/* tests:
* 1. each sampled trace must validate.
* 2. each trace must be <= viterbi trace score
* 3. in a large # of traces, one is "equal" to the viterbi trace score.
* (this of course is stochastic; but it's true for the particular
* choice of RNG seed used in tests here.)
*/
static void
utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, P7_PROFILE *gm, P7_OPROFILE *om, ESL_DSQ *dsq, int L, int ntrace)
{
P7_GMX *gx = NULL;
P7_OMX *ox = NULL;
P7_TRACE *tr = NULL;
char errbuf[eslERRBUFSIZE];
int idx;
float maxsc = -eslINFINITY;
float vsc, sc;
if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("generic DP matrix creation failed");
if ((ox = p7_omx_Create(gm->M, L, L)) == NULL) esl_fatal("optimized DP matrix create failed");
if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed");
if (p7_GViterbi(dsq, L, gm, gx, &vsc) != eslOK) esl_fatal("viterbi failed");
if (p7_Forward (dsq, L, om, ox, NULL) != eslOK) esl_fatal("forward failed");
for (idx = 0; idx < ntrace; idx++)
{
if (p7_StochasticTrace(rng, dsq, L, om, ox, tr) != eslOK) esl_fatal("stochastic trace failed");
if (p7_trace_Validate(tr, abc, dsq, errbuf) != eslOK) esl_fatal("trace invalid:\n%s", errbuf);
if (p7_trace_Score(tr, dsq, gm, &sc) != eslOK) esl_fatal("trace scoring failed");
maxsc = ESL_MAX(sc, maxsc);
if (sc > vsc) esl_fatal("sampled trace has score > optimal Viterbi path; not possible");
p7_trace_Reuse(tr);
}
if (esl_FCompare(maxsc, vsc, 0.1) != eslOK) esl_fatal("stochastic trace failed to sample the Viterbi path");
p7_trace_Destroy(tr);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
ESL_RANDOMNESS *rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
char *hmmfile = esl_opt_GetArg(go, 1);
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_TRACE *tr = p7_trace_Create();
ESL_SQ *sq = NULL;
char errbuf[eslERRBUFSIZE];
int i;
int status;
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);
if (status == eslEFORMAT) p7_Fail("Bad file format in HMM file %s:\n%s\n", hfp->fname, hfp->errbuf);
else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
else if (status == eslEOF) p7_Fail("Empty HMM file %s? No HMM data found.\n", hfp->fname);
else if (status != eslOK) p7_Fail("Unexpected error in reading HMMs from %s\n", hfp->fname);
p7_hmmfile_Close(hfp);
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);
sq = esl_sq_CreateDigital(abc);
for (i = 0; i < N; i++)
{
p7_ProfileEmit(rng, hmm, gm, bg, sq, tr);
esl_sq_FormatName(sq, "%s-sample%d", hmm->name, i);
esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);
if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) esl_fatal(errbuf);
esl_sq_Reuse(sq);
p7_trace_Reuse(tr);
}
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(rng);
esl_getopts_Destroy(go);
return 0;
}
/* Viterbi validation is done by comparing the returned score
* to the score of the optimal trace. Not foolproof, but catches
* many kinds of errors.
*
* Another check is that the average score should be <= 0,
* since the random sequences are drawn from the null model.
*/
static void
utest_viterbi(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, P7_PROFILE *gm, int nseq, int L)
{
float avg_sc = 0.;
char errbuf[eslERRBUFSIZE];
ESL_DSQ *dsq = NULL;
P7_GMX *gx = NULL;
P7_TRACE *tr = NULL;
int idx;
float sc1, sc2;
if ((dsq = malloc(sizeof(ESL_DSQ) *(L+2))) == NULL) esl_fatal("malloc failed");
if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed");
if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("matrix creation failed");
for (idx = 0; idx < nseq; idx++)
{
if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal("seq generation failed");
if (p7_GViterbi(dsq, L, gm, gx, &sc1) != eslOK) esl_fatal("viterbi failed");
if (p7_GTrace (dsq, L, gm, gx, tr) != eslOK) esl_fatal("trace failed");
if (p7_trace_Validate(tr, abc, dsq, errbuf) != eslOK) esl_fatal("trace invalid:\n%s", errbuf);
if (p7_trace_Score(tr, dsq, gm, &sc2) != eslOK) esl_fatal("trace score failed");
if (esl_FCompare(sc1, sc2, 1e-6) != eslOK) esl_fatal("Trace score != Viterbi score");
if (p7_bg_NullOne(bg, dsq, L, &sc2) != eslOK) esl_fatal("null score failed");
avg_sc += (sc1 - sc2);
if (esl_opt_GetBoolean(go, "--vv"))
printf("utest_viterbi: Viterbi score: %.4f (null %.4f) (total so far: %.4f)\n", sc1, sc2, avg_sc);
p7_trace_Reuse(tr);
}
avg_sc /= (float) nseq;
if (avg_sc > 0.) esl_fatal("Viterbi scores have positive expectation (%f nats)", avg_sc);
p7_gmx_Destroy(gx);
p7_trace_Destroy(tr);
free(dsq);
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_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);
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;
}
/*
* 1. Compare accscore to GOptimalAccuracy().
* 2. Compare trace to GOATrace().
*
* Note: This test is subject to some expected noise and can fail
* for entirely innocent reasons. Generic Forward/Backward calculations with
* p7_GForward(), p7_GBackward() use coarse-grain table lookups to sum
* log probabilities, and sufficient roundoff error can accumulate to
* change the optimal accuracy traceback, causing this test to fail.
* So, if optacc_utest fails, before you go looking for bugs, first
* go to ../logsum.c, change the #ifdef to activate the slow/accurate
* version, recompile and rerun optacc_utest. If the failure goes away,
* you can ignore it. - SRE, Wed Dec 17 09:45:31 2008
*/
static void
utest_optacc(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
char *msg = "optimal accuracy unit test failed";
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_SQ *sq = esl_sq_CreateDigital(abc);
P7_OMX *ox1 = p7_omx_Create(M, L, L);
P7_OMX *ox2 = p7_omx_Create(M, L, L);
P7_GMX *gx1 = p7_gmx_Create(M, L);
P7_GMX *gx2 = p7_gmx_Create(M, L);
P7_TRACE *tr = p7_trace_CreateWithPP();
P7_TRACE *trg = p7_trace_CreateWithPP();
P7_TRACE *tro = p7_trace_CreateWithPP();
float accscore_o;
float fsc, bsc, accscore;
float fsc_g, bsc_g, accscore_g, accscore_g2;
float pptol = 0.01;
float sctol = 0.001;
float gtol;
p7_FLogsumInit();
gtol = ( (p7_FLogsumError(-0.4, -0.5) > 0.0001) ? 0.1 : 0.001);
if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om)!= eslOK) esl_fatal(msg);
while (N--)
{
if (p7_ProfileEmit(r, hmm, gm, bg, sq, tro) != eslOK) esl_fatal(msg);
if (p7_omx_GrowTo(ox1, M, sq->n, sq->n) != eslOK) esl_fatal(msg);
if (p7_omx_GrowTo(ox2, M, sq->n, sq->n) != eslOK) esl_fatal(msg);
if (p7_gmx_GrowTo(gx1, M, sq->n) != eslOK) esl_fatal(msg);
if (p7_gmx_GrowTo(gx2, M, sq->n) != eslOK) esl_fatal(msg);
if (p7_Forward (sq->dsq, sq->n, om, ox1, &fsc) != eslOK) esl_fatal(msg);
if (p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc) != eslOK) esl_fatal(msg);
if (p7_Decoding(om, ox1, ox2, ox2) != eslOK) esl_fatal(msg);
if (p7_OptimalAccuracy(om, ox2, ox1, &accscore) != eslOK) esl_fatal(msg);
#if 0
p7_omx_FDeconvert(ox1, gx1);
p7_gmx_Dump(stdout, gx1, p7_DEFAULT);
p7_omx_FDeconvert(ox2, gx1);
p7_gmx_Dump(stdout, gx1, p7_DEFAULT);
#endif
if (p7_OATrace(om, ox2, ox1, tr) != eslOK) esl_fatal(msg);
if (p7_GForward (sq->dsq, sq->n, gm, gx1, &fsc_g) != eslOK) esl_fatal(msg);
if (p7_GBackward(sq->dsq, sq->n, gm, gx2, &bsc_g) != eslOK) esl_fatal(msg);
#if 0
p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* fwd */
p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* bck */
#endif
if (p7_GDecoding(gm, gx1, gx2, gx2) != eslOK) esl_fatal(msg);
if (p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g) != eslOK) esl_fatal(msg);
#if 0
p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* oa */
p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* pp */
#endif
if (p7_GOATrace(gm, gx2, gx1, trg) != eslOK) esl_fatal(msg);
if (p7_trace_SetPP(tro, gx2) != eslOK) esl_fatal(msg);
if (esl_opt_GetBoolean(go, "--traces"))
{
p7_trace_Dump(stdout, tro, gm, sq->dsq);
p7_trace_Dump(stdout, tr, gm, sq->dsq);
p7_trace_Dump(stdout, trg, gm, sq->dsq);
}
if (p7_trace_Validate(tr, abc, sq->dsq, NULL) != eslOK) esl_fatal(msg);
if (p7_trace_Validate(trg, abc, sq->dsq, NULL) != eslOK) esl_fatal(msg);
if (p7_trace_Compare(tr, trg, pptol) != eslOK) esl_fatal(msg);
accscore_o = p7_trace_GetExpectedAccuracy(tro); /* according to gx2; see p7_trace_SetPP() call above */
accscore_g2 = p7_trace_GetExpectedAccuracy(trg);
#if 0
printf("%f %f %f %f\n", accscore, accscore_g, accscore_g2, accscore_o);
#endif
if (esl_FCompare(fsc, bsc, sctol) != eslOK) esl_fatal(msg);
if (esl_FCompare(fsc_g, bsc_g, gtol) != eslOK) esl_fatal(msg);
if (esl_FCompare(fsc, fsc_g, gtol) != eslOK) esl_fatal(msg);
if (esl_FCompare(accscore, accscore_g, gtol) != eslOK) esl_fatal(msg);
if (esl_FCompare(accscore_g, accscore_g2, gtol) != eslOK) esl_fatal(msg);
if (accscore_g2 < accscore_o) esl_fatal(msg);
/* the above deserves explanation:
* - accscore_o is the accuracy of the originally emitted trace, according
* to the generic posterior decoding matrix <gx2>. This is a lower bound
* on the expected # of accurately aligned residues found by a DP
* optimization.
* - accscore is the accuracy found by the fast (vector) code DP implementation.
* - accscore_g is the accuracy found by the generic DP implementation.
* accscore and accscore_g should be nearly identical,
* within tolerance of roundoff error accumulation and
* the imprecision of Logsum() tables.
* - accscore_g2 is the accuracy of the traceback identified by the generic
* DP implementation. It should be identical (within order-of-evaluation
* roundoff error) to accscore_g.
*
* the "accscore_g2 < accscore_o" test is carefully contrived.
* accscore_o is a theoretical lower bound but because of fp error,
* accscore and (much more rarely) even accscore_g can exceed accscore_o.
* accscore_g2, however, is calculated with identical order of evaluation
* as accscore_o if the optimal trace does turn out to be identical to
* the originally emitted trace. It should be extremely unlikely (though
* not impossible) for accscore_o to exceed accscore_g2. (The DP algorithm
* would have to identify a trace that was different than the original trace,
* which the DP algorithm, by order-of-evaluation, assigned higher accuracy,
* but order-of-evaluation in traceback dependent code assigned lower accuracy.
* [xref J5/29]
*/
esl_sq_Reuse(sq);
p7_trace_Reuse(tr);
p7_trace_Reuse(trg);
p7_trace_Reuse(tro);
}
p7_trace_Destroy(tro);
p7_trace_Destroy(trg);
p7_trace_Destroy(tr);
p7_gmx_Destroy(gx2);
p7_gmx_Destroy(gx1);
p7_omx_Destroy(ox2);
p7_omx_Destroy(ox1);
esl_sq_Destroy(sq);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
}
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;
}
/* utest_fragments()
* This exercises the building code that deals with fragments,
* creating traces with B->X->{MDI}k and {MDI}k->X->E
* transitions, and making sure we can make MSAs correctly
* from them using p7_tracealign_MSA(). This code was initially
* buggy when first written; bugs first detected by Elena,
* Nov 2009
*/
static void
utest_fragments(void)
{
char *failmsg = "failure in build.c::utest_fragments() unit test";
char msafile[16] = "p7tmpXXXXXX"; /* tmpfile name template */
FILE *ofp = NULL;
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
ESL_MSA *dmsa = NULL;
ESL_MSA *postmsa = NULL;
P7_HMM *hmm = NULL;
P7_TRACE **trarr = NULL;
int i;
/* Write an MSA that tests fragment/missing data transitions.
* When built with Handmodelmaker (using the RF line):
* seq1 forces B->X->Mk and Mk->X->E missing data transitions;
* seq2 forces B->X->Ik and Ik->X->E missing data transitions;
* seq3 forces B->X->Dk and Dk->X->E missing data transitions.
*
* The first two cases can arise from fragment definition in
* model construction, or in an input file.
*
* The X->Dk and Dk->X cases should never happen, but we don't
* prohibit them. They can only arise in an input file, because
* esl_msa_MarkFragments() converts everything before/after
* first/last residue to ~, and won't leave a gap character in
* between.
*
* There's nothing being tested by seq4 and seq5; they're just there.
*/
if (esl_tmpfile_named(msafile, &ofp) != eslOK) esl_fatal(failmsg);
fprintf(ofp, "# STOCKHOLM 1.0\n");
fprintf(ofp, "#=GC RF xxxxx.xxxxxxxxxxxx.xxx\n");
fprintf(ofp, "seq1 ~~~~~~GHIKLMNPQRST~~~~\n");
fprintf(ofp, "seq2 ~~~~~aGHIKLMNPQRSTa~~~\n");
fprintf(ofp, "seq3 ~~~~~~~HIKLMNPQRS~~~~~\n");
fprintf(ofp, "seq4 ACDEF.GHIKLMNPQRST.VWY\n");
fprintf(ofp, "seq5 ACDEF.GHIKLMNPQRST.VWY\n");
fprintf(ofp, "//\n");
fclose(ofp);
/* Read the original as text for comparison to postmsa. Make a digital copy for construction */
if (esl_msafile_Open(NULL, msafile, NULL, eslMSAFILE_UNKNOWN, NULL, &afp)!= eslOK) esl_fatal(failmsg);
if (esl_msafile_Read(afp, &msa) != eslOK) esl_fatal(failmsg);
if ((dmsa = esl_msa_Clone(msa)) == NULL) esl_fatal(failmsg);
if (esl_msa_Digitize(abc, dmsa, NULL) != eslOK) esl_fatal(failmsg);
if (p7_Handmodelmaker(dmsa, NULL, &hmm, &trarr) != eslOK) esl_fatal(failmsg);
for (i = 0; i < dmsa->nseq; i++)
if (p7_trace_Validate(trarr[i], abc, dmsa->ax[i], NULL) != eslOK) esl_fatal(failmsg);
/* The example is contrived such that the traces should give exactly the
* same (text) alignment as the input alignment; no tracedoctoring.
* Not a trivial test; for example, sequence 2 has a B->X->I transition that
* can be problematic to handle.
*/
if (p7_tracealign_MSA(dmsa, trarr, hmm->M, p7_DEFAULT, &postmsa) != eslOK) esl_fatal(failmsg);
for (i = 0; i < msa->nseq; i++)
if (strcmp(msa->aseq[i], postmsa->aseq[i]) != 0) esl_fatal(failmsg);
p7_trace_DestroyArray(trarr, msa->nseq);
p7_hmm_Destroy(hmm);
esl_msa_Destroy(msa);
esl_msa_Destroy(dmsa);
esl_msa_Destroy(postmsa);
esl_msafile_Close(afp);
esl_alphabet_Destroy(abc);
remove(msafile);
return;
}
/* Function: matassign2hmm()
*
* Purpose: Given an assignment of alignment columns to match vs.
* insert, finish the final part of the model construction
* calculation that is constant between model construction
* algorithms.
*
* Args: msa - multiple sequence alignment
* matassign - 1..alen bit flags for column assignments
* ret_hmm - RETURN: counts-form HMM
* opt_tr - optRETURN: array of tracebacks for aseq's
*
* Return: <eslOK> on success.
* <eslENORESULT> if no consensus columns are identified.
*
* ret_hmm and opt_tr alloc'ed here.
*/
static int
matassign2hmm(ESL_MSA *msa, int *matassign, P7_HMM **ret_hmm, P7_TRACE ***opt_tr)
{
int status; /* return status */
P7_HMM *hmm = NULL; /* RETURN: new hmm */
P7_TRACE **tr = NULL; /* RETURN: 0..nseq-1 fake traces */
int M; /* length of new model in match states */
int idx; /* counter over sequences */
int apos; /* counter for aligned columns */
#ifdef p7_DEBUGGING
char errbuf[eslERRBUFSIZE];
#endif
/* apply the model mask in the 'GC MM' row */
do_modelmask(msa);
/* How many match states in the HMM? */
for (M = 0, apos = 1; apos <= msa->alen; apos++)
if (matassign[apos]) M++;
if (M == 0) { status = eslENORESULT; goto ERROR; }
/* Make fake tracebacks for each seq */
ESL_ALLOC(tr, sizeof(P7_TRACE *) * msa->nseq);
if ((status = p7_trace_FauxFromMSA(msa, matassign, p7_MSA_COORDS, tr)) != eslOK) goto ERROR;
for (idx = 0; idx < msa->nseq; idx++)
{
if ((status = p7_trace_Doctor(tr[idx], NULL, NULL)) != eslOK) goto ERROR;
#ifdef p7_DEBUGGING
if ((status = p7_trace_Validate(tr[idx], msa->abc, msa->ax[idx], errbuf)) != eslOK)
ESL_XEXCEPTION(eslFAIL, "validation failed: %s", errbuf);
#endif
}
/* Build count model from tracebacks */
if ((hmm = p7_hmm_Create(M, msa->abc)) == NULL) { status = eslEMEM; goto ERROR; }
if ((status = p7_hmm_Zero(hmm)) != eslOK) goto ERROR;
for (idx = 0; idx < msa->nseq; idx++) {
if (tr[idx] == NULL) continue; /* skip rare examples of empty sequences */
if ((status = p7_trace_Count(hmm, msa->ax[idx], msa->wgt[idx], tr[idx])) != eslOK) goto ERROR;
}
hmm->nseq = msa->nseq;
hmm->eff_nseq = msa->nseq;
/* Transfer annotation from the MSA to the new model
*/
if ((status = annotate_model(hmm, matassign, msa)) != eslOK) goto ERROR;
/* Reset #=RF line of alignment to reflect our assignment
* of match, delete. matassign is valid from 1..alen and is off
* by one from msa->rf.
*/
if (msa->rf == NULL) ESL_ALLOC(msa->rf, sizeof(char) * (msa->alen + 1));
for (apos = 1; apos <= msa->alen; apos++)
msa->rf[apos-1] = matassign[apos] ? 'x' : '.';
msa->rf[msa->alen] = '\0';
if (opt_tr != NULL) *opt_tr = tr;
else p7_trace_DestroyArray(tr, msa->nseq);
*ret_hmm = hmm;
return eslOK;
ERROR:
if (tr != NULL) p7_trace_DestroyArray(tr, msa->nseq);
if (hmm != NULL) p7_hmm_Destroy(hmm);
if (opt_tr != NULL) *opt_tr = NULL;
*ret_hmm = NULL;
return status;
}
