X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=EM.cpp;h=7016b8944def26003c755697627019fe0dd0d6ea;hp=fdc75cce046eb533755b4f99a669d48cf8e13c7b;hb=refs%2Fheads%2Fupstream;hpb=d484af5f8ab839e296f01d01ff713c37a8db6e02 diff --git a/EM.cpp b/EM.cpp index fdc75cc..7016b89 100644 --- a/EM.cpp +++ b/EM.cpp @@ -44,6 +44,8 @@ #include "HitWrapper.h" #include "BamWriter.h" +#include "WriteResults.h" + using namespace std; const double STOP_CRITERIA = 0.001; @@ -68,7 +70,7 @@ bool genGibbsOut; // generate file for Gibbs sampler char refName[STRLEN], outName[STRLEN]; char imdName[STRLEN], statName[STRLEN]; -char refF[STRLEN], groupF[STRLEN], cntF[STRLEN], tiF[STRLEN]; +char refF[STRLEN], cntF[STRLEN], tiF[STRLEN]; char mparamsF[STRLEN]; char modelF[STRLEN], thetaF[STRLEN]; @@ -83,11 +85,13 @@ vector theta, eel; // eel : expected effective length double *probv, **countvs; Refs refs; -GroupInfo gi; Transcripts transcripts; ModelParams mparams; +bool hasSeed; +seedType seed; + template void init(ReadReader **&readers, HitContainer **&hitvs, double **&ncpvs, ModelType **&mhps) { READ_INT_TYPE nReads; @@ -271,185 +275,11 @@ void* calcConProbs(void* arg) { return NULL; } -template -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; -} - -void polishTheta(vector& theta, const vector& eel, const double* mw) { - double sum = 0.0; - - /* The reason that for noise gene, mw value is 1 is : - * currently, all masked positions are for poly(A) sites, which in theory should be filtered out. - * So the theta0 does not containing reads from any masked position - */ - - for (int i = 0; i <= M; i++) { - // i == 0, mw[i] == 1 - if (i > 0 && (mw[i] < EPSILON || eel[i] < EPSILON)) { - theta[i] = 0.0; - continue; - } - theta[i] = theta[i] / mw[i]; - sum += theta[i]; - } - // currently is OK, since no transcript should be masked totally, only the poly(A) tail related part will be masked - general_assert(sum >= EPSILON, "No effective length is no less than" + ftos(MINEEL, 6) + " !"); - for (int i = 0; i <= M; i++) theta[i] /= sum; -} - -void calcExpressionValues(const vector& theta, const vector& eel, vector& tpm, vector& fpkm) { - double denom; - vector frac; - - //calculate fraction of count over all mappabile reads - denom = 0.0; - frac.assign(M + 1, 0.0); - for (int i = 1; i <= M; i++) - if (eel[i] >= EPSILON) { - frac[i] = theta[i]; - denom += frac[i]; - } - general_assert(denom > 0, "No alignable reads?!"); - for (int i = 1; i <= M; i++) frac[i] /= denom; - - //calculate FPKM - fpkm.assign(M + 1, 0.0); - for (int i = 1; i <= M; i++) - if (eel[i] >= EPSILON) fpkm[i] = frac[i] * 1e9 / eel[i]; - - //calculate TPM - tpm.assign(M + 1, 0.0); - denom = 0.0; - for (int i = 1; i <= M; i++) denom += fpkm[i]; - for (int i = 1; i <= M; i++) tpm[i] = fpkm[i] / denom * 1e6; -} - template void writeResults(ModelType& model, double* counts) { - char outF[STRLEN]; - FILE *fo; - - sprintf(modelF, "%s.model", statName); - model.write(modelF); - - vector tlens; - vector fpkm, tpm, isopct; - vector glens, gene_eels, gene_counts, gene_tpm, gene_fpkm; - - calcExpressionValues(theta, eel, tpm, fpkm); - - //calculate IsoPct, etc. - isopct.assign(M + 1, 0.0); - tlens.assign(M + 1, 0); - - glens.assign(m, 0.0); gene_eels.assign(m, 0.0); - gene_counts.assign(m, 0.0); gene_tpm.assign(m, 0.0); gene_fpkm.assign(m, 0.0); - - for (int i = 0; i < m; i++) { - int b = gi.spAt(i), e = gi.spAt(i + 1); - for (int j = b; j < e; j++) { - const Transcript& transcript = transcripts.getTranscriptAt(j); - tlens[j] = transcript.getLength(); - - gene_counts[i] += counts[j]; - gene_tpm[i] += tpm[j]; - gene_fpkm[i] += fpkm[j]; - } - - if (gene_tpm[i] < EPSILON) { - double frac = 1.0 / (e - b); - for (int j = b; j < e; j++) { - glens[i] += tlens[j] * frac; - gene_eels[i] += eel[j] * frac; - } - } - else { - for (int j = b; j < e; j++) { - isopct[j] = tpm[j] / gene_tpm[i]; - glens[i] += tlens[j] * isopct[j]; - gene_eels[i] += eel[j] * isopct[j]; - } - } - } - - //isoform level results - sprintf(outF, "%s.iso_res", imdName); - fo = fopen(outF, "w"); - for (int i = 1; i <= M; i++) { - const Transcript& transcript = transcripts.getTranscriptAt(i); - fprintf(fo, "%s%c", transcript.getTranscriptID().c_str(), (i < M ? '\t' : '\n')); - } - for (int i = 1; i <= M; i++) { - const Transcript& transcript = transcripts.getTranscriptAt(i); - fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < M ? '\t' : '\n')); - } - for (int i = 1; i <= M; i++) - fprintf(fo, "%d%c", tlens[i], (i < M ? '\t' : '\n')); - for (int i = 1; i <= M; i++) - fprintf(fo, "%.2f%c", eel[i], (i < M ? '\t' : '\n')); - for (int i = 1; i <= M; i++) - fprintf(fo, "%.2f%c", counts[i], (i < M ? '\t' : '\n')); - for (int i = 1; i <= M; i++) - fprintf(fo, "%.2f%c", tpm[i], (i < M ? '\t' : '\n')); - for (int i = 1; i <= M; i++) - fprintf(fo, "%.2f%c", fpkm[i], (i < M ? '\t' : '\n')); - for (int i = 1; i <= M; i++) - fprintf(fo, "%.2f%c", isopct[i] * 1e2, (i < M ? '\t' : '\n')); - fclose(fo); - - //gene level results - sprintf(outF, "%s.gene_res", imdName); - fo = fopen(outF, "w"); - for (int i = 0; i < m; i++) { - const Transcript& transcript = transcripts.getTranscriptAt(gi.spAt(i)); - fprintf(fo, "%s%c", transcript.getGeneID().c_str(), (i < m - 1 ? '\t' : '\n')); - } - for (int i = 0; i < m; i++) { - int b = gi.spAt(i), e = gi.spAt(i + 1); - for (int j = b; j < e; j++) { - fprintf(fo, "%s%c", transcripts.getTranscriptAt(j).getTranscriptID().c_str(), (j < e - 1 ? ',' : (i < m - 1 ? '\t' :'\n'))); - } - } - for (int i = 0; i < m; i++) - fprintf(fo, "%.2f%c", glens[i], (i < m - 1 ? '\t' : '\n')); - for (int i = 0; i < m; i++) - fprintf(fo, "%.2f%c", gene_eels[i], (i < m - 1 ? '\t' : '\n')); - for (int i = 0; i < m; i++) - fprintf(fo, "%.2f%c", gene_counts[i], (i < m - 1 ? '\t' : '\n')); - for (int i = 0; i < m; i++) - fprintf(fo, "%.2f%c", gene_tpm[i], (i < m - 1 ? '\t' : '\n')); - for (int i = 0; i < m; i++) - fprintf(fo, "%.2f%c", gene_fpkm[i], (i < m - 1 ? '\t' : '\n')); - fclose(fo); - - if (verbose) { printf("Expression Results are written!\n"); } + sprintf(modelF, "%s.model", statName); + model.write(modelF); + writeResultsEM(M, refName, imdName, transcripts, theta, eel, countvs[0]); } template @@ -658,8 +488,8 @@ void EM() { fprintf(fo, "%.15g\n", theta[M]); //calculate expected effective lengths for each isoform - calcExpectedEffectiveLengths(model); - polishTheta(theta, eel, model.getMW()); + calcExpectedEffectiveLengths(M, refs, model, eel); + polishTheta(M, theta, eel, model.getMW()); // output theta for (int i = 0; i < M; i++) fprintf(fo, "%.15g ", theta[i]); @@ -676,7 +506,9 @@ void EM() { READ_INT_TYPE local_N; HIT_INT_TYPE fr, to, len, id; vector arr; - uniform01 rg(engine_type(time(NULL))); + engine_type engine(hasSeed ? seed : time(NULL)); + uniform_01_dist uniform_01; + uniform_01_generator rg(engine, uniform_01); if (verbose) cout<< "Begin to sample reads from their posteriors."<< endl; for (int i = 0; i < nThreads; i++) { @@ -709,7 +541,7 @@ int main(int argc, char* argv[]) { bool quiet = false; if (argc < 6) { - printf("Usage : rsem-run-em refName read_type sampleName imdName statName [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling]\n\n"); + printf("Usage : rsem-run-em refName read_type sampleName imdName statName [-p #Threads] [-b samInpType samInpF has_fn_list_? [fn_list]] [-q] [--gibbs-out] [--sampling] [--seed seed]\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(" sampleName: sample's name, including the path\n"); @@ -719,6 +551,7 @@ int main(int argc, char* argv[]) { printf(" -q: set it quiet\n"); printf(" --gibbs-out: generate output file used by Gibbs sampler. (default: off)\n"); printf(" --sampling: sample each read from its posterior distribution when bam file is generated. (default: off)\n"); + printf(" --seed uint32: the seed used for the BAM sampling. (default: off)\n"); printf("// model parameters should be in imdName.mparams.\n"); exit(-1); } @@ -737,6 +570,7 @@ int main(int argc, char* argv[]) { bamSampling = false; genGibbsOut = false; pt_fn_list = pt_chr_list = NULL; + hasSeed = false; for (int i = 6; i < argc; i++) { if (!strcmp(argv[i], "-p")) { nThreads = atoi(argv[i + 1]); } @@ -752,6 +586,12 @@ int main(int argc, char* argv[]) { if (!strcmp(argv[i], "-q")) { quiet = true; } if (!strcmp(argv[i], "--gibbs-out")) { genGibbsOut = true; } if (!strcmp(argv[i], "--sampling")) { bamSampling = 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'); + } } general_assert(nThreads > 0, "Number of threads should be bigger than 0!"); @@ -762,9 +602,6 @@ int main(int argc, char* argv[]) { sprintf(refF, "%s.seq", refName); refs.loadRefs(refF); M = refs.getM(); - sprintf(groupF, "%s.grp", refName); - gi.load(groupF); - m = gi.getm(); sprintf(tiF, "%s.ti", refName); transcripts.readFrom(tiF);