/* ViterbiFilter() unit test
*
* We can check that scores are identical (within machine error) to
* scores of generic DP with scores rounded the same way. Do this for
* a random model of length <M>, for <N> test sequences of length <L>.
*
* We assume that we don't accidentally generate a high-scoring random
* sequence that overflows ViterbiFilter()'s limited range.
*
*/
static void
utest_viterbi_filter(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
P7_OMX *ox = p7_omx_Create(M, 0, 0);
P7_GMX *gx = p7_gmx_Create(M, L);
float sc1, sc2;
p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
p7_profile_SameAsVF(om, gm); /* round and scale the scores in <gm> the same as in <om> */
#if 0
p7_oprofile_Dump(stdout, om); // dumps the optimized profile
p7_omx_SetDumpMode(stdout, ox, TRUE); // makes the fast DP algorithms dump their matrices
#endif
while (N--)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_ViterbiFilter(dsq, L, om, ox, &sc1);
p7_GViterbi (dsq, L, gm, gx, &sc2);
#if 0
p7_gmx_Dump(stdout, gx); // dumps a generic DP matrix
#endif
sc2 /= om->scale_w;
sc2 -= 3.0;
if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi filter unit test failed: scores differ (%.2f, %.2f)", sc1, sc2);
}
free(dsq);
p7_hmm_Destroy(hmm);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_profile_Destroy(gm);
p7_oprofile_Destroy(om);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
ESL_RANDOMNESS *rng = esl_randomness_CreateFast(0);
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx = NULL;
P7_OMX *fwd = NULL;
P7_TRACE *tr = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
int N = esl_opt_GetInteger(go, "-N");
int i;
float vsc, fsc, tsc;
char errbuf[eslERRBUFSIZE];
int status;
/* Read in one HMM */
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
if (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
/* create default null model, then create and optimize profile */
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
if (esl_opt_GetBoolean(go, "-p")) p7_oprofile_Dump(stdout, om);
fwd = p7_omx_Create(gm->M, sq->n, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
tr = p7_trace_Create();
if (esl_opt_GetBoolean(go, "-m") == TRUE) p7_omx_SetDumpMode(stdout, fwd, TRUE);
p7_GViterbi(sq->dsq, sq->n, gm, gx, &vsc);
p7_Forward (sq->dsq, sq->n, om, fwd, &fsc);
for (i = 0; i < N; i++)
{
p7_StochasticTrace(rng, sq->dsq, sq->n, om, fwd, tr);
p7_trace_Score(tr, sq->dsq, gm, &tsc);
if (esl_opt_GetBoolean(go, "-t") == TRUE) p7_trace_Dump(stdout, tr, gm, sq->dsq);
if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace %d fails validation:\n%s\n", i, errbuf);
printf("Sampled trace: %.4f nats\n", tsc);
p7_trace_Reuse(tr);
}
printf("Forward score: %.4f nats\n", fsc);
printf("Viterbi score: %.4f nats\n", vsc);
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
p7_trace_Destroy(tr);
p7_omx_Destroy(fwd);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_randomness_Destroy(rng);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = 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_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float msvraw, nullsc, msvscore;
float graw, gscore;
double P, gP;
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");
/* 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_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, 0); /* one row version */
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(stdout, ox, TRUE); makes the fast DP algorithms dump their matrices
p7_gmx_Dump(stdout, gx, p7_DEFAULT); dumps a generic DP matrix
p7_oprofile_SameMSV(om, gm);
*/
p7_omx_SetDumpMode(stdout, ox, 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(ox, om->M, 0, sq->n);
p7_gmx_GrowTo(gx, gm->M, sq->n);
p7_MSVFilter (sq->dsq, sq->n, om, ox, &msvraw);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
msvscore = (msvraw - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(msvscore, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
p7_GMSV(sq->dsq, sq->n, gm, gx, 2.0, &graw);
gscore = (graw - nullsc) / eslCONST_LOG2;
gP = esl_gumbel_surv(gscore, gm->evparam[p7_MMU], gm->evparam[p7_MLAMBDA]);
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-30s %-20s %9.2g %7.2f %9.2g %7.2f\n", sq->name, hmm->name, P, msvscore, gP, gscore);
}
else if (esl_opt_GetBoolean(go, "-P"))
{ /* output suitable for direct use in profmark benchmark postprocessors: */
printf("%g %.2f %s %s\n", P, msvscore, sq->name, hmm->name);
}
else
{
printf("target sequence: %s\n", sq->name);
printf("msv filter raw score: %.2f nats\n", msvraw);
printf("null score: %.2f nats\n", nullsc);
printf("per-seq score: %.2f bits\n", msvscore);
printf("P-value: %g\n", P);
printf("GMSV raw score: %.2f nats\n", graw);
printf("GSMV per-seq score: %.2f bits\n", gscore);
printf("GSMV 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;
}
