/* tests: * 1. each sampled trace must validate. * 2. each trace must be <= viterbi trace score * 3. in a large # of traces, one is "equal" to the viterbi trace score. * (this of course is stochastic; but it's true for the particular * choice of RNG seed used in tests here.) */ static void utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, P7_PROFILE *gm, P7_OPROFILE *om, ESL_DSQ *dsq, int L, int ntrace) { P7_GMX *gx = NULL; P7_OMX *ox = NULL; P7_TRACE *tr = NULL; char errbuf[eslERRBUFSIZE]; int idx; float maxsc = -eslINFINITY; float vsc, sc; if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("generic DP matrix creation failed"); if ((ox = p7_omx_Create(gm->M, L, L)) == NULL) esl_fatal("optimized DP matrix create failed"); if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed"); if (p7_GViterbi(dsq, L, gm, gx, &vsc) != eslOK) esl_fatal("viterbi failed"); if (p7_Forward (dsq, L, om, ox, NULL) != eslOK) esl_fatal("forward failed"); for (idx = 0; idx < ntrace; idx++) { if (p7_StochasticTrace(rng, dsq, L, om, ox, tr) != eslOK) esl_fatal("stochastic trace failed"); if (p7_trace_Validate(tr, abc, dsq, errbuf) != eslOK) esl_fatal("trace invalid:\n%s", errbuf); if (p7_trace_Score(tr, dsq, gm, &sc) != eslOK) esl_fatal("trace scoring failed"); maxsc = ESL_MAX(sc, maxsc); if (sc > vsc) esl_fatal("sampled trace has score > optimal Viterbi path; not possible"); p7_trace_Reuse(tr); } if (esl_FCompare(maxsc, vsc, 0.1) != eslOK) esl_fatal("stochastic trace failed to sample the Viterbi path"); p7_trace_Destroy(tr); p7_omx_Destroy(ox); p7_gmx_Destroy(gx); }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage); char *hmmfile = esl_opt_GetArg(go, 1); ESL_STOPWATCH *w = esl_stopwatch_Create(); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; P7_OMX *ox1 = NULL; P7_OMX *ox2 = NULL; int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N"); ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); float null2[p7_MAXCODE]; int i,j,d,pos; int nsamples = 200; float fsc, bsc; double Mcs; if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_ReconfigLength(om, L); ox1 = p7_omx_Create(gm->M, L, L); ox2 = p7_omx_Create(gm->M, L, L); esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_Forward (dsq, L, om, ox1, &fsc); if (esl_opt_GetBoolean(go, "-t")) { P7_TRACE *tr = p7_trace_Create(); float *n2sc = malloc(sizeof(float) * (L+1)); esl_stopwatch_Start(w); for (i = 0; i < N; i++) { /* This is approximately what p7_domaindef.c::region_trace_ensemble() is doing: */ for (j = 0; j < nsamples; j++) { p7_StochasticTrace(r, dsq, L, om, ox1, tr); p7_trace_Index(tr); pos = 1; for (d = 0; d < tr->ndom; d++) { p7_Null2_ByTrace(om, tr, tr->tfrom[d], tr->tto[d], ox2, null2); for (; pos <= tr->sqfrom[d]; pos++) n2sc[pos] += 1.0; for (; pos < tr->sqto[d]; pos++) n2sc[pos] += null2[dsq[pos]]; } for (; pos <= L; pos++) n2sc[pos] += 1.0; p7_trace_Reuse(tr); } for (pos = 1; pos <= L; pos++) n2sc[pos] = logf(n2sc[pos] / nsamples); } esl_stopwatch_Stop(w); free(n2sc); p7_trace_Destroy(tr); } else { p7_Backward(dsq, L, om, ox1, ox2, &bsc); p7_Decoding(om, ox1, ox2, ox2); esl_stopwatch_Start(w); for (i = 0; i < N; i++) p7_Null2_ByExpectation(om, ox2, null2); esl_stopwatch_Stop(w); } Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user; esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("# M = %d\n", gm->M); printf("# %.1f Mc/s\n", Mcs); free(dsq); p7_omx_Destroy(ox1); p7_omx_Destroy(ox2); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); p7_hmmfile_Close(hfp); esl_alphabet_Destroy(abc); esl_stopwatch_Destroy(w); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage); char *hmmfile = esl_opt_GetArg(go, 1); char *seqfile = esl_opt_GetArg(go, 2); ESL_ALPHABET *abc = NULL; ESL_RANDOMNESS *rng = esl_randomness_CreateFast(0); P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; P7_GMX *gx = NULL; P7_OMX *fwd = NULL; P7_TRACE *tr = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; int format = eslSQFILE_UNKNOWN; int N = esl_opt_GetInteger(go, "-N"); int i; float vsc, fsc, tsc; char errbuf[eslERRBUFSIZE]; int status; /* Read in one HMM */ if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); /* Read in one sequence */ sq = esl_sq_CreateDigital(abc); status = esl_sqfile_Open(seqfile, format, NULL, &sqfp); if (status == eslENOTFOUND) p7_Fail("No such file."); else if (status == eslEFORMAT) p7_Fail("Format unrecognized."); else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz."); else if (status != eslOK) p7_Fail("Open failed, code %d.", status); if (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence"); /* create default null model, then create and optimize profile */ bg = p7_bg_Create(abc); p7_bg_SetLength(bg, sq->n); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); if (esl_opt_GetBoolean(go, "-p")) p7_oprofile_Dump(stdout, om); fwd = p7_omx_Create(gm->M, sq->n, sq->n); gx = p7_gmx_Create(gm->M, sq->n); tr = p7_trace_Create(); if (esl_opt_GetBoolean(go, "-m") == TRUE) p7_omx_SetDumpMode(stdout, fwd, TRUE); p7_GViterbi(sq->dsq, sq->n, gm, gx, &vsc); p7_Forward (sq->dsq, sq->n, om, fwd, &fsc); for (i = 0; i < N; i++) { p7_StochasticTrace(rng, sq->dsq, sq->n, om, fwd, tr); p7_trace_Score(tr, sq->dsq, gm, &tsc); if (esl_opt_GetBoolean(go, "-t") == TRUE) p7_trace_Dump(stdout, tr, gm, sq->dsq); if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace %d fails validation:\n%s\n", i, errbuf); printf("Sampled trace: %.4f nats\n", tsc); p7_trace_Reuse(tr); } printf("Forward score: %.4f nats\n", fsc); printf("Viterbi score: %.4f nats\n", vsc); /* cleanup */ esl_sq_Destroy(sq); esl_sqfile_Close(sqfp); p7_trace_Destroy(tr); p7_omx_Destroy(fwd); p7_gmx_Destroy(gx); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); p7_hmmfile_Close(hfp); esl_randomness_Destroy(rng); esl_alphabet_Destroy(abc); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage); char *hmmfile = esl_opt_GetArg(go, 1); ESL_STOPWATCH *w = esl_stopwatch_Create(); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; P7_GMX *gx = NULL; P7_OMX *fwd = NULL; P7_TRACE *tr = NULL; int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N"); ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); int i; float sc, fsc, vsc; float bestsc = -eslINFINITY; if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); fwd = p7_omx_Create(gm->M, L, L); gx = p7_gmx_Create(gm->M, L); tr = p7_trace_Create(); esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_GViterbi(dsq, L, gm, gx, &vsc); p7_Forward (dsq, L, om, fwd, &fsc); esl_stopwatch_Start(w); for (i = 0; i < N; i++) { p7_StochasticTrace(r, dsq, L, om, fwd, tr); p7_trace_Score(tr, dsq, gm, &sc); bestsc = ESL_MAX(bestsc, sc); p7_trace_Reuse(tr); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("forward sc = %.4f nats\n", fsc); printf("viterbi sc = %.4f nats\n", vsc); printf("max trace sc = %.4f nats\n", bestsc); free(dsq); p7_trace_Destroy(tr); p7_gmx_Destroy(gx); p7_omx_Destroy(fwd); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); p7_hmmfile_Close(hfp); esl_alphabet_Destroy(abc); esl_stopwatch_Destroy(w); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }