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; 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_OMX *bck = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; int format = eslSQFILE_UNKNOWN; float fraw, braw, nullsc, fsc; float gfraw, gbraw, gfsc; double P, gP; 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"); /* Open sequence file for reading */ 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); /* 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_UNILOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); /* p7_oprofile_Dump(stdout, om); */ /* allocate DP matrices for O(M+L) parsers */ fwd = p7_omx_Create(gm->M, 0, sq->n); bck = p7_omx_Create(gm->M, 0, sq->n); gx = p7_gmx_Create(gm->M, sq->n); /* allocate DP matrices for O(ML) fills */ /* fwd = p7_omx_Create(gm->M, sq->n, sq->n); */ /* bck = p7_omx_Create(gm->M, sq->n, sq->n); */ /* p7_omx_SetDumpMode(stdout, fwd, TRUE); */ /* makes the fast DP algorithms dump their matrices */ /* p7_omx_SetDumpMode(stdout, bck, TRUE); */ while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { p7_oprofile_ReconfigLength(om, sq->n); p7_ReconfigLength(gm, sq->n); p7_bg_SetLength(bg, sq->n); p7_omx_GrowTo(fwd, om->M, 0, sq->n); p7_omx_GrowTo(bck, om->M, 0, sq->n); p7_gmx_GrowTo(gx, gm->M, sq->n); p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc); p7_ForwardParser (sq->dsq, sq->n, om, fwd, &fraw); p7_BackwardParser(sq->dsq, sq->n, om, fwd, bck, &braw); /* p7_Forward (sq->dsq, sq->n, om, fwd, &fsc); printf("forward: %.2f nats\n", fsc); */ /* p7_Backward(sq->dsq, sq->n, om, fwd, bck, &bsc); printf("backward: %.2f nats\n", bsc); */ /* Comparison to other F/B implementations */ p7_GForward (sq->dsq, sq->n, gm, gx, &gfraw); p7_GBackward (sq->dsq, sq->n, gm, gx, &gbraw); /* p7_gmx_Dump(stdout, gx); */ fsc = (fraw-nullsc) / eslCONST_LOG2; gfsc = (gfraw-nullsc) / eslCONST_LOG2; P = esl_exp_surv(fsc, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]); gP = esl_exp_surv(gfsc, gm->evparam[p7_FTAU], gm->evparam[p7_FLAMBDA]); if (esl_opt_GetBoolean(go, "-1")) { printf("%-30s\t%-20s\t%9.2g\t%6.1f\t%9.2g\t%6.1f\n", sq->name, hmm->name, P, fsc, gP, gfsc); } else if (esl_opt_GetBoolean(go, "-P")) { /* output suitable for direct use in profmark benchmark postprocessors: */ printf("%g\t%.2f\t%s\t%s\n", P, fsc, sq->name, hmm->name); } else { printf("target sequence: %s\n", sq->name); printf("fwd filter raw score: %.2f nats\n", fraw); printf("bck filter raw score: %.2f nats\n", braw); printf("null score: %.2f nats\n", nullsc); printf("per-seq score: %.2f bits\n", fsc); printf("P-value: %g\n", P); printf("GForward raw score: %.2f nats\n", gfraw); printf("GBackward raw score: %.2f nats\n", gbraw); printf("GForward seq score: %.2f bits\n", gfsc); printf("GForward P-value: %g\n", gP); } esl_sq_Reuse(sq); } /* cleanup */ esl_sq_Destroy(sq); esl_sqfile_Close(sqfp); p7_omx_Destroy(bck); 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_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_OMX *bck = 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 fsc, bsc; float fsc2, bsc2; double base_time, bench_time, Mcs; p7_FLogsumInit(); 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_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_ReconfigLength(om, L); if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001) p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode"); if (esl_opt_GetBoolean(go, "-P")) { fwd = p7_omx_Create(gm->M, 0, L); bck = p7_omx_Create(gm->M, 0, L); } else { fwd = p7_omx_Create(gm->M, L, L); bck = p7_omx_Create(gm->M, L, L); } gx = p7_gmx_Create(gm->M, L); /* Get a baseline time: how long it takes just to generate the sequences */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); esl_stopwatch_Stop(w); base_time = w->user; esl_stopwatch_Start(w); for (i = 0; i < N; i++) { esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); if (esl_opt_GetBoolean(go, "-P")) { if (! esl_opt_GetBoolean(go, "-B")) p7_ForwardParser (dsq, L, om, fwd, &fsc); if (! esl_opt_GetBoolean(go, "-F")) p7_BackwardParser(dsq, L, om, fwd, bck, &bsc); } else { if (! esl_opt_GetBoolean(go, "-B")) p7_Forward (dsq, L, om, fwd, &fsc); if (! esl_opt_GetBoolean(go, "-F")) p7_Backward(dsq, L, om, fwd, bck, &bsc); } if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x")) { p7_GForward (dsq, L, gm, gx, &fsc2); p7_GBackward(dsq, L, gm, gx, &bsc2); printf("%.4f %.4f %.4f %.4f\n", fsc, bsc, fsc2, bsc2); } } esl_stopwatch_Stop(w); bench_time = w->user - base_time; Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time; esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("# M = %d\n", gm->M); printf("# %.1f Mc/s\n", Mcs); free(dsq); p7_omx_Destroy(bck); 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_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, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); char template[13]= "esltmpXXXXXX";
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; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; ESL_SQFILE *sqfp = NULL; int format = eslSQFILE_UNKNOWN; ESL_SQ *sq = NULL; float nullsc, filtersc, H; int status; /* Read one HMM from <hmmfile> */ 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"); p7_hmmfile_Close(hfp); /* Open <seqfile> for reading */ status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp); if (status == eslENOTFOUND) esl_fatal("No such file."); else if (status == eslEFORMAT) esl_fatal("Format unrecognized."); else if (status != eslOK) esl_fatal("Open failed, code %d.", status); sq = esl_sq_CreateDigital(abc); bg = p7_bg_Create(abc); p7_bg_SetFilterByHMM(bg, hmm); H = esl_vec_FEntropy(bg->f, bg->abc->K); printf("bg iid H = %.4f\n", H); H = esl_vec_FEntropy(bg->mcomp, bg->abc->K); printf("modelcomp H = %.4f\n", H); while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { p7_bg_SetLength(bg, sq->n); p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc); p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc); printf("%-20s %5d %8.5f %8.5f %8.5f\n", sq->name, (int) sq->n, nullsc, filtersc, filtersc-nullsc); esl_sq_Reuse(sq); } if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s line %" PRId64 "):\n%s\n", sqfp->filename, sqfp->linenumber, sqfp->errbuf); else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename); esl_sqfile_Close(sqfp); esl_sq_Destroy(sq); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); 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); int N = esl_opt_GetInteger(go, "-N"); 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_TRACE *tr = NULL; ESL_SQ *sq = NULL; P7_ALIDISPLAY *ad = NULL; int i,z; 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"); p7_hmmfile_Close(hfp); bg = p7_bg_Create(abc); p7_bg_SetLength(bg, 0); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, 0, p7_UNIGLOCAL); /* that sets N,C,J to generate nothing */ om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); if (esl_opt_GetBoolean(go, "-p")) tr = p7_trace_CreateWithPP(); else tr = p7_trace_Create(); sq = esl_sq_CreateDigital(abc); esl_stopwatch_Start(w); for (i = 0; i < N; i++) { p7_ProfileEmit(r, hmm, gm, bg, sq, tr); esl_sq_SetName(sq, "random"); if (! esl_opt_GetBoolean(go, "-b")) { if (esl_opt_GetBoolean(go, "-p")) for (z = 0; z < tr->N; z++) if (tr->i[z] > 0) tr->pp[z] = esl_random(r); ad = p7_alidisplay_Create(tr, 0, om, sq); p7_alidisplay_Print(stdout, ad, 40, 80, FALSE); p7_alidisplay_Destroy(ad); } p7_trace_Reuse(tr); esl_sq_Reuse(sq); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); esl_sq_Destroy(sq); p7_trace_Destroy(tr); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_randomness_Destroy(r); esl_stopwatch_Destroy(w); 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; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_GMX *fwd = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; P7_TRACE *tr = NULL; int format = eslSQFILE_UNKNOWN; char errbuf[eslERRBUFSIZE]; float sc; int d; 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"); p7_hmmfile_Close(hfp); /* 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"); esl_sqfile_Close(sqfp); /* Configure a profile from the HMM */ 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); /* Allocate matrix and a trace */ fwd = p7_gmx_Create(gm->M, sq->n); tr = p7_trace_Create(); /* Run Viterbi; do traceback */ p7_GViterbi (sq->dsq, sq->n, gm, fwd, &sc); p7_GTrace (sq->dsq, sq->n, gm, fwd, tr); /* Dump and validate the trace. */ p7_trace_Dump(stdout, tr, gm, sq->dsq); if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace fails validation:\n%s\n", errbuf); /* Domain info in the trace. */ p7_trace_Index(tr); printf("# Viterbi: %d domains :\n", tr->ndom); for (d = 0; d < tr->ndom; d++) printf("%6d %6d %6d %6d\n", tr->sqfrom[d], tr->sqto[d], tr->hmmfrom[d], tr->hmmto[d]); /* Cleanup */ p7_trace_Destroy(tr); p7_gmx_Destroy(fwd); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); 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_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_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_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, 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_GMX *gx = 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; double base_time, bench_time, Mcs; 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); gx = p7_gmx_Create(gm->M, L); /* Baseline time. */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); esl_stopwatch_Stop(w); base_time = w->user; /* Benchmark time. */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) { esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_GMSV (dsq, L, gm, gx, 2.0, &sc); } esl_stopwatch_Stop(w); bench_time = w->user - base_time; Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time; esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("# M = %d\n", gm->M); printf("# %.1f Mc/s\n", Mcs); free(dsq); p7_gmx_Destroy(gx); 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); float nu = esl_opt_GetReal(go, "--nu"); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_GMX *fwd = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; P7_TRACE *tr = NULL; int format = eslSQFILE_UNKNOWN; float sc, nullsc, seqscore, P; 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"); p7_hmmfile_Close(hfp); /* Open sequence file */ 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); /* Configure a profile from the HMM */ bg = p7_bg_Create(abc); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL); /* Allocate matrix */ fwd = p7_gmx_Create(gm->M, sq->n); while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { p7_ReconfigLength(gm, sq->n); p7_bg_SetLength(bg, sq->n); p7_gmx_GrowTo(fwd, gm->M, sq->n); /* Run MSV */ p7_GMSV(sq->dsq, sq->n, gm, fwd, nu, &sc); /* Calculate bit score and P-value using standard null1 model*/ p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc); seqscore = (sc - nullsc) / eslCONST_LOG2; P = esl_gumbel_surv(seqscore, gm->evparam[p7_MMU], gm->evparam[p7_MLAMBDA]); /* output suitable for direct use in profmark benchmark postprocessors: * <Pvalue> <bitscore> <target name> <query name> */ printf("%g\t%.2f\t%s\t%s\n", P, seqscore, sq->name, hmm->name); esl_sq_Reuse(sq); } if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename); /* Cleanup */ esl_sqfile_Close(sqfp); esl_sq_Destroy(sq); p7_trace_Destroy(tr); p7_gmx_Destroy(fwd); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); 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; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_GMX *fwd = NULL; P7_GMX *bck = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; int format = eslSQFILE_UNKNOWN; float fsc, bsc; 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"); p7_hmmfile_Close(hfp); /* 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"); esl_sqfile_Close(sqfp); /* Configure a profile from the HMM */ 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_UNILOCAL); /* Allocate matrices */ fwd = p7_gmx_Create(gm->M, sq->n); bck = p7_gmx_Create(gm->M, sq->n); /* Run Forward, Backward */ p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc); p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc); printf("fwd = %.4f nats\n", fsc); printf("bck = %.4f nats\n", bsc); /* Cleanup */ esl_sq_Destroy(sq); p7_gmx_Destroy(fwd); p7_gmx_Destroy(bck); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); 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; 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; P7_GMX *gx = NULL; ESL_SQ *sq = NULL; ESL_SQFILE *sqfp = NULL; P7_TRACE *tr = NULL; int format = eslSQFILE_UNKNOWN; char errbuf[eslERRBUFSIZE]; float fsc, bsc; float accscore; 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"); p7_hmmfile_Close(hfp); /* Read in one sequence */ sq = esl_sq_CreateDigital(abc); status = esl_sqfile_OpenDigital(abc, 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"); esl_sqfile_Close(sqfp); /* Configure a profile from the HMM */ 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); /* multihit local: H3 default */ om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); /* Allocations */ ox1 = p7_omx_Create(gm->M, sq->n, sq->n); ox2 = p7_omx_Create(gm->M, sq->n, sq->n); gx = p7_gmx_Create(gm->M, sq->n); tr = p7_trace_CreateWithPP(); p7_FLogsumInit(); /* Run Forward, Backward; do OA fill and trace */ p7_Forward (sq->dsq, sq->n, om, ox1, &fsc); p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc); p7_Decoding(om, ox1, ox2, ox2); /* <gx2> is now the posterior decoding matrix */ p7_OptimalAccuracy(om, ox2, ox1, &accscore); /* <gx1> is now the OA matrix */ p7_OATrace(om, ox2, ox1, tr); if (esl_opt_GetBoolean(go, "-d")) { p7_omx_FDeconvert(ox2, gx); p7_gmx_Dump(stdout, gx); } if (esl_opt_GetBoolean(go, "-m")) { p7_omx_FDeconvert(ox1, gx); p7_gmx_Dump(stdout, gx); } p7_trace_Dump(stdout, tr, gm, sq->dsq); if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace fails validation:\n%s\n", errbuf); printf("fwd = %.4f nats\n", fsc); printf("bck = %.4f nats\n", bsc); printf("acc = %.4f (%.2f%%)\n", accscore, accscore * 100. / (float) sq->n); /* Cleanup */ esl_sq_Destroy(sq); p7_trace_Destroy(tr); p7_omx_Destroy(ox1); p7_omx_Destroy(ox2); p7_gmx_Destroy(gx); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); 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 *gx1 = NULL; P7_GMX *gx2 = NULL; P7_OMX *ox1 = NULL; P7_OMX *ox2 = 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 fsc, bsc, accscore; float fsc_g, bsc_g, accscore_g; double Mcs; p7_FLogsumInit(); 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_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_ReconfigLength(om, L); if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001) p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode"); ox1 = p7_omx_Create(gm->M, L, L); ox2 = p7_omx_Create(gm->M, L, L); tr = p7_trace_CreateWithPP(); esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_Forward (dsq, L, om, ox1, &fsc); 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_OptimalAccuracy(om, ox2, ox1, &accscore); if (! esl_opt_GetBoolean(go, "--notrace")) { p7_OATrace(om, ox2, ox1, tr); p7_trace_Reuse(tr); } } 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); if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x") ) { gx1 = p7_gmx_Create(gm->M, L); gx2 = p7_gmx_Create(gm->M, L); p7_GForward (dsq, L, gm, gx1, &fsc_g); p7_GBackward(dsq, L, gm, gx2, &bsc_g); p7_GDecoding(gm, gx1, gx2, gx2); p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g); printf("generic: fwd=%8.4f bck=%8.4f acc=%8.4f\n", fsc_g, bsc_g, accscore_g); printf("VMX: fwd=%8.4f bck=%8.4f acc=%8.4f\n", fsc, bsc, accscore); p7_gmx_Destroy(gx1); p7_gmx_Destroy(gx2); } free(dsq); p7_omx_Destroy(ox1); p7_omx_Destroy(ox2); p7_trace_Destroy(tr); 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, 1, argc, argv, banner, usage); ESL_ALPHABET *abc = NULL; char *hmmfile = esl_opt_GetArg(go, 1); P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; char *fname = NULL; char *pname = NULL; FILE *ffp = NULL; FILE *pfp = NULL; int nmodel = 0; uint64_t totM = 0; int status; status = p7_hmmfile_Open(hmmfile, NULL, &hfp); if (status == eslENOTFOUND) esl_fatal("Failed to open HMM file %s for reading.\n", hmmfile); else if (status == eslEFORMAT) esl_fatal("File %s does not appear to be in a recognized HMM format.\n", hmmfile); else if (status != eslOK) esl_fatal("Unexpected error %d in opening HMM file %s.\n", status, hmmfile); esl_sprintf(&fname, "%s.h3f", hmmfile); esl_sprintf(&pname, "%s.h3f", hmmfile); if ((ffp = fopen(fname, "wb")) == NULL) esl_fatal("failed to open %s\n", fname); if ((pfp = fopen(pname, "wb")) == NULL) esl_fatal("failed to open %s\n", pname); free(fname); free(pname); while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) == eslOK) { if (nmodel == 0) { /* first time initialization, now that alphabet known */ bg = p7_bg_Create(abc); p7_bg_SetLength(bg, 400); } if (esl_opt_GetBoolean(go, "-v")) printf("%s\n", hmm->name); nmodel++; totM += hmm->M; gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, 400, p7_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_Write(ffp, pfp, om); p7_profile_Destroy(gm); p7_oprofile_Destroy(om); p7_hmm_Destroy(hmm); } if (status == eslEFORMAT) esl_fatal("bad file format in HMM file %s", hmmfile); else if (status == eslEINCOMPAT) esl_fatal("HMM file %s contains different alphabets", hmmfile); else if (status != eslEOF) esl_fatal("Unexpected error in reading HMMs from %s", hmmfile); fclose(ffp); fclose(pfp); p7_bg_Destroy(bg); p7_hmmfile_Close(hfp); 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_ALPHABET *abc = esl_alphabet_Create(eslAMINO); P7_BG *bg = p7_bg_Create(abc); int my_rank; int nproc; char *buf = NULL; int nbuf = 0; int subtotalM = 0; int allM = 0; int stalling = esl_opt_GetBoolean(go, "--stall"); MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &my_rank); MPI_Comm_size(MPI_COMM_WORLD, &nproc); while (stalling); /* Master MPI process: */ if (my_rank == 0) { ESL_STOPWATCH *w = esl_stopwatch_Create(); P7_HMMFILE *hfp = NULL; P7_OPROFILE *om = NULL; P7_HMM *hmm = NULL; /* Read HMMs from a file. */ if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); esl_stopwatch_Start(w); while (p7_oprofile_ReadMSV(hfp, &abc, &om) == eslOK && p7_oprofile_ReadRest(hfp, om) == eslOK) { if (!esl_opt_GetBoolean(go, "-b")) p7_oprofile_MPISend(om, 1, 0, MPI_COMM_WORLD, &buf, &nbuf); /* 1 = dest; 0 = tag */ p7_hmm_Destroy(hmm); p7_oprofile_Destroy(om); } p7_oprofile_MPISend(NULL, 1, 0, MPI_COMM_WORLD, &buf, &nbuf); /* send the "no more HMMs" sign */ MPI_Reduce(&subtotalM, &allM, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD); printf("total: %d\n", allM); esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "CPU Time: "); esl_stopwatch_Destroy(w); } /* Worker MPI process: */ else { P7_OPROFILE *om_recd = NULL; while (p7_oprofile_MPIRecv(0, 0, MPI_COMM_WORLD, &buf, &nbuf, &abc, &om_recd) == eslOK) { subtotalM += om_recd->M; p7_oprofile_Destroy(om_recd); } MPI_Reduce(&subtotalM, &allM, 1, MPI_INT, MPI_SUM, 0, MPI_COMM_WORLD); } free(buf); p7_bg_Destroy(bg); esl_alphabet_Destroy(abc); esl_getopts_Destroy(go); MPI_Finalize(); exit(0); }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); double mu = esl_opt_GetReal(go, "-m"); double lambda = esl_opt_GetReal(go, "-l"); double tau = esl_opt_GetReal(go, "-t"); ESL_RANDOMNESS *r = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); ESL_HISTOGRAM *h = esl_histogram_CreateFull(mu, 100., esl_opt_GetReal(go, "-w"));; int n = esl_opt_GetInteger(go, "-n"); int be_verbose = esl_opt_GetBoolean(go, "-v"); char *plotfile = esl_opt_GetString(go, "-o"); FILE *pfp = stdout; int plot_pdf = esl_opt_GetBoolean(go, "--P"); int plot_logpdf = esl_opt_GetBoolean(go, "--LP"); int plot_cdf = esl_opt_GetBoolean(go, "--C"); int plot_logcdf = esl_opt_GetBoolean(go, "--LC"); int plot_surv = esl_opt_GetBoolean(go, "--S"); int plot_logsurv = esl_opt_GetBoolean(go, "--LS"); double xmin = esl_opt_IsOn(go, "--XL") ? esl_opt_GetReal(go, "--XL") : mu; double xmax = esl_opt_IsOn(go, "--XH") ? esl_opt_GetReal(go, "--XH") : mu+40*(1./lambda); double xstep = esl_opt_IsOn(go, "--XS") ? esl_opt_GetReal(go, "--XS") : 0.1; double emu, elambda, etau; int i; double x; double *data; int ndata; if (be_verbose) printf("Parametric: mu = %f lambda = %f tau = %f\n", mu, lambda, tau); if (plotfile != NULL) { if ((pfp = fopen(plotfile, "w")) == NULL) esl_fatal("Failed to open plotfile"); } for (i = 0; i < n; i++) { x = esl_sxp_Sample(r, mu, lambda, tau); esl_histogram_Add(h, x); } esl_histogram_GetData(h, &data, &ndata); esl_sxp_FitComplete(data, ndata, &emu, &elambda, &etau); if (be_verbose) printf("Complete data fit: mu = %f lambda = %f tau = %f\n", emu, elambda, etau); if (fabs( (emu-mu)/mu ) > 0.01) esl_fatal("Error in (complete) fitted mu > 1%\n"); if (fabs( (elambda-lambda)/lambda ) > 0.10) esl_fatal("Error in (complete) fitted lambda > 10%\n"); if (fabs( (etau-tau)/tau ) > 0.10) esl_fatal("Error in (complete) fitted tau > 10%\n"); esl_sxp_FitCompleteBinned(h, &emu, &elambda, &etau); if (be_verbose) printf("Binned data fit: mu = %f lambda = %f tau = %f\n", emu, elambda, etau); if (fabs( (emu-mu)/mu ) > 0.01) esl_fatal("Error in (binned) fitted mu > 1%\n"); if (fabs( (elambda-lambda)/lambda ) > 0.10) esl_fatal("Error in (binned) fitted lambda > 10%\n"); if (fabs( (etau-tau)/tau ) > 0.10) esl_fatal("Error in (binned) fitted tau > 10%\n"); if (plot_pdf) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_pdf, xmin, xmax, xstep); if (plot_logpdf) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_logpdf, xmin, xmax, xstep); if (plot_cdf) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_cdf, xmin, xmax, xstep); if (plot_logcdf) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_logcdf, xmin, xmax, xstep); if (plot_surv) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_surv, xmin, xmax, xstep); if (plot_logsurv) esl_sxp_Plot(pfp, mu, lambda, tau, &esl_sxp_logsurv, xmin, xmax, xstep); if (plotfile != NULL) fclose(pfp); esl_histogram_Destroy(h); esl_randomness_Destroy(r); 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 *msafile = esl_opt_GetArg(go, 1); int infmt = eslMSAFILE_UNKNOWN; int outfmt = eslMSAFILE_UNKNOWN; ESL_ALPHABET *abc = NULL; ESL_MSAFILE *afp = NULL; ESL_MSA *msa = NULL; int nali = 0; int status; /* Alphabet specification from cmdline? */ if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA); else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA); /* MSA input file format from cmdline? */ if (esl_opt_IsOn(go, "--informat") && (infmt = esl_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN) esl_fatal("Your --informat, %s, is not a recognized multiple alignment file format", esl_opt_GetString(go, "--informat")); /* Open in digital mode. Autoguess alphabet, format if we haven't set them already. */ if (( status = esl_msafile_Open(&abc, msafile, NULL, infmt, NULL, &afp)) != eslOK) esl_msafile_OpenFailure(afp, status); /* Reverse complementation only makes sense for alphabets that have abc->complement set */ if (! abc->complement) esl_fatal("File %s appears to use the %s alphabet.\nThat alphabet cannot be reverse complemented.\n", msafile, esl_abc_DecodeType(abc->type)); /* Set the output format, if requested. * By default, write in the same format we read in. * Remember, it's afp->format that gets set; infmt was only a hint. */ if ( esl_opt_IsOn(go, "--outformat") ) { outfmt = esl_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat")); if (outfmt == eslMSAFILE_UNKNOWN) esl_fatal("Your --outformat, %s, is not a recognized multiple alignment file format.\n", esl_opt_GetString(go, "--outformat")); } else outfmt = afp->format; /* Here we go. */ while ((status = esl_msafile_Read(afp, &msa)) == eslOK) { nali++; status = esl_msa_ReverseComplement(msa); esl_msafile_Write(stdout, msa, outfmt); esl_msa_Destroy(msa); } if (nali == 0) esl_fatal("No alignments found in input file %s\n", msafile); if (status != eslEOF) esl_msafile_ReadFailure(afp, status); esl_msafile_Close(afp); 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; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); double mu = esl_opt_GetReal (go, "-m"); double lambda = esl_opt_GetReal (go, "-l"); double tau = esl_opt_GetReal (go, "-t"); int n = esl_opt_GetInteger(go, "-n"); double binwidth = esl_opt_GetReal (go, "-w"); int plot_cdf = esl_opt_GetBoolean(go, "--cdf"); int plot_logcdf = esl_opt_GetBoolean(go, "--logcdf"); int plot_pdf = esl_opt_GetBoolean(go, "--pdf"); int plot_logpdf = esl_opt_GetBoolean(go, "--logpdf"); int plot_surv = esl_opt_GetBoolean(go, "--surv"); int plot_logsurv = esl_opt_GetBoolean(go, "--logsurv"); int be_verbose = esl_opt_GetBoolean(go, "-v"); char *plotfile = esl_opt_GetString (go, "-o"); ESL_HISTOGRAM *h = NULL; int xmin_set = esl_opt_IsOn(go, "--xL"); double xmin = xmin_set ? esl_opt_GetReal(go, "--xL") : mu; int xmax_set = esl_opt_IsOn(go, "--xH"); double xmax = xmax_set ? esl_opt_GetReal(go, "--xH") : mu+40*(1./lambda); int xstep_set = esl_opt_IsOn(go, "--xH"); double xstep = xstep_set ? esl_opt_GetReal(go, "--xS") : 0.1; FILE *pfp = stdout; double emu, elambda, etau; int i; double x; double *data; int ndata; fprintf(stderr, "## %s\n", argv[0]); fprintf(stderr, "# rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(rng)); if (be_verbose) printf("Parametric: mu = %f lambda = %f tau = %f\n", mu, lambda, tau); h = esl_histogram_CreateFull(mu, 100., binwidth); if (plotfile && (pfp = fopen(plotfile, "w")) == NULL) ESL_EXCEPTION(eslFAIL, "Failed to open plotfile"); for (i = 0; i < n; i++) { x = esl_wei_Sample(rng, mu, lambda, tau); esl_histogram_Add(h, x); } esl_histogram_GetData(h, &data, &ndata); esl_wei_FitComplete(data, ndata, &emu, &elambda, &etau); if (be_verbose) printf("Complete data fit: mu = %f lambda = %f tau = %f\n", emu, elambda, etau); if (fabs( (emu-mu)/mu ) > 0.01) ESL_EXCEPTION(eslFAIL, "Error in (complete) fitted mu > 1%\n"); if (fabs( (elambda-lambda)/lambda ) > 0.10) ESL_EXCEPTION(eslFAIL, "Error in (complete) fitted lambda > 10%\n"); if (fabs( (etau-tau)/tau ) > 0.10) ESL_EXCEPTION(eslFAIL, "Error in (complete) fitted tau > 10%\n"); esl_wei_FitCompleteBinned(h, &emu, &elambda, &etau); if (be_verbose) printf("Binned data fit: mu = %f lambda = %f tau = %f\n", emu, elambda, etau); if (fabs( (emu-mu)/mu ) > 0.01) ESL_EXCEPTION(eslFAIL, "Error in (binned) fitted mu > 1%\n"); if (fabs( (elambda-lambda)/lambda ) > 0.10) ESL_EXCEPTION(eslFAIL, "Error in (binned) fitted lambda > 10%\n"); if (fabs( (etau-tau)/tau ) > 0.10) ESL_EXCEPTION(eslFAIL, "Error in (binned) fitted lambda > 10%\n"); if (plot_pdf) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_pdf, xmin, xmax, xstep); if (plot_logpdf) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_logpdf, xmin, xmax, xstep); if (plot_cdf) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_cdf, xmin, xmax, xstep); if (plot_logcdf) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_logcdf, xmin, xmax, xstep); if (plot_surv) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_surv, xmin, xmax, xstep); if (plot_logsurv) esl_wei_Plot(pfp, mu, lambda, tau, &esl_wei_logsurv, xmin, xmax, xstep); if (plotfile) fclose(pfp); esl_histogram_Destroy(h); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); fprintf(stderr, "# status = ok\n"); 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_OMX *ox = NULL; P7_GMX *gx = 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 sc1, sc2; double base_time, bench_time, Mcs; 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_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_ReconfigLength(om, L); p7_oprofile_Logify(om); ox = p7_omx_Create(gm->M, 0, 0); gx = p7_gmx_Create(gm->M, L); /* Get a baseline time: how long it takes just to generate the sequences */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); esl_stopwatch_Stop(w); base_time = w->user; /* Run the benchmark */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) { esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_ViterbiScore (dsq, L, om, ox, &sc1); if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x")) { p7_GViterbi(dsq, L, gm, gx, &sc2); printf("%.4f %.4f\n", sc1, sc2); } } esl_stopwatch_Stop(w); bench_time = w->user - base_time; Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time; esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("# M = %d\n", gm->M); printf("# %.1f Mc/s\n", Mcs); free(dsq); p7_omx_Destroy(ox); 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_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, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; ESL_HMM *hmm = NULL; ESL_DSQ *dsq = NULL; int *path = NULL; ESL_HMX *fwd = NULL; ESL_HMX *bck = NULL; ESL_HMX *pp = NULL; int be_verbose = esl_opt_GetBoolean(go, "-v"); float fsc, bsc; int L; int i; float fsum, bsum; make_occasionally_dishonest_casino(&hmm, &abc); esl_hmm_Emit(r, hmm, &dsq, &path, &L); fwd = esl_hmx_Create(L, hmm->M); bck = esl_hmx_Create(L, hmm->M); pp = esl_hmx_Create(L, hmm->M); esl_hmm_Forward (dsq, L, hmm, fwd, &fsc); esl_hmm_Backward(dsq, L, hmm, bck, &bsc); esl_hmm_PosteriorDecoding(dsq, L, hmm, fwd, bck, pp); fsum = 0.0; bsum = bsc; fsum += fwd->sc[0]; if (be_verbose) printf("%4d %c %s %8.3f %8.3f\n", 0, '-', "--", fwd->sc[0], bck->sc[0]); bsum -= bck->sc[0]; for (i = 1; i <= L; i++) { fsum += fwd->sc[i]; if (be_verbose) printf("%4d %c %s %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", i, abc->sym[dsq[i]], path[i] == 0 ? "F " : " L", fwd->sc[i], bck->sc[i], fsum, bsum, fsum+bsum, pp->dp[i][0], pp->dp[i][1]); bsum -= fwd->sc[i]; } if (be_verbose) { printf("%4d %c %s %8.3f %8.3f\n", 0, '-', "--", fwd->sc[L+1], bck->sc[L+1]); printf("Forward score = %f\n", fsc); printf("Backward score = %f\n", bsc); } free(path); free(dsq); esl_hmx_Destroy(pp); esl_hmx_Destroy(bck); esl_hmx_Destroy(fwd); esl_alphabet_Destroy(abc); esl_hmm_Destroy(hmm); 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_STOPWATCH *w = esl_stopwatch_Create(); ESL_RANDOMNESS*r = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET*abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm1, *gm2; int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N") / SSE16_NVALS; int MaxPart = esl_opt_GetInteger(go, "-M"); int NROUNDS = esl_opt_GetInteger(go, "-R"); int check = esl_opt_GetBoolean(go, "-c"); __m128 resdata[10]; int i, j; float *sc1 = (float*) resdata; ESL_SQFILE *sqfp = NULL; DATA_COPS16 *dcops; struct timeb tbstart, tbend; int sumlengths = 0; float* results = NULL; srand(time(NULL)); 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); gm1 = p7_profile_Create(hmm->M, abc); gm2 = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm1, L, p7_UNILOCAL); p7_ProfileConfig(hmm, bg, gm2, L, p7_UNILOCAL); dcops = p7_ViterbiCOPSw_Create(gm1); p7_ViterbiCOPSW_Setup(dcops, L+100, MaxPart); // use max L dcops->L = L; int dbsize = SSE16_NVALS*N; SEQ **seqsdb= calloc(dbsize+1, sizeof(SEQ*)); int equallength = 1; if (esl_sqfile_OpenDigital(abc, seqfile, eslSQFILE_FASTA, NULL, &sqfp) == eslOK) { // Use Sequence file ESL_SQ* sq = esl_sq_CreateDigital(abc); int maxseqs, len=0; if (esl_opt_IsDefault(go, "-N")) // N not specified in cmdline maxseqs = INT_MAX; // no limit else maxseqs = SSE16_NVALS*N; // use cmdline limit for (j = 0; j < maxseqs && esl_sqio_Read(sqfp, sq) == eslOK; j++) { if (equallength && sq->n != len && j > 0) equallength = 0; len = sq->n; if (j > dbsize) { seqsdb = realloc(seqsdb, 2*(dbsize+1)*sizeof(SEQ*)); dbsize *= 2; } ESL_DSQ* dsq = sq->dsq; seqsdb[j] = malloc(sizeof(SEQ)); seqsdb[j]->length = len; seqsdb[j]->seq = malloc((len+4)*sizeof(ESL_DSQ)); memcpy(seqsdb[j]->seq, dsq, len+2); sumlengths += len; esl_sq_Reuse(sq); } N = j/SSE16_NVALS; } else // Not found database. Generate random sequences for (i = 0; i < N; i++) for (j = 0; j < SSE16_NVALS; j++) { int len = L; // - rand()%1000; seqsdb[i*SSE16_NVALS+j] = malloc(sizeof(SEQ)); seqsdb[i*SSE16_NVALS+j]->seq = malloc(len+4); seqsdb[i*SSE16_NVALS+j]->length = len; esl_rsq_xfIID(r, bg->f, abc->K, len, seqsdb[i*SSE16_NVALS+j]->seq); sumlengths += len; } printf("Viterbi COPS Word with %d threads, model %s. ModelLen: %d, #Segms: %d, SeqL.: %d, #seqs: %d, Partition: %d, #parts: %d\n", NTHREADS, hmmfile, gm1->M, (int) ceil(gm1->M/SSE16_NVALS), L, SSE16_NVALS*N*NROUNDS, dcops->partition, dcops->Npartitions); /* // No. of partitions computed without full parallelism ( == no. of threads active while some are idle) int Niters_part = dcops->Npartitions % NTHREADS; // No. of Model lines that could be computed but are wasted by idle threads waiting on the end int Nwasted_threads = dcops->partition * ((NTHREADS-Niters_part) % NTHREADS); // No. of lines in the last partition that go beyond M. It's wasted comp time by a single thread int Nwasted_leftover= (dcops->partition - gm1->M % dcops->partition) % dcops->partition; // Total number of wasted lines int wastedcomp = Nwasted_threads + Nwasted_leftover; // Total number of lines computed and waited for int totalcomp = wastedcomp + gm1->M; // same as: roundtop(gm1->M, dcops->partition * NTHREADS); printf("Total Comp Lines: %d | Wasted Comp Lines: %d\n", totalcomp, wastedcomp); */ if (check) results = (float*) alloc_m128_aligned64((N+1)*2); ftime(&tbstart); if (!equallength) { // Sort sequences by length qsort(seqsdb, N*SSE16_NVALS, sizeof(SEQ*), compare_seqs); } for (j = 0; j < NROUNDS; j++) for (i = 0; i < N; i++) { // if (i % 1000 == 0) printf("Seq %d\n", i); p7_ViterbiCOPSw_run(dcops, seqsdb+i*SSE16_NVALS, sc1); if (check) memcpy(results+i*SSE16_NVALS, sc1, 32); // 32 bytes indeed! SSE16_NVALS floats } ftime(&tbend); double secs = TIMEDIFF(tbstart,tbend); w->elapsed = w->user = secs; esl_stopwatch_Display(stdout, w, "# Opt CPU time: "); double compmillioncells = NROUNDS * (double) sumlengths * (double) hmm->M * 1e-6; printf("# %.0fM cells in %.1f Mc/s\n", compmillioncells, compmillioncells / secs); if (check) { P7_OPROFILE *om = p7_oprofile_Create(hmm->M, gm1->abc); p7_oprofile_Convert(gm1, om); P7_OMX *ox = p7_omx_Create(hmm->M, 0, 0); printf("Compare results against base version\n"); for (i = 0; i < N; i++) { int maxll = 0; float sc2; for (j = 0; j < SSE16_NVALS; j++) if (maxll < seqsdb[i*SSE16_NVALS+j]->length) maxll = seqsdb[i*SSE16_NVALS+j]->length; p7_oprofile_ReconfigRestLength(om, maxll); // p7_ReconfigLength(gm2, maxll); // emulate the lock-step inter-sequence reconfigs for (j = 0; j < SSE16_NVALS; j++) { // p7_ReconfigLength(gm2, seqsdb[i*SSE16_NVALS+j]->length); // p7_Viterbi_unilocal(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc3); // p7_Viterbi_unilocal_word(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc2); // p7_oprofile_ReconfigLength(om, seqsdb[i*SSE16_NVALS+j]->length); p7_ViterbiFilter(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, om, ox, &sc2); sc2 += 1.0; // -2.0nat optimization, Local to Unilocal mode if (fabs(results[i*SSE16_NVALS+j] - sc2) > 0.0001) { printf("Seq %d Len %4d: %f - %f\tdiff: %f\n", i*SSE16_NVALS+j, seqsdb[i*SSE16_NVALS+j]->length, results[i*SSE16_NVALS+j], sc2, fabs(results[i*SSE16_NVALS+j] - sc2)); } } } } 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_OMX *fwd = NULL; P7_OMX *bck = NULL; P7_OMX *pp = 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 fsc, bsc; double Mcs; 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_LOCAL); om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om); p7_oprofile_ReconfigLength(om, L); fwd = p7_omx_Create(gm->M, L, L); bck = p7_omx_Create(gm->M, L, L); pp = p7_omx_Create(gm->M, L, L); esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_Forward (dsq, L, om, fwd, &fsc); p7_Backward(dsq, L, om, fwd, bck, &bsc); esl_stopwatch_Start(w); for (i = 0; i < N; i++) p7_Decoding(om, fwd, bck, pp); 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(fwd); p7_omx_Destroy(bck); p7_omx_Destroy(pp); 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 eslOK; }