "%s.seq", refName);
refs.loadRefs(refF, 1);
M = refs.getM();
- sprintf(groupF, "%s.grp", argv[1]);
+
+ sprintf(groupF, "%s.grp", refName);
gi.load(groupF);
m = gi.getm();
+ // allele-specific
+ alleleS = isAlleleSpecific(refName, NULL, &ta);
+ if (alleleS) m_trans = ta.getm();
+
nSamples = nCV * nSpC;
- cvlen = M + 1;
- assert(nSamples > 0 && cvlen > 1); // for Buffter.h: (bufsize_type)nSamples
+ assert(nSamples > 0 && M > 0); // for Buffter.h: (bufsize_type)nSamples
+ l_bars = new float[nSamples];
- sprintf(imdName, "%s.temp/%s", argv[2], argv[3]);
- sprintf(statName, "%s.stat/%s", argv[2], argv[3]);
sprintf(tmpF, "%s.tmp", imdName);
sprintf(cvsF, "%s.countvectors", imdName);
// Phase II
calculate_credibility_intervals(imdName);
- /*
- sprintf(command, "rm -f %s", tmpF);
- int status = system(command);
- if (status != 0) {
- fprintf(stderr, "Cannot delete %s!\n", tmpF);
- exit(-1);
- }
- */
+ delete l_bars;
return 0;
}
projects / rsem.git / blobdiff