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 = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
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;
double lambda = 0.0;
double mmu = 0.0;
double vmu = 0.0;
double ftau = 0.0;
int Z = esl_opt_GetInteger(go, "-Z");
int EmL = esl_opt_GetInteger(go, "--EmL");
int EmN = esl_opt_GetInteger(go, "--EmN");
int EvL = esl_opt_GetInteger(go, "--EvL");
int EvN = esl_opt_GetInteger(go, "--EvN");
int EfL = esl_opt_GetInteger(go, "--EfL");
int EfN = esl_opt_GetInteger(go, "--EfN");
int Eft = esl_opt_GetReal (go, "--Eft");
int iteration;
int do_msv, do_vit, do_fwd;
int status;
if (esl_opt_GetBoolean(go, "--msvonly") == TRUE) { do_msv = TRUE; do_vit = FALSE; do_fwd = FALSE; }
else if (esl_opt_GetBoolean(go, "--vitonly") == TRUE) { do_msv = FALSE; do_vit = TRUE; do_fwd = FALSE; }
else if (esl_opt_GetBoolean(go, "--fwdonly") == TRUE) { do_msv = FALSE; do_vit = FALSE; do_fwd = TRUE; }
else { do_msv = TRUE; do_vit = TRUE; do_fwd = TRUE; }
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
{
if (bg == NULL) bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL); /* the EvL doesn't matter */
om = p7_oprofile_Create(hmm->M, abc);
p7_oprofile_Convert(gm, om);
if (esl_opt_IsOn(go, "--lambda")) lambda = esl_opt_GetReal(go, "--lambda");
else p7_Lambda(hmm, bg, &lambda);
for (iteration = 0; iteration < Z; iteration++)
{
if (do_msv) p7_MSVMu (r, om, bg, EmL, EmN, lambda, &mmu);
if (do_vit) p7_ViterbiMu (r, om, bg, EvL, EvN, lambda, &vmu);
if (do_fwd) p7_Tau (r, om, bg, EfL, EfN, lambda, Eft, &ftau);
printf("%s %.4f %.4f %.4f %.4f\n", hmm->name, lambda, mmu, vmu, ftau);
}
p7_hmm_Destroy(hmm);
p7_profile_Destroy(gm);
p7_oprofile_Destroy(om);
}
p7_hmmfile_Close(hfp);
p7_bg_Destroy(bg);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
int i, j;
int status = eslOK;
P7_HMMFILE *hfp = NULL; /* open input HMM file */
P7_HMM *hmm = NULL; /* one HMM query */
ESL_ALPHABET *abc = NULL; /* digital alphabet */
P7_BG *bg = NULL;
char errbuf[eslERRBUFSIZE];
char* hmmfile;
float *rel_ents = NULL;
float **heights = NULL;
float **probs = NULL;
float *ins_P = NULL;
float *ins_expL = NULL;
float *occupancy = NULL;
int mode = HMMLOGO_RELENT_ALL; //default
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) {
p7_banner (stdout, argv[0], banner);
esl_usage (stdout, argv[0], usage);
puts("\nOptions:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 100);
exit(0);
}
if (esl_opt_ArgNumber(go) != 1) esl_fatal(argv[0], "Incorrect number of command line arguments.\n");
hmmfile = esl_opt_GetArg(go, 1);
if (esl_opt_IsOn(go, "--height_relent_all"))
mode = HMMLOGO_RELENT_ALL;
else if (esl_opt_IsOn(go, "--height_relent_abovebg"))
mode = HMMLOGO_RELENT_ABOVEBG;
else if (esl_opt_IsOn(go, "--height_score"))
mode = HMMLOGO_SCORE;
else
mode = HMMLOGO_RELENT_ALL; //default
/* Open the query profile HMM file */
status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile, errbuf);
status = p7_hmmfile_Read(hfp, &abc, &hmm);
bg = p7_bg_Create(abc);
ESL_ALLOC(rel_ents, (hmm->M+1) * sizeof(float));
ESL_ALLOC(heights, (hmm->M+1) * sizeof(float*));
ESL_ALLOC(probs, (hmm->M+1) * sizeof(float*));
for (i = 1; i <= hmm->M; i++) {
ESL_ALLOC(heights[i], abc->K * sizeof(float));
ESL_ALLOC(probs[i], abc->K * sizeof(float));
}
/* residue heights */
if (mode == HMMLOGO_RELENT_ALL) {
printf ("max expected height = %.2f\n", hmmlogo_maxHeight(bg) );
hmmlogo_RelativeEntropy_all(hmm, bg, rel_ents, probs, heights);
} else if (mode == HMMLOGO_RELENT_ABOVEBG) {
printf ("max expected height = %.2f\n", hmmlogo_maxHeight(bg) );
hmmlogo_RelativeEntropy_above_bg(hmm, bg, rel_ents, probs, heights);
} else if (mode == HMMLOGO_SCORE) {
hmmlogo_ScoreHeights(hmm, bg, heights );
}
printf ("Residue heights\n");
for (i = 1; i <= hmm->M; i++) {
printf("%d: ", i);
for (j=0; j<abc->K; j++)
printf("%6.3f ", heights[i][j] );
if (mode != HMMLOGO_SCORE)
printf(" (%6.3f)", rel_ents[i]);
printf("\n");
}
if (rel_ents != NULL) free(rel_ents);
if (heights != NULL) {
for (i = 1; i <= hmm->M; i++)
if (heights[i] != NULL) free(heights[i]);
free(heights);
}
/* indel values */
if (! esl_opt_IsOn(go, "--no_indel")) {
ESL_ALLOC(ins_P, (hmm->M+1) * sizeof(float));
ESL_ALLOC(ins_expL, (hmm->M+1) * sizeof(float));
ESL_ALLOC(occupancy, (hmm->M+1) * sizeof(float));
hmmlogo_IndelValues(hmm, ins_P, ins_expL, occupancy);
printf ("Indel values\n");
for (i = 1; i <= hmm->M; i++)
printf("%d: %6.3f %6.3f %6.3f\n", i, ins_P[i], ins_expL[i], occupancy[i] );
free(ins_P);
free(ins_expL);
free(occupancy);
}
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
exit(0);
ERROR:
if (rel_ents != NULL) free(rel_ents);
if (heights != NULL) {
for (i = 1; i <= hmm->M; i++)
if (heights[i] != NULL) free(heights[i]);
free(heights);
}
if (hfp != NULL) p7_hmmfile_Close(hfp);
if (abc != NULL) esl_alphabet_Destroy(abc);
if (ins_P != NULL) free(ins_P);
if (ins_expL != NULL) free(ins_expL);
if (occupancy != NULL) free(occupancy);
}
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, 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);
if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsVF(om, gm);
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_ViterbiFilter(dsq, L, om, ox, &sc1);
if (esl_opt_GetBoolean(go, "-c"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
printf("%.4f %.4f\n", sc1, sc2);
}
if (esl_opt_GetBoolean(go, "-x"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
sc2 /= om->scale_w;
if (om->mode == p7_UNILOCAL) sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
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, 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_GViterbi (dsq, L, gm, gx, &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 = 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_GMX *gx1 = NULL;
P7_GMX *gx2 = 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;
double Mcs;
p7_FLogsumInit();
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_UNILOCAL);
gx1 = p7_gmx_Create(gm->M, L);
gx2 = p7_gmx_Create(gm->M, L);
tr = p7_trace_CreateWithPP();
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_GForward (dsq, L, gm, gx1, &fsc);
p7_GBackward(dsq, L, gm, gx2, &bsc);
p7_GDecoding(gm, gx1, gx2, gx2); /* <gx2> is now the posterior decoding matrix */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
p7_GOptimalAccuracy(gm, gx2, gx1, &accscore); /* <gx1> is now the OA matrix */
if (! esl_opt_GetBoolean(go, "--notrace"))
{
p7_GOATrace(gm, gx2, gx1, tr);
p7_trace_Reuse(tr);
}
}
esl_stopwatch_Stop(w);
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_trace_Destroy(tr);
p7_gmx_Destroy(gx1);
p7_gmx_Destroy(gx2);
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 = p7_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_OpenE(hmmfile, NULL, &hfp, NULL) != 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, 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);
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 = NULL; /* command line processing */
ESL_ALPHABET *abc = NULL;
char *hmmfile = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
int nhmm;
double x;
float KL;
int status;
char errbuf[eslERRBUFSIZE];
float nseq;
int do_eval2score = 0;
int do_score2eval = 0;
int z_val;
float e_val;
float s_val;
/* Process the command line options.
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK ||
esl_opt_VerifyConfig(go) != eslOK)
{
printf("Failed to parse command line: %s\n", go->errbuf);
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
p7_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
puts("\nOptions:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=docgroup, 2 = indentation; 80=textwidth*/
exit(0);
}
if (esl_opt_ArgNumber(go) != 1)
{
puts("Incorrect number of command line arguments.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if ((hmmfile = esl_opt_GetArg(go, 1)) == NULL)
{
puts("Failed to read <hmmfile> argument from command line.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
output_header(stdout, go);
if ( esl_opt_IsOn(go, "--eval2score") ) {
do_eval2score = TRUE;
e_val = esl_opt_GetReal(go, "-E");
} else if ( esl_opt_IsOn(go, "--score2eval") ) {
do_score2eval = TRUE;
s_val = esl_opt_GetReal(go, "-S");
} else if ( esl_opt_IsUsed(go, "--baseZ") || esl_opt_IsUsed(go, "--baseZ1") || esl_opt_IsUsed(go, "-Z") ) {
puts("The flags -Z, --baseZ, and --baseZ1 are for use with --eval2score and --score2eval.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_IsUsed(go, "--baseZ") ) {
z_val = 1000000 * 2 * (long)(esl_opt_GetInteger(go, "--baseZ"));
} else if (esl_opt_IsUsed(go, "--baseZ1") ) {
z_val = 1000000 * (long)(esl_opt_GetInteger(go, "--baseZ1"));
} else {
z_val = esl_opt_GetInteger(go, "-Z");
}
/* Initializations: open the HMM file
*/
status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile, errbuf);
/* Main body: read HMMs one at a time, print one line of stats
*/
printf("#\n");
printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s", "idx", "name", "accession", "nseq", "eff_nseq", "M", "relent", "info", "p relE", "compKL");
if (do_eval2score)
printf (" %6s %6.2g", "sc for", e_val);
if (do_score2eval)
printf (" %6s %6.2f", "E-val for", s_val);
printf("\n");
printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s", "----", "--------------------", "------------", "--------", "--------", "------", "------", "------", "------", "------");
if (do_eval2score)
printf (" %13s", "-------------");
if (do_score2eval)
printf (" %13s", "-------------");
printf("\n");
nhmm = 0;
while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
{
if (status == eslEOD) esl_fatal("read failed, HMM file %s may be truncated?", hmmfile);
else 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 != eslOK) esl_fatal("Unexpected error in reading HMMs from %s", hmmfile);
nhmm++;
if ( esl_opt_IsOn(go, "--eval2score") || esl_opt_IsOn(go, "--score2eval") ) {
if (esl_opt_IsUsed(go, "--baseZ") || esl_opt_IsUsed(go, "--baseZ1" ) ) {
if ( hmm->abc->type != eslRNA && hmm->abc->type != eslDNA) {
puts("The flags --baseZ and --baseZ1 can't be used with non-nucleotide models.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
} else if ( hmm->abc->type != eslAMINO && hmm->abc->type != eslRNA && hmm->abc->type != eslDNA) {
puts("The flags --eval2score and --score2eval can't be used with non-sequence models.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
}
if (esl_opt_IsUsed(go, "--baseZ") ) {
nseq = (float)z_val / (float)(hmm->max_length);
} else if (esl_opt_IsUsed(go, "--baseZ1") ) {
nseq = (float)z_val / (float)(hmm->max_length);
} else {
nseq = z_val;
}
if (bg == NULL) bg = p7_bg_Create(abc);
p7_MeanPositionRelativeEntropy(hmm, bg, &x);
p7_hmm_CompositionKLDist(hmm, bg, &KL, NULL);
printf("%-6d %-20s %-12s %8d %8.2f %6d %6.2f %6.2f %6.2f %6.2f",
nhmm,
hmm->name,
hmm->acc == NULL ? "-" : hmm->acc,
hmm->nseq,
hmm->eff_nseq,
hmm->M,
p7_MeanMatchRelativeEntropy(hmm, bg),
p7_MeanMatchInfo(hmm, bg),
x,
KL);
if ( do_eval2score )
{
float sc;
sc = esl_exp_invsurv( e_val / nseq , hmm->evparam[p7_FTAU], hmm->evparam[p7_FLAMBDA]);
printf("%13.2f", sc);
}
else if ( do_score2eval)
{
float e;
e = nseq * esl_exp_surv( s_val , hmm->evparam[p7_FTAU], hmm->evparam[p7_FLAMBDA]);
printf("%13.2g", e);
}
printf("\n");
/* p7_MeanForwardScore(hmm, bg)); */
p7_hmm_Destroy(hmm);
}
p7_bg_Destroy(bg);
esl_alphabet_Destroy(abc);
p7_hmmfile_Close(hfp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
char *hmmfile = argv[1];
char *seqfile = argv[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 *ox = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float sc;
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);
p7_oprofile_Logify(om);
/* allocate DP matrices, both a generic and an optimized one */
ox = p7_omx_Create(gm->M, 0, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
/* Useful to place and compile in for debugging:
p7_oprofile_Dump(stdout, om); dumps the optimized profile
p7_omx_SetDumpMode(ox, TRUE); makes the fast DP algorithms dump their matrices
p7_gmx_Dump(stdout, gx); dumps a generic DP matrix
*/
p7_ViterbiScore(sq->dsq, sq->n, om, ox, &sc); printf("viterbi (non-optimized): %.2f nats\n", sc);
p7_GViterbi (sq->dsq, sq->n, gm, gx, &sc); printf("viterbi (generic): %.2f nats\n", sc);
/* now in a real app, you'd need to convert raw nat scores to final bit
* scores, by subtracting the null model score and rescaling.
*/
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
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);
return 0;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmdb> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail().
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* output file for results (default stdout) */
FILE *tblfp = NULL; /* output stream for tabular per-seq (--tblout) */
FILE *dfamtblfp = NULL; /* output stream for tabular Dfam format (--dfamtblout) */
FILE *aliscoresfp = NULL; /* output stream for alignment scores (--aliscoresout) */
// P7_HMM *hmm = NULL; /* one HMM query */
// P7_SCOREDATA *scoredata = NULL;
int seqfmt = eslSQFILE_UNKNOWN; /* format of seqfile */
ESL_SQFILE *sqfp = NULL; /* open seqfile */
P7_HMMFILE *hfp = NULL; /* open HMM database file */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
P7_OPROFILE *om = NULL; /* target profile */
ESL_STOPWATCH *w = NULL; /* timing */
ESL_SQ *qsq = NULL; /* query sequence */
int nquery = 0;
int textw;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
P7_OM_BLOCK *block = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errbuf[eslERRBUFSIZE];
double window_beta = -1.0 ;
int window_length = -1;
if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) < 0 || window_beta > 1 ) esl_fatal("Invalid window-length beta value\n"); }
if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4 ) esl_fatal("Invalid window length value\n"); }
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
/* If caller declared an input format, decode it */
if (esl_opt_IsOn(go, "--qformat")) {
seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
}
/* validate options if running as a daemon */
// if (esl_opt_IsOn(go, "--daemon")) {
/* running as a daemon, the input format must be type daemon */
// if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
// esl_fatal("Input format %s not supported. Must be daemon\n", esl_opt_GetString(go, "--qformat"));
// seqfmt = eslSQFILE_DAEMON;
// if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
// }
/* Open the target profile database to get the sequence alphabet */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem, trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, cfg->hmmfile, errbuf);
if (! hfp->is_pressed) p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n", hfp->fname);
hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
if (hstatus == eslEFORMAT) p7_Fail("bad format, binary auxfiles, %s:\n%s", cfg->hmmfile, hfp->errbuf);
else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
else if (hstatus != eslOK) p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
p7_oprofile_Destroy(om);
p7_hmmfile_Close(hfp);
/* Open the query sequence database */
status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->seqfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->seqfile);
else if (status == eslEINVAL) p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
if (sqfp->format > 100) // breaking the law! That range is reserved for msa, for aligned formats
p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n", cfg->seqfile);
qsq = esl_sq_CreateDigital(abc);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
output_header(ofp, go, cfg->hmmfile, cfg->seqfile);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(abc);
#ifdef HMMER_THREADS
info[i].queue = queue;
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
block = p7_oprofile_CreateBlock(BLOCK_SIZE);
if (block == NULL) esl_fatal("Failed to allocate sequence block");
status = esl_workqueue_Init(queue, block);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
/* Outside loop: over each query sequence in <seqfile>. */
while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
{
if (sstatus == eslEMEM) p7_Fail("Memory allocation error reading sequence file\n", status);
if (sstatus == eslEINCONCEIVABLE) p7_Fail("Unexpected error %d reading sequence file\n", status);
// if (qsq->L > NHMMER_MAX_RESIDUE_COUNT) p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n", qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);
nquery++;
esl_stopwatch_Start(w);
/* Open the target profile database */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
if (status != eslOK) p7_Fail("Unexpected error %d in opening hmm file %s.\n", status, cfg->hmmfile);
#ifdef HMMER_THREADS
/* if we are threaded, create a lock to prevent multiple readers */
if (ncpus > 0)
{
status = p7_hmmfile_CreateLock(hfp);
if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
}
#endif
if (fprintf(ofp, "Query: %s [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->acc[0] != 0 && fprintf(ofp, "Accession: %s\n", qsq->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
info[i].pli->hfp = hfp; /* for two-stage input, pipeline needs <hfp> */
p7_pli_NewSeq(info[i].pli, qsq);
info[i].qsq = qsq;
if ( esl_opt_IsUsed(go, "--toponly") )
info[i].pli->strand = p7_STRAND_TOPONLY;
else if ( esl_opt_IsUsed(go, "--bottomonly") )
info[i].pli->strand = p7_STRAND_BOTTOMONLY;
else
info[i].pli->strand = p7_STRAND_BOTH;
#ifdef HMMER_THREADS
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
if (ncpus > 0) hstatus = thread_loop(threadObj, queue, hfp);
else hstatus = serial_loop(info, hfp);
#else
hstatus = serial_loop(info, hfp);
#endif
switch(hstatus)
{
case eslEFORMAT: p7_Fail("bad file format in HMM file %s", cfg->hmmfile); break;
case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile); break;
case eslEOF:
case eslOK: /* do nothing */
break;
default: p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
}
/* merge the results of the search results */
for (i = 1; i < infocnt; ++i)
{
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
}
/* modify e-value to account for number of models */
for (i = 0; i < info->th->N ; i++)
{
info->th->unsrt[i].lnP += log((float)info->pli->nmodels);
info->th->unsrt[i].dcl[0].lnP = info->th->unsrt[i].lnP;
info->th->unsrt[i].sortkey = -1.0 * info->th->unsrt[i].lnP;
}
/* it's possible to have duplicates based on how viterbi ranges can overlap */
p7_tophits_SortByModelnameAndAlipos(info->th);
p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);
/* Print results */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
//tally up total number of hits and target coverage
info->pli->n_output = info->pli->pos_output = 0;
for (i = 0; i < info->th->N; i++) {
if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
info->pli->n_output++;
info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
}
}
p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (tblfp) p7_tophits_TabularTargets(tblfp, qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp, qsq->name, NULL, info->th, info->pli);
if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );
esl_stopwatch_Stop(w);
info->pli->nseqs = 1;
p7_pli_Statistics(ofp, info->pli, w);
if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
fflush(ofp);
p7_hmmfile_Close(hfp);
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
esl_sq_Reuse(qsq);
}
if (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (sstatus != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
sstatus, sqfp->filename);
/* Terminate outputs - any last words?
*/
if (tblfp) p7_tophits_TabularTail(tblfp, "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
if (ofp) { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Cleanup - prepare for successful exit
*/
for (i = 0; i < infocnt; ++i)
p7_bg_Destroy(info[i].bg);
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
p7_oprofile_DestroyBlock(block);
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
esl_sq_Destroy(qsq);
esl_stopwatch_Destroy(w);
esl_alphabet_Destroy(abc);
esl_sqfile_Close(sqfp);
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return eslOK;
ERROR:
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return status;
}
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;
}
static void
search_thread(void *arg)
{
int i;
int count;
int seed;
int status;
int workeridx;
WORKER_INFO *info;
ESL_THREADS *obj;
ESL_SQ dbsq;
ESL_STOPWATCH *w = NULL; /* timing stopwatch */
P7_BUILDER *bld = NULL; /* HMM construction configuration */
P7_BG *bg = NULL; /* null model */
P7_PIPELINE *pli = NULL; /* work pipeline */
P7_TOPHITS *th = NULL; /* top hit results */
P7_PROFILE *gm = NULL; /* generic model */
P7_OPROFILE *om = NULL; /* optimized query profile */
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
w = esl_stopwatch_Create();
bg = p7_bg_Create(info->abc);
esl_stopwatch_Start(w);
/* set up the dummy description and accession fields */
dbsq.desc = "";
dbsq.acc = "";
/* process a query sequence or hmm */
if (info->seq != NULL) {
bld = p7_builder_Create(NULL, info->abc);
if ((seed = esl_opt_GetInteger(info->opts, "--seed")) > 0) {
esl_randomness_Init(bld->r, seed);
bld->do_reseeding = TRUE;
}
bld->EmL = esl_opt_GetInteger(info->opts, "--EmL");
bld->EmN = esl_opt_GetInteger(info->opts, "--EmN");
bld->EvL = esl_opt_GetInteger(info->opts, "--EvL");
bld->EvN = esl_opt_GetInteger(info->opts, "--EvN");
bld->EfL = esl_opt_GetInteger(info->opts, "--EfL");
bld->EfN = esl_opt_GetInteger(info->opts, "--EfN");
bld->Eft = esl_opt_GetReal (info->opts, "--Eft");
if (esl_opt_IsOn(info->opts, "--mxfile")) status = p7_builder_SetScoreSystem (bld, esl_opt_GetString(info->opts, "--mxfile"), NULL, esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
else status = p7_builder_LoadScoreSystem(bld, esl_opt_GetString(info->opts, "--mx"), esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
if (status != eslOK) {
//client_error(info->sock, status, "hmmgpmd: failed to set single query sequence score system: %s", bld->errbuf);
fprintf(stderr, "hmmpgmd: failed to set single query sequence score system: %s", bld->errbuf);
pthread_exit(NULL);
return;
}
p7_SingleBuilder(bld, info->seq, bg, NULL, NULL, NULL, &om); /* bypass HMM - only need model */
p7_builder_Destroy(bld);
} else {
gm = p7_profile_Create (info->hmm->M, info->abc);
om = p7_oprofile_Create(info->hmm->M, info->abc);
p7_ProfileConfig(info->hmm, bg, gm, 100, p7_LOCAL);
p7_oprofile_Convert(gm, om);
}
/* Create processing pipeline and hit list */
th = p7_tophits_Create();
pli = p7_pipeline_Create(info->opts, om->M, 100, FALSE, p7_SEARCH_SEQS);
p7_pli_NewModel(pli, om, bg);
if (pli->Z_setby == p7_ZSETBY_NTARGETS) pli->Z = info->db_Z;
/* loop until all sequences have been processed */
count = 1;
while (count > 0) {
int inx;
int blksz;
HMMER_SEQ **sq;
/* grab the next block of sequences */
if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
inx = *info->inx;
blksz = *info->blk_size;
if (inx > *info->limit) {
blksz /= 5;
if (blksz < 1000) {
*info->limit = info->sq_cnt * 2;
} else {
*info->limit = inx + (info->sq_cnt - inx) * 2 / 3;
}
}
*info->blk_size = blksz;
*info->inx += blksz;
if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");
sq = info->sq_list + inx;
count = info->sq_cnt - inx;
if (count > blksz) count = blksz;
/* Main loop: */
for (i = 0; i < count; ++i, ++sq) {
if ( !(info->range_list) || hmmpgmd_IsWithinRanges ((*sq)->idx, info->range_list)) {
dbsq.name = (*sq)->name;
dbsq.dsq = (*sq)->dsq;
dbsq.n = (*sq)->n;
dbsq.idx = (*sq)->idx;
if((*sq)->desc != NULL) dbsq.desc = (*sq)->desc;
p7_bg_SetLength(bg, dbsq.n);
p7_oprofile_ReconfigLength(om, dbsq.n);
p7_Pipeline(pli, om, bg, &dbsq, th);
p7_pipeline_Reuse(pli);
}
}
}
/* make available the pipeline objects to the main thread */
info->th = th;
info->pli = pli;
/* clean up */
p7_bg_Destroy(bg);
p7_oprofile_Destroy(om);
if (gm != NULL) p7_profile_Destroy(gm);
esl_stopwatch_Stop(w);
info->elapsed = w->elapsed;
esl_stopwatch_Destroy(w);
esl_threads_Finished(obj, workeridx);
pthread_exit(NULL);
return;
}
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;
}
static void
scan_thread(void *arg)
{
int i;
int count;
int workeridx;
WORKER_INFO *info;
ESL_THREADS *obj;
ESL_STOPWATCH *w;
P7_BG *bg = NULL; /* null model */
P7_PIPELINE *pli = NULL; /* work pipeline */
P7_TOPHITS *th = NULL; /* top hit results */
obj = (ESL_THREADS *) arg;
esl_threads_Started(obj, &workeridx);
info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
w = esl_stopwatch_Create();
esl_stopwatch_Start(w);
/* Convert to an optimized model */
bg = p7_bg_Create(info->abc);
/* Create processing pipeline and hit list */
th = p7_tophits_Create();
pli = p7_pipeline_Create(info->opts, 100, 100, FALSE, p7_SCAN_MODELS);
p7_pli_NewSeq(pli, info->seq);
/* loop until all sequences have been processed */
count = 1;
while (count > 0) {
int inx;
int blksz;
P7_OPROFILE **om;
/* grab the next block of sequences */
if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
inx = *info->inx;
blksz = *info->blk_size;
if (inx > *info->limit) {
blksz /= 5;
if (blksz < 1000) {
*info->limit = info->om_cnt * 2;
} else {
*info->limit = inx + (info->om_cnt - inx) * 2 / 3;
}
}
*info->blk_size = blksz;
*info->inx += blksz;
if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");
om = info->om_list + inx;
count = info->om_cnt - inx;
if (count > blksz) count = blksz;
/* Main loop: */
for (i = 0; i < count; ++i, ++om) {
p7_pli_NewModel(pli, *om, bg);
p7_bg_SetLength(bg, info->seq->n);
p7_oprofile_ReconfigLength(*om, info->seq->n);
p7_Pipeline(pli, *om, bg, info->seq, th);
p7_pipeline_Reuse(pli);
}
}
/* make available the pipeline objects to the main thread */
info->th = th;
info->pli = pli;
/* clean up */
p7_bg_Destroy(bg);
esl_stopwatch_Stop(w);
info->elapsed = w->elapsed;
esl_stopwatch_Destroy(w);
esl_threads_Finished(obj, workeridx);
pthread_exit(NULL);
return;
}
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, 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 : ", tr->ndom);
for (d = 0; d < tr->ndom; d++) printf("%6d %6d %6d %6d ", tr->sqfrom[d], tr->sqto[d], tr->hmmfrom[d], tr->hmmto[d]);
printf("\n");
/* Cleanup */
p7_trace_Destroy(tr);
p7_gmx_Destroy(fwd);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_sq_Destroy(sq);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
ESL_RANDOMNESS *rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
char *ghmmfile = esl_opt_GetArg(go, 1); /* HMMs parameterized for sequence generation */
char *ahmmfile = esl_opt_GetArg(go, 2); /* HMMs parameterized for alignment */
int N = esl_opt_GetInteger(go, "-N");
P7_HMMFILE *ghfp = NULL;
P7_HMMFILE *ahfp = NULL;
P7_HMM *ghmm = NULL;
P7_HMM *ahmm = NULL;
P7_PROFILE *ggm = NULL;
P7_PROFILE *agm = NULL;
P7_OPROFILE *aom = NULL;
P7_BG *bg = NULL;
ESL_SQ *sq = NULL;
P7_TRACE *reftr = p7_trace_Create();
P7_TRACE *testtr = p7_trace_Create();
P7_TRACE_METRICS *tmetrics = p7_trace_metrics_Create();
P7_REFMX *rmx = p7_refmx_Create(100,100);
// P7_FILTERMX *ox = NULL;
P7_HARDWARE *hw;
if ((hw = p7_hardware_Create ()) == NULL) p7_Fail("Couldn't get HW information data structure");
P7_SPARSEMASK *sm = p7_sparsemask_Create(100, 100, hw->simd);
P7_SPARSEMX *sxv = p7_sparsemx_Create(NULL);
int idx;
char errbuf[eslERRBUFSIZE];
int status;
p7_Init();
/* open HMM file containing models parameterized for generation (sampling) of seqs */
status = p7_hmmfile_OpenE(ghmmfile, NULL, &ghfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", ghmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", ghmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, ghmmfile, errbuf);
/* open HMM file containing models parameterized for alignment (may be the same as ghmmfile) */
status = p7_hmmfile_OpenE(ahmmfile, NULL, &ahfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", ahmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", ahmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, ahmmfile, errbuf);
while ( (status = p7_hmmfile_Read(ghfp, &abc, &ghmm)) == eslOK) /* <abc> gets set on first read */
{
/* read the counterpart HMM from <ahfp> */
status = p7_hmmfile_Read(ahfp, &abc, &ahmm);
if (status == eslEFORMAT) p7_Fail("Bad file format in HMM file %s:\n%s\n", ahfp->fname, ahfp->errbuf);
else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", ahfp->fname, esl_abc_DecodeType(abc->type));
else if (status == eslEOF) p7_Fail("Empty HMM file %s? No HMM data found.\n", ahfp->fname);
else if (status != eslOK) p7_Fail("Unexpected error in reading HMMs from %s\n", ahfp->fname);
/* try to validate that they're the "same" */
if (ahmm->M != ghmm->M || strcmp(ahmm->name, ghmm->name) != 0) p7_Fail("<gen-hmmfile>, <ali-hmmfile> contain different set or order of models");
/* deferred one-time creation of structures that need to know the alphabet */
if (!bg) bg = p7_bg_Create(abc);
if (!sq) sq = esl_sq_CreateDigital(abc);
ggm = p7_profile_Create(ghmm->M, abc);
agm = p7_profile_Create(ahmm->M, abc);
aom = p7_oprofile_Create(ahmm->M, abc, hw->simd);
p7_profile_ConfigCustom(ggm, ghmm, bg, esl_opt_GetInteger(go, "--gL"), esl_opt_GetReal(go, "--gnj"), esl_opt_GetReal(go, "--gpglocal"));
p7_profile_ConfigCustom(agm, ahmm, bg, 100, esl_opt_GetReal(go, "--anj"), esl_opt_GetReal(go, "--apglocal"));
p7_oprofile_Convert(agm, aom);
for (idx = 1; idx <= N; idx++)
{
p7_ProfileEmit(rng, ghmm, ggm, bg, sq, reftr);
if (esl_opt_GetBoolean(go, "--dumpseqs")) {
esl_sq_FormatName(sq, "seq%d", idx);
esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);
}
p7_bg_SetLength(bg, sq->n);
p7_profile_SetLength(agm, sq->n);
p7_sparsemask_Reinit(sm, agm->M, sq->n);
p7_sparsemask_AddAll(sm);
if (esl_opt_GetBoolean(go, "--vit")) p7_ReferenceViterbi(sq->dsq, sq->n, agm, rmx, testtr, /*opt_vsc=*/NULL);
else p7_SparseViterbi (sq->dsq, sq->n, agm, sm, sxv, testtr, /*opt_vsc=*/NULL);
p7_trace_metrics(reftr, testtr, tmetrics);
p7_sparsemask_Reuse(sm);
p7_sparsemx_Reuse(sxv);
//p7_filtermx_Reuse(ox);
p7_refmx_Reuse(rmx);
esl_sq_Reuse(sq);
p7_trace_Reuse(reftr);
p7_trace_Reuse(testtr);
}
p7_oprofile_Destroy(aom);
p7_profile_Destroy(ggm);
p7_profile_Destroy(agm);
p7_hmm_Destroy(ghmm);
p7_hmm_Destroy(ahmm);
}
/* we leave the loop with <status> set by a p7_hmmfile_Read() on ghfp; if all is well, status=eslEOF */
if (status == eslEFORMAT) p7_Fail("Bad file format in HMM file %s:\n%s\n", ghfp->fname, ghfp->errbuf);
else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", ghfp->fname, esl_abc_DecodeType(abc->type));
else if (status != eslEOF) p7_Fail("Unexpected error in reading HMMs from %s\n", ghfp->fname);
p7_trace_metrics_Dump(stdout, tmetrics);
p7_hmmfile_Close(ghfp);
p7_hmmfile_Close(ahfp);
// p7_filtermx_Destroy(ox);
p7_sparsemask_Destroy(sm);
p7_sparsemx_Destroy(sxv);
p7_refmx_Destroy(rmx);
p7_trace_metrics_Destroy(tmetrics);
p7_trace_Destroy(testtr);
p7_trace_Destroy(reftr);
p7_bg_Destroy(bg);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(rng);
esl_getopts_Destroy(go);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_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 *gx1 = NULL;
P7_GMX *gx2 = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
P7_TRACE *tr = NULL;
int format = eslSQFILE_UNKNOWN;
char errbuf[eslERRBUFSIZE];
float fsc, bsc, vsc;
float accscore;
int status;
/* Read in one HMM */
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");
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 */
/* Allocations */
gx1 = p7_gmx_Create(gm->M, sq->n);
gx2 = p7_gmx_Create(gm->M, sq->n);
tr = p7_trace_CreateWithPP();
p7_FLogsumInit();
/* Run Forward, Backward; do OA fill and trace */
p7_GForward (sq->dsq, sq->n, gm, gx1, &fsc);
p7_GBackward(sq->dsq, sq->n, gm, gx2, &bsc);
p7_GDecoding(gm, gx1, gx2, gx2); /* <gx2> is now the posterior decoding matrix */
p7_GOptimalAccuracy(gm, gx2, gx1, &accscore); /* <gx1> is now the OA matrix */
p7_GOATrace(gm, gx2, gx1, tr);
if (esl_opt_GetBoolean(go, "-d")) p7_gmx_Dump(stdout, gx2, p7_DEFAULT);
if (esl_opt_GetBoolean(go, "-m")) p7_gmx_Dump(stdout, gx1, p7_DEFAULT);
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);
p7_trace_Reuse(tr);
p7_GViterbi(sq->dsq, sq->n, gm, gx1, &vsc);
p7_GTrace (sq->dsq, sq->n, gm, gx1, tr);
p7_trace_SetPP(tr, gx2);
p7_trace_Dump(stdout, tr, gm, sq->dsq);
printf("vit = %.4f nats\n", vsc);
printf("acc = %.4f\n", p7_trace_GetExpectedAccuracy(tr));
/* Cleanup */
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
p7_gmx_Destroy(gx1);
p7_gmx_Destroy(gx2);
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 = 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_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_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);
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_ALPHABET *abc = NULL; /* sequence alphabet */
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_RANDOMNESS *r = NULL; /* source of randomness */
P7_HMM *hmm = NULL; /* sampled HMM to emit from */
P7_HMM *core = NULL; /* safe copy of the HMM, before config */
P7_BG *bg = NULL; /* null model */
ESL_SQ *sq = NULL; /* sampled sequence */
P7_TRACE *tr = NULL; /* sampled trace */
P7_PROFILE *gm = NULL; /* profile */
int i,j;
int i1,i2;
int k1,k2;
int iseq;
FILE *fp = NULL;
double expected;
int do_ilocal;
char *hmmfile = NULL;
int nseq;
int do_swlike;
int do_ungapped;
int L;
int M;
int do_h2;
char *ipsfile = NULL;
char *kpsfile = NULL;
ESL_DMATRIX *imx = NULL;
ESL_DMATRIX *kmx = NULL;
ESL_DMATRIX *iref = NULL; /* reference matrix: expected i distribution under ideality */
int Lbins;
int status;
char errbuf[eslERRBUFSIZE];
/*****************************************************************
* Parse the command line
*****************************************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") == TRUE) {
puts(usage);
puts("\n where options are:\n");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2 = indentation; 80=textwidth*/
return eslOK;
}
do_ilocal = esl_opt_GetBoolean(go, "-i");
hmmfile = esl_opt_GetString (go, "-m");
nseq = esl_opt_GetInteger(go, "-n");
do_swlike = esl_opt_GetBoolean(go, "-s");
do_ungapped = esl_opt_GetBoolean(go, "-u");
L = esl_opt_GetInteger(go, "-L");
M = esl_opt_GetInteger(go, "-M");
do_h2 = esl_opt_GetBoolean(go, "-2");
ipsfile = esl_opt_GetString (go, "--ips");
kpsfile = esl_opt_GetString (go, "--kps");
if (esl_opt_ArgNumber(go) != 0) {
puts("Incorrect number of command line arguments.");
printf("Usage: %s [options]\n", argv[0]);
return eslFAIL;
}
r = esl_randomness_CreateFast(0);
if (hmmfile != NULL)
{ /* Read the HMM (and get alphabet from it) */
P7_HMMFILE *hfp = NULL;
status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile, errbuf);
if ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslOK) {
if (status == eslEOD) esl_fatal("read failed, HMM file %s may be truncated?", hmmfile);
else 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 esl_fatal("Unexpected error in reading HMMs");
}
M = hmm->M;
p7_hmmfile_Close(hfp);
}
else
{ /* Or sample the HMM (create alphabet first) */
abc = esl_alphabet_Create(eslAMINO);
if (do_ungapped) p7_hmm_SampleUngapped(r, M, abc, &hmm);
else if (do_swlike) p7_hmm_SampleUniform (r, M, abc, 0.05, 0.5, 0.05, 0.2, &hmm); /* tmi, tii, tmd, tdd */
else p7_hmm_Sample (r, M, abc, &hmm);
}
Lbins = M;
imx = esl_dmatrix_Create(Lbins, Lbins);
iref = esl_dmatrix_Create(Lbins, Lbins);
kmx = esl_dmatrix_Create(M, M);
esl_dmatrix_SetZero(imx);
esl_dmatrix_SetZero(iref);
esl_dmatrix_SetZero(kmx);
tr = p7_trace_Create();
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
core = p7_hmm_Clone(hmm);
if (do_h2) {
gm = p7_profile_Create(hmm->M, abc);
p7_H2_ProfileConfig(hmm, bg, gm, p7_UNILOCAL);
} else {
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
if (p7_hmm_Validate (hmm, NULL, 0.0001) != eslOK) esl_fatal("whoops, HMM is bad!");
if (p7_profile_Validate(gm, NULL, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!");
}
/* Sample endpoints.
* Also sample an ideal reference distribution for i endpoints. i
* endpoints are prone to discretization artifacts, when emitted
* sequences have varying lengths. Taking log odds w.r.t. an ideal
* reference that is subject to the same discretization artifacts
* cancels out the effect.
*/
for (iseq = 0; iseq < nseq; iseq++)
{
if (do_ilocal) ideal_local_endpoints (r, core, sq, tr, Lbins, &i1, &i2, &k1, &k2);
else profile_local_endpoints(r, core, gm, sq, tr, Lbins, &i1, &i2, &k1, &k2);
imx->mx[i1-1][i2-1] += 1.;
kmx->mx[k1-1][k2-1] += 1.;
/* reference distribution for i */
ideal_local_endpoints (r, core, sq, tr, Lbins, &i1, &i2, &k1, &k2);
iref->mx[i1-1][i2-1] += 1.;
}
/* Adjust both mx's to log_2(obs/exp) ratio */
printf("Before normalization/log-odds:\n");
printf(" i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
printf(" k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));
printf("iref matrix values range from %f to %f\n", dmx_upper_min(iref), dmx_upper_max(iref));
expected = (double) nseq * 2. / (double) (M*(M+1));
for (i = 0; i < kmx->m; i++)
for (j = i; j < kmx->n; j++)
kmx->mx[i][j] = log(kmx->mx[i][j] / expected) / log(2.0);
for (i = 0; i < imx->m; i++)
for (j = i; j < imx->m; j++)
if (iref->mx[i][j] == 0. && imx->mx[i][j] == 0.)
imx->mx[i][j] = 0.;
else if (iref->mx[i][j] == 0.)
imx->mx[i][j] = eslINFINITY;
else if (imx->mx[i][j] == 0.)
imx->mx[i][j] = -eslINFINITY;
else
imx->mx[i][j] = log(imx->mx[i][j] / iref->mx[i][j]) / log(2.0);
/* Print ps files */
if (kpsfile != NULL) {
if ((fp = fopen(kpsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", kpsfile);
dmx_Visualize(fp, kmx, -4., 5.);
fclose(fp);
}
if (ipsfile != NULL) {
if ((fp = fopen(ipsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", ipsfile);
dmx_Visualize(fp, imx, -4., 5.);
/* dmx_Visualize(fp, imx, dmx_upper_min(imx), dmx_upper_max(imx)); */
fclose(fp);
}
printf("After normalization/log-odds:\n");
printf("i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
printf("k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(core);
p7_hmm_Destroy(hmm);
p7_trace_Destroy(tr);
esl_sq_Destroy(sq);
esl_dmatrix_Destroy(imx);
esl_dmatrix_Destroy(kmx);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return eslOK;
}
/* serial_master()
* The serial version of hmmbuild.
* For each MSA, build an HMM and save it.
*
* A master can only return if it's successful. All errors are handled immediately and fatally with p7_Fail().
*/
static int
serial_master(const ESL_GETOPTS *go, struct cfg_s *cfg)
{
int status;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
WORK_ITEM *item = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errmsg[eslERRBUFSIZE];
if ((status = init_master_cfg(go, cfg, errmsg)) != eslOK) p7_Fail(errmsg);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(cfg->abc);
info[i].bld = p7_builder_Create(go, cfg->abc);
if (info[i].bld == NULL) p7_Fail("p7_builder_Create failed");
#ifdef HMMER_THREADS
info[i].queue = queue;
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
ESL_ALLOC(item, sizeof(*item));
item->nali = 0;
item->processed = FALSE;
item->postmsa = NULL;
item->msa = NULL;
item->hmm = NULL;
item->entropy = 0.0;
status = esl_workqueue_Init(queue, item);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
#ifdef HMMER_THREADS
if (ncpus > 0) status = thread_loop(threadObj, queue, cfg);
else status = serial_loop(info, cfg);
#else
status = serial_loop(info, cfg);
#endif
if (status == eslEFORMAT) esl_fatal("Alignment file parse error:\n%s\n", cfg->afp->errbuf);
else if (status == eslEINVAL) esl_fatal("Alignment file parse error:\n%s\n", cfg->afp->errbuf);
else if (status != eslEOF) esl_fatal("Alignment file read failed with error code %d\n", status);
for (i = 0; i < infocnt; ++i)
{
p7_bg_Destroy(info[i].bg);
p7_builder_Destroy(info[i].bld);
}
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &item) == eslOK)
{
free(item);
}
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
return eslOK;
ERROR:
return eslFAIL;
}
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 *ox = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float vfraw, nullsc, vfscore;
float graw, gscore;
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");
/* 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);
/* 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);
/* allocate DP matrices, both a generic and an optimized one */
ox = p7_omx_Create(gm->M, 0, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
/* Useful to place and compile in for debugging:
p7_oprofile_Dump(stdout, om); dumps the optimized profile
p7_omx_SetDumpMode(ox, TRUE); makes the fast DP algorithms dump their matrices
p7_gmx_Dump(stdout, gx); dumps a generic DP matrix
*/
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(ox, om->M, 0, sq->n);
p7_gmx_GrowTo(gx, gm->M, sq->n);
p7_ViterbiFilter (sq->dsq, sq->n, om, ox, &vfraw);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
vfscore = (vfraw - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(vfscore, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
p7_GViterbi (sq->dsq, sq->n, gm, gx, &graw);
gscore = (graw - nullsc) / eslCONST_LOG2;
gP = esl_gumbel_surv(gscore, gm->evparam[p7_VMU], gm->evparam[p7_VLAMBDA]);
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-30s\t%-20s\t%9.2g\t%7.2f\t%9.2g\t%7.2f\n", sq->name, hmm->name, P, vfscore, gP, gscore);
}
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, vfscore, sq->name, hmm->name);
}
else
{
printf("target sequence: %s\n", sq->name);
printf("vit filter raw score: %.2f nats\n", vfraw);
printf("null score: %.2f nats\n", nullsc);
printf("per-seq score: %.2f bits\n", vfscore);
printf("P-value: %g\n", P);
printf("GViterbi raw score: %.2f nats\n", graw);
printf("GViterbi seq score: %.2f bits\n", gscore);
printf("GViterbi P-value: %g\n", gP);
}
esl_sq_Reuse(sq);
}
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
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_getopts_Destroy(go);
return 0;
}
/* mpi_master()
* The MPI version of hmmbuild.
* Follows standard pattern for a master/worker load-balanced MPI program (J1/78-79).
*
* A master can only return if it's successful.
* Errors in an MPI master come in two classes: recoverable and nonrecoverable.
*
* Recoverable errors include all worker-side errors, and any
* master-side error that do not affect MPI communication. Error
* messages from recoverable messages are delayed until we've cleanly
* shut down the workers.
*
* Unrecoverable errors are master-side errors that may affect MPI
* communication, meaning we cannot count on being able to reach the
* workers and shut them down. Unrecoverable errors result in immediate
* p7_Fail()'s, which will cause MPI to shut down the worker processes
* uncleanly.
*/
static void
mpi_master(const ESL_GETOPTS *go, struct cfg_s *cfg)
{
int xstatus = eslOK; /* changes from OK on recoverable error */
int status;
int have_work = TRUE; /* TRUE while alignments remain */
int nproc_working = 0; /* number of worker processes working, up to nproc-1 */
int wi; /* rank of next worker to get an alignment to work on */
char *buf = NULL; /* input/output buffer, for packed MPI messages */
int bn = 0;
ESL_MSA *msa = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
ESL_MSA **msalist = NULL;
ESL_MSA *postmsa = NULL;
int *msaidx = NULL;
char errmsg[eslERRBUFSIZE];
MPI_Status mpistatus;
int n;
int pos;
double entropy;
/* Master initialization: including, figure out the alphabet type.
* If any failure occurs, delay printing error message until we've shut down workers.
*/
if (xstatus == eslOK) { if ((status = init_master_cfg(go, cfg, errmsg)) != eslOK) xstatus = status; }
if (xstatus == eslOK) { bn = 4096; if ((buf = malloc(sizeof(char) * bn)) == NULL) { sprintf(errmsg, "allocation failed"); xstatus = eslEMEM; } }
if (xstatus == eslOK) { if ((msalist = malloc(sizeof(ESL_MSA *) * cfg->nproc)) == NULL) { sprintf(errmsg, "allocation failed"); xstatus = eslEMEM; } }
if (xstatus == eslOK) { if ((msaidx = malloc(sizeof(int) * cfg->nproc)) == NULL) { sprintf(errmsg, "allocation failed"); xstatus = eslEMEM; } }
MPI_Bcast(&xstatus, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (xstatus != eslOK) { MPI_Finalize(); p7_Fail(errmsg); }
ESL_DPRINTF1(("MPI master is initialized\n"));
bg = p7_bg_Create(cfg->abc);
for (wi = 0; wi < cfg->nproc; wi++) { msalist[wi] = NULL; msaidx[wi] = 0; }
/* Worker initialization:
* Because we've already successfully initialized the master before we start
* initializing the workers, we don't expect worker initialization to fail;
* so we just receive a quick OK/error code reply from each worker to be sure,
* and don't worry about an informative message.
*/
MPI_Bcast(&(cfg->abc->type), 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Reduce(&xstatus, &status, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
if (status != eslOK) { MPI_Finalize(); p7_Fail("One or more MPI worker processes failed to initialize."); }
ESL_DPRINTF1(("%d workers are initialized\n", cfg->nproc-1));
/* Main loop: combining load workers, send/receive, clear workers loops;
* also, catch error states and die later, after clean shutdown of workers.
*
* When a recoverable error occurs, have_work = FALSE, xstatus !=
* eslOK, and errmsg is set to an informative message. No more
* errmsg's can be received after the first one. We wait for all the
* workers to clear their work units, then send them shutdown signals,
* then finally print our errmsg and exit.
*
* Unrecoverable errors just crash us out with p7_Fail().
*/
wi = 1;
while (have_work || nproc_working)
{
if (have_work)
{
if ((status = esl_msa_Read(cfg->afp, &msa)) == eslOK)
{
cfg->nali++;
ESL_DPRINTF1(("MPI master read MSA %s\n", msa->name == NULL? "" : msa->name));
}
else
{
have_work = FALSE;
if (status == eslEFORMAT) { xstatus = eslEFORMAT; snprintf(errmsg, eslERRBUFSIZE, "Alignment file parse error:\n%s\n", cfg->afp->errbuf); }
else if (status == eslEINVAL) { xstatus = eslEFORMAT; snprintf(errmsg, eslERRBUFSIZE, "Alignment file parse error:\n%s\n", cfg->afp->errbuf); }
else if (status != eslEOF) { xstatus = status; snprintf(errmsg, eslERRBUFSIZE, "Alignment file read unexpectedly failed with code %d\n", status); }
ESL_DPRINTF1(("MPI master has run out of MSAs (having read %d)\n", cfg->nali));
}
}
if ((have_work && nproc_working == cfg->nproc-1) || (!have_work && nproc_working > 0))
{
if (MPI_Probe(MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &mpistatus) != 0) { MPI_Finalize(); p7_Fail("mpi probe failed"); }
if (MPI_Get_count(&mpistatus, MPI_PACKED, &n) != 0) { MPI_Finalize(); p7_Fail("mpi get count failed"); }
wi = mpistatus.MPI_SOURCE;
ESL_DPRINTF1(("MPI master sees a result of %d bytes from worker %d\n", n, wi));
if (n > bn) {
if ((buf = realloc(buf, sizeof(char) * n)) == NULL) p7_Fail("reallocation failed");
bn = n;
}
if (MPI_Recv(buf, bn, MPI_PACKED, wi, 0, MPI_COMM_WORLD, &mpistatus) != 0) { MPI_Finalize(); p7_Fail("mpi recv failed"); }
ESL_DPRINTF1(("MPI master has received the buffer\n"));
/* If we're in a recoverable error state, we're only clearing worker results;
* just receive them, don't unpack them or print them.
* But if our xstatus is OK, go ahead and process the result buffer.
*/
if (xstatus == eslOK)
{
pos = 0;
if (MPI_Unpack(buf, bn, &pos, &xstatus, 1, MPI_INT, MPI_COMM_WORLD) != 0) { MPI_Finalize(); p7_Fail("mpi unpack failed");}
if (xstatus == eslOK) /* worker reported success. Get the HMM. */
{
ESL_DPRINTF1(("MPI master sees that the result buffer contains an HMM\n"));
if (p7_hmm_MPIUnpack(buf, bn, &pos, MPI_COMM_WORLD, &(cfg->abc), &hmm) != eslOK) { MPI_Finalize(); p7_Fail("HMM unpack failed"); }
ESL_DPRINTF1(("MPI master has unpacked the HMM\n"));
if (cfg->postmsafile != NULL) {
if (esl_msa_MPIUnpack(cfg->abc, buf, bn, &pos, MPI_COMM_WORLD, &postmsa) != eslOK) { MPI_Finalize(); p7_Fail("postmsa unpack failed");}
}
entropy = p7_MeanMatchRelativeEntropy(hmm, bg);
if ((status = output_result(cfg, errmsg, msaidx[wi], msalist[wi], hmm, postmsa, entropy)) != eslOK) xstatus = status;
esl_msa_Destroy(postmsa); postmsa = NULL;
p7_hmm_Destroy(hmm); hmm = NULL;
}
else /* worker reported an error. Get the errmsg. */
{
if (MPI_Unpack(buf, bn, &pos, errmsg, eslERRBUFSIZE, MPI_CHAR, MPI_COMM_WORLD) != 0) { MPI_Finalize(); p7_Fail("mpi unpack of errmsg failed"); }
ESL_DPRINTF1(("MPI master sees that the result buffer contains an error message\n"));
}
}
esl_msa_Destroy(msalist[wi]);
msalist[wi] = NULL;
msaidx[wi] = 0;
nproc_working--;
}
if (have_work)
{
ESL_DPRINTF1(("MPI master is sending MSA %s to worker %d\n", msa->name == NULL ? "":msa->name, wi));
if (esl_msa_MPISend(msa, wi, 0, MPI_COMM_WORLD, &buf, &bn) != eslOK) p7_Fail("MPI msa send failed");
msalist[wi] = msa;
msaidx[wi] = cfg->nali; /* 1..N for N alignments in the MSA database */
msa = NULL;
wi++;
nproc_working++;
}
}
/* On success or recoverable errors:
* Shut down workers cleanly.
*/
ESL_DPRINTF1(("MPI master is done. Shutting down all the workers cleanly\n"));
for (wi = 1; wi < cfg->nproc; wi++)
if (esl_msa_MPISend(NULL, wi, 0, MPI_COMM_WORLD, &buf, &bn) != eslOK) p7_Fail("MPI msa send failed");
free(buf);
free(msaidx);
free(msalist);
p7_bg_Destroy(bg);
if (xstatus != eslOK) { MPI_Finalize(); p7_Fail(errmsg); }
else return;
}
/* Function: p7_Calibrate()
* Synopsis: Calibrate the E-value parameters of a model.
* Incept: SRE, Thu Dec 25 09:29:31 2008 [Magallon]
*
* Purpose: Calibrate the E-value parameters of a model with
* one calculation ($\lambda$) and two brief simulations
* (Viterbi $\mu$, Forward $\tau$).
*
* Args: hmm - HMM to be calibrated
* cfg_b - OPTCFG: ptr to optional build configuration;
* if <NULL>, use default parameters.
* byp_rng - BYPASS optimization: pass ptr to <ESL_RANDOMNESS> generator
* if already known;
* <*byp_rng> == NULL> if <rng> return is desired;
* pass <NULL> to use and discard internal default.
* byp_bg - BYPASS optimization: pass ptr to <P7_BG> if already known;
* <*byp_bg == NULL> if <bg> return is desired;
* pass <NULL> to use and discard internal default.
* byp_gm - BYPASS optimization: pass ptr to <gm> profile if already known;
* pass <*byp_gm == NULL> if <gm> return desired;
* pass <NULL> to use and discard internal default.
* byp_om - BYPASS optimization: pass ptr to <om> profile if already known;
* pass <*byp_om == NULL> if <om> return desired;
* pass <NULL> to use and discard internal default.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
* <eslEINVAL> if <hmm>, <gm>, <om> aren't compatible somehow.
*
* Xref: J4/41
*/
int
p7_Calibrate(P7_HMM *hmm, P7_BUILDER *cfg_b, ESL_RANDOMNESS **byp_rng, P7_BG **byp_bg, P7_PROFILE **byp_gm, P7_OPROFILE **byp_om)
{
P7_BG *bg = (esl_byp_IsProvided(byp_bg) ? *byp_bg : NULL);
P7_PROFILE *gm = (esl_byp_IsProvided(byp_gm) ? *byp_gm : NULL);
P7_OPROFILE *om = (esl_byp_IsProvided(byp_om) ? *byp_om : NULL);
ESL_RANDOMNESS *r = (esl_byp_IsProvided(byp_rng) ? *byp_rng : NULL);
char *errbuf = ((cfg_b != NULL) ? cfg_b->errbuf : NULL);
int EmL = ((cfg_b != NULL) ? cfg_b->EmL : 200);
int EmN = ((cfg_b != NULL) ? cfg_b->EmN : 200);
int EvL = ((cfg_b != NULL) ? cfg_b->EvL : 200);
int EvN = ((cfg_b != NULL) ? cfg_b->EvN : 200);
int EfL = ((cfg_b != NULL) ? cfg_b->EfL : 100);
int EfN = ((cfg_b != NULL) ? cfg_b->EfN : 200);
double Eft = ((cfg_b != NULL) ? cfg_b->Eft : 0.04);
double lambda, mmu, vmu, tau;
int status;
/* Configure any objects we need
* that weren't already passed to us as a bypass optimization
*/
if (r == NULL) {
if ((r = esl_randomness_CreateFast(42)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create RNG");
} else if (cfg_b != NULL && cfg_b->do_reseeding) {
esl_randomness_Init(r, esl_randomness_GetSeed(r));
}
if (bg == NULL) {
if ((bg = p7_bg_Create(hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to allocate background");
}
/* there's an odd case where the <om> is provided and a <gm> isn't going to be returned
* where we don't need a <gm> at all, and <gm> stays <NULL> after the next block.
* Note that the <EvL> length in the ProfileConfig doesn't matter; the individual
* calibration routines MSVMu(), etc. contain their own length reconfig calls.
*/
if ((esl_byp_IsInternal(byp_gm) && ! esl_byp_IsProvided(byp_om)) || esl_byp_IsReturned(byp_gm)) {
if ( (gm = p7_profile_Create(hmm->M, hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to allocate profile");
if ( (status = p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL)) != eslOK) ESL_XFAIL(status, errbuf, "failed to configure profile");
}
if (om == NULL) {
if ((om = p7_oprofile_Create(hmm->M, hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create optimized profile");
if ((status = p7_oprofile_Convert(gm, om)) != eslOK) ESL_XFAIL(status, errbuf, "failed to convert to optimized profile");
}
/* The calibration steps themselves */
if ((status = p7_Lambda(hmm, bg, &lambda)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine lambda");
if ((status = p7_MSVMu (r, om, bg, EmL, EmN, lambda, &mmu)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine msv mu");
if ((status = p7_ViterbiMu(r, om, bg, EvL, EvN, lambda, &vmu)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine vit mu");
if ((status = p7_Tau (r, om, bg, EfL, EfN, lambda, Eft, &tau)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine fwd tau");
/* Store results */
hmm->evparam[p7_MLAMBDA] = om->evparam[p7_MLAMBDA] = lambda;
hmm->evparam[p7_VLAMBDA] = om->evparam[p7_VLAMBDA] = lambda;
hmm->evparam[p7_FLAMBDA] = om->evparam[p7_FLAMBDA] = lambda;
hmm->evparam[p7_MMU] = om->evparam[p7_MMU] = mmu;
hmm->evparam[p7_VMU] = om->evparam[p7_VMU] = vmu;
hmm->evparam[p7_FTAU] = om->evparam[p7_FTAU] = tau;
hmm->flags |= p7H_STATS;
if (gm != NULL) {
gm->evparam[p7_MLAMBDA] = lambda;
gm->evparam[p7_VLAMBDA] = lambda;
gm->evparam[p7_FLAMBDA] = lambda;
gm->evparam[p7_MMU] = mmu;
gm->evparam[p7_VMU] = vmu;
gm->evparam[p7_FTAU] = tau;
}
if (byp_rng != NULL) *byp_rng = r; else esl_randomness_Destroy(r); /* bypass convention: no-op if rng was provided.*/
if (byp_bg != NULL) *byp_bg = bg; else p7_bg_Destroy(bg); /* bypass convention: no-op if bg was provided. */
if (byp_gm != NULL) *byp_gm = gm; else p7_profile_Destroy(gm); /* bypass convention: no-op if gm was provided. */
if (byp_om != NULL) *byp_om = om; else p7_oprofile_Destroy(om); /* bypass convention: no-op if om was provided. */
return eslOK;
ERROR:
if (! esl_byp_IsProvided(byp_rng)) esl_randomness_Destroy(r);
if (! esl_byp_IsProvided(byp_bg)) p7_bg_Destroy(bg);
if (! esl_byp_IsProvided(byp_gm)) p7_profile_Destroy(gm);
if (! esl_byp_IsProvided(byp_om)) p7_oprofile_Destroy(om);
return status;
}
static void
mpi_worker(const ESL_GETOPTS *go, struct cfg_s *cfg)
{
int xstatus = eslOK;
int status;
int type;
P7_BUILDER *bld = NULL;
ESL_MSA *msa = NULL;
ESL_MSA *postmsa = NULL;
ESL_MSA **postmsa_ptr = (cfg->postmsafile != NULL) ? &postmsa : NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
char *wbuf = NULL; /* packed send/recv buffer */
void *tmp; /* for reallocation of wbuf */
int wn = 0; /* allocation size for wbuf */
int sz, n; /* size of a packed message */
int pos;
char errmsg[eslERRBUFSIZE];
/* After master initialization: master broadcasts its status.
*/
MPI_Bcast(&xstatus, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (xstatus != eslOK) return; /* master saw an error code; workers do an immediate normal shutdown. */
ESL_DPRINTF2(("worker %d: sees that master has initialized\n", cfg->my_rank));
/* Master now broadcasts worker initialization information (alphabet type)
* Workers returns their status post-initialization.
* Initial allocation of wbuf must be large enough to guarantee that
* we can pack an error result into it, because after initialization,
* errors will be returned as packed (code, errmsg) messages.
*/
MPI_Bcast(&type, 1, MPI_INT, 0, MPI_COMM_WORLD);
if (xstatus == eslOK) { if ((cfg->abc = esl_alphabet_Create(type)) == NULL) xstatus = eslEMEM; }
if (xstatus == eslOK) { wn = 4096; if ((wbuf = malloc(wn * sizeof(char))) == NULL) xstatus = eslEMEM; }
if (xstatus == eslOK) { if ((bld = p7_builder_Create(go, cfg->abc)) == NULL) xstatus = eslEMEM; }
MPI_Reduce(&xstatus, &status, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD); /* everyone sends xstatus back to master */
if (xstatus != eslOK) {
if (wbuf != NULL) free(wbuf);
if (bld != NULL) p7_builder_Destroy(bld);
return; /* shutdown; we passed the error back for the master to deal with. */
}
bg = p7_bg_Create(cfg->abc);
ESL_DPRINTF2(("worker %d: initialized\n", cfg->my_rank));
/* source = 0 (master); tag = 0 */
while (esl_msa_MPIRecv(0, 0, MPI_COMM_WORLD, cfg->abc, &wbuf, &wn, &msa) == eslOK)
{
/* Build the HMM */
ESL_DPRINTF2(("worker %d: has received MSA %s (%d columns, %d seqs)\n", cfg->my_rank, msa->name, msa->alen, msa->nseq));
if ((status = p7_Builder(bld, msa, bg, &hmm, NULL, NULL, NULL, postmsa_ptr)) != eslOK) { strcpy(errmsg, bld->errbuf); goto ERROR; }
ESL_DPRINTF2(("worker %d: has produced an HMM %s\n", cfg->my_rank, hmm->name));
/* Calculate upper bound on size of sending status, HMM, and optional postmsa; make sure wbuf can hold it. */
n = 0;
if (MPI_Pack_size(1, MPI_INT, MPI_COMM_WORLD, &sz) != 0) goto ERROR; n += sz;
if (p7_hmm_MPIPackSize( hmm, MPI_COMM_WORLD, &sz) != eslOK) goto ERROR; n += sz;
if (esl_msa_MPIPackSize(postmsa, MPI_COMM_WORLD, &sz) != eslOK) goto ERROR; n += sz;
if (n > wn) { ESL_RALLOC(wbuf, tmp, sizeof(char) * n); wn = n; }
ESL_DPRINTF2(("worker %d: has calculated that HMM will pack into %d bytes\n", cfg->my_rank, n));
/* Send status, HMM, and optional postmsa back to the master */
pos = 0;
if (MPI_Pack (&status, 1, MPI_INT, wbuf, wn, &pos, MPI_COMM_WORLD) != 0) goto ERROR;
if (p7_hmm_MPIPack (hmm, wbuf, wn, &pos, MPI_COMM_WORLD) != eslOK) goto ERROR;
if (esl_msa_MPIPack(postmsa, wbuf, wn, &pos, MPI_COMM_WORLD) != eslOK) goto ERROR;
MPI_Send(wbuf, pos, MPI_PACKED, 0, 0, MPI_COMM_WORLD);
ESL_DPRINTF2(("worker %d: has sent HMM to master in message of %d bytes\n", cfg->my_rank, pos));
esl_msa_Destroy(msa); msa = NULL;
esl_msa_Destroy(postmsa); postmsa = NULL;
p7_hmm_Destroy(hmm); hmm = NULL;
}
if (wbuf != NULL) free(wbuf);
p7_builder_Destroy(bld);
return;
ERROR:
ESL_DPRINTF2(("worker %d: fails, is sending an error message, as follows:\n%s\n", cfg->my_rank, errmsg));
pos = 0;
MPI_Pack(&status, 1, MPI_INT, wbuf, wn, &pos, MPI_COMM_WORLD);
MPI_Pack(errmsg, eslERRBUFSIZE, MPI_CHAR, wbuf, wn, &pos, MPI_COMM_WORLD);
MPI_Send(wbuf, pos, MPI_PACKED, 0, 0, MPI_COMM_WORLD);
if (wbuf != NULL) free(wbuf);
if (msa != NULL) esl_msa_Destroy(msa);
if (hmm != NULL) p7_hmm_Destroy(hmm);
if (bld != NULL) p7_builder_Destroy(bld);
return;
}
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 *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_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);
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;
}
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;
}
