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;
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;
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);
gx1 = p7_gmx_Create(gm->M, L);
gx2 = p7_gmx_Create(gm->M, L);
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);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
p7_GNull2_ByExpectation(gm, gx2, null2);
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_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;
}
/* compare results to GDecoding(). */
static void
utest_null2_expectation(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
char *msg = "decoding unit test failed";
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
P7_OMX *fwd = p7_omx_Create(M, L, L);
P7_OMX *bck = p7_omx_Create(M, L, L);
P7_OMX *pp = p7_omx_Create(M, L, L);
P7_GMX *gxf = p7_gmx_Create(M, L);
P7_GMX *gxb = p7_gmx_Create(M, L);
P7_GMX *gpp = p7_gmx_Create(M, L);
float *on2 = malloc(sizeof(float) * abc->Kp);
float *gn2 = malloc(sizeof(float) * abc->Kp);
float fsc1, fsc2;
float bsc1, bsc2;
if (!gn2 || !on2) esl_fatal(msg);
if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
while (N--)
{
if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
if (p7_Forward (dsq, L, om, fwd, &fsc1) != eslOK) esl_fatal(msg);
if (p7_Backward (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
if (p7_Decoding(om, fwd, bck, pp) != eslOK) esl_fatal(msg);
if (p7_Null2_ByExpectation(om, pp, on2) != eslOK) esl_fatal(msg);
if (p7_GForward (dsq, L, gm, gxf, &fsc2) != eslOK) esl_fatal(msg);
if (p7_GBackward(dsq, L, gm, gxb, &bsc2) != eslOK) esl_fatal(msg);
if (p7_GDecoding(gm, gxf, gxb, gpp) != eslOK) esl_fatal(msg);
if (p7_GNull2_ByExpectation(gm, gpp, gn2) != eslOK) esl_fatal(msg);
if (esl_vec_FCompare(gn2, on2, abc->Kp, tolerance) != eslOK) esl_fatal(msg);
}
p7_gmx_Destroy(gpp);
p7_gmx_Destroy(gxf);
p7_gmx_Destroy(gxb);
p7_omx_Destroy(pp);
p7_omx_Destroy(fwd);
p7_omx_Destroy(bck);
free(on2);
free(gn2);
free(dsq);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
}
/* compare results to GDecoding(). */
static void
utest_decoding(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
char *msg = "decoding unit test failed";
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
P7_OMX *fwd = p7_omx_Create(M, L, L);
P7_OMX *bck = p7_omx_Create(M, L, L);
P7_OMX *pp = p7_omx_Create(M, L, L);
P7_GMX *gxf = p7_gmx_Create(M, L);
P7_GMX *gxb = p7_gmx_Create(M, L);
P7_GMX *gxp1 = p7_gmx_Create(M, L);
P7_GMX *gxp2 = p7_gmx_Create(M, L);
float fsc1, fsc2;
float bsc1, bsc2;
if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
while (N--)
{
if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
if (p7_Forward (dsq, L, om, fwd, &fsc1) != eslOK) esl_fatal(msg);
if (p7_Backward (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
if (p7_Decoding(om, fwd, bck, pp) != eslOK) esl_fatal(msg);
if (p7_omx_FDeconvert(pp, gxp1) != eslOK) esl_fatal(msg);
if (p7_GForward (dsq, L, gm, gxf, &fsc2) != eslOK) esl_fatal(msg);
if (p7_GBackward(dsq, L, gm, gxb, &bsc2) != eslOK) esl_fatal(msg);
if (p7_GDecoding(gm, gxf, gxb, gxp2) != eslOK) esl_fatal(msg);
// p7_gmx_Dump(stdout, gxp1, p7_DEFAULT);
// p7_gmx_Dump(stdout, gxp2, p7_DEFAULT);
if (p7_gmx_Compare(gxp1, gxp2, tolerance) != eslOK) esl_fatal(msg);
}
p7_gmx_Destroy(gxp1);
p7_gmx_Destroy(gxp2);
p7_gmx_Destroy(gxf);
p7_gmx_Destroy(gxb);
p7_omx_Destroy(fwd);
p7_omx_Destroy(bck);
p7_omx_Destroy(pp);
free(dsq);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
}
/* Function: p7_Decoding()
* Synopsis: Posterior decoding of residue assignment.
* Incept: MSF Tue Nov 3, 2009 [Janelia]
*
* Purpose: Identical to <p7_GDecoding()>. See <p7_GDecoding()>
* documentation for more info.
*
* Args: om - profile (must be the same that was used to fill <oxf>, <oxb>).
* oxf - filled Forward matrix
* oxb - filled Backward matrix
* pp - RESULT: posterior decoding matrix.
*
* Returns: <eslOK> on success.
*
* Returns <eslERANGE> if numeric range of floating-point
* values is exceeded during posterior probability
* calculations. In this case, the <pp> matrix must not be
* used by the caller; it will contain <NaN> values. To be
* safe, the caller should recalculate a generic posterior
* decoding matrix instead -- generic calculations are done
* in log probability space and are robust.
*
* However, I currently believe that this overflow only
* occurs on an unusual and ignorable situation: when a
* <p7_UNILOCAL> model is used on a region that contains
* two or more high scoring distinct alignments to the
* model. And that only happens if domain definition fails,
* after stochastic clustering, and an envelope that we
* pass to p7_domaindef.c::rescore_isolated_domain()
* erroneously contains 2+ distinct domains. (Note that
* this is different from having 2+ expected B states: that
* can happen normally, if a single consistent domain is
* better described by 2+ passes through the model). And I
* strongly believe all this only can happen on repetitive
* or biased-composition junk that we want to ignore anyway.
* Therefore the caller should be safe in ignoring any domain
* for which <p7_Decoding()> returns <eslERANGE>.
*/
int
p7_Decoding(const P7_OPROFILE *om, const P7_OMX *oxf, P7_OMX *oxb, P7_OMX *pp)
{
return p7_GDecoding(om, oxf, oxb, pp);
}
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_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;
}
/*
* 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 = 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;
}
void run_hmmer_pipeline(const char* seq) {
int index, i, status;
ESL_SQ* sq = esl_sq_CreateFrom(NULL, seq, NULL, NULL, NULL);
P7_OPROFILE *om = NULL;
P7_PROFILE *gm = NULL;
float usc, vfsc, fwdsc; /* filter scores */
float filtersc; /* HMM null filter score */
float nullsc; /* null model score */
float seqbias;
float seq_score; /* the corrected per-seq bit score */
double P;
WRAPPER_RESULT* result;
num_results = 0;
if(sq->n == 0) {
esl_sq_Destroy(sq);
return;
}
esl_sq_Digitize(abc, sq);
int n = 0;
float oasc;
for(index = 0;index < num_models;index++) {
om = models[index];
p7_omx_Reuse(oxf);
p7_omx_Reuse(oxb);
p7_omx_GrowTo(oxf, om->M, sq->n, sq->n);
p7_omx_GrowTo(oxb, om->M, sq->n, sq->n);
p7_oprofile_ReconfigLength(om, sq->n);
p7_bg_SetFilter(bg, om->M, om->compo);
p7_bg_SetLength(bg, sq->n);
//Calibrate null model
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
//MSV Filter
p7_MSVFilter(sq->dsq, sq->n, om, oxf, &usc);
seq_score = (usc - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Bias filter (model compo)
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
seq_score = (usc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Viterbi filter (Only do if P value from Bias is high)
if(P > f2) {
p7_ViterbiFilter(sq->dsq, sq->n, om, oxf, &vfsc);
seq_score = (vfsc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
if (P > f2) continue;
}
//Get the real probability (forward)
p7_Forward(sq->dsq, sq->n, om, oxf, &fwdsc);
seq_score = (fwdsc - filtersc) / eslCONST_LOG2;
P = esl_exp_surv(seq_score, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]);
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
if (P > f3) continue;
//Real hit, go in to posterior decoding and alignment
p7_omx_Reuse(oxb);
p7_trace_Reuse(tr);
p7_Backward(sq->dsq, sq->n, om, oxf, oxb, NULL);
status = p7_Decoding(om, oxf, oxb, oxb);
if(status == eslOK) {
//And then trace the result
p7_OptimalAccuracy(om, oxb, oxf, &oasc);
p7_OATrace(om, oxb, oxf, tr);
} else if(status == eslERANGE) {
fprintf(stderr, "Decoding overflow on model %s\n", om->name);
gm = gmodels[index];
if(gxf == NULL) {
gxf = p7_gmx_Create(gm->M, sq->n);
gxb = p7_gmx_Create(gm->M, sq->n);
} else {
p7_gmx_GrowTo(gxf, gm->M, sq->n);
p7_gmx_GrowTo(gxb, gm->M, sq->n);
}
p7_ReconfigLength(gm, sq->n);
p7_GForward (sq->dsq, sq->n, gm, gxf, &fwdsc);
p7_GBackward(sq->dsq, sq->n, gm, gxb, NULL);
p7_GDecoding(gm, gxf, gxb, gxb);
p7_GOptimalAccuracy(gm, gxb, gxf, &oasc);
p7_GOATrace (gm, gxb, gxf, tr);
p7_gmx_Reuse(gxf);
p7_gmx_Reuse(gxb);
}
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
result = wrapper_results[num_results];
reuse_result(result, tr->N + om->M, om->name); //We're way overallocating here, but it's hard to know at this point how much space we'll need for the alignment (plus leading and trailing gaps)
trace_into(tr, result, sq, abc, om->M);
result->bits = seq_score;
num_results++;
}
esl_sq_Destroy(sq);
}
/* glocal_rescore_isolated_domain()
* EPN, Tue Oct 5 10:16:12 2010
*
* Based on p7_domaindef.c's rescore_isolated_domain(). Modified
* so that generic matrices (which can be used for glocally configured
* models) can be used. This function finds a single glocal domain, not a
* single local one.
*
* Also modified to optionally remove the Backward and OA alignment.
* The decision to do these is determined by three input parameters:
* <null2_is_done>: TRUE if we've already computed the null2 scores for
* this region (see Sean's notes below).
* <do_null2>: TRUE if we will apply a null2 penalty eventually
* to this domain
* <do_aln>: TRUE if we need the OA alignment
*
* Notes (verbatim) from p7_domaindef.c::rescore_isolated_domain():
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* SRE, Fri Feb 8 09:18:33 2008 [Janelia]
*
* We have isolated a single domain's envelope from <i>..<j> in
* sequence <sq>, and now we want to score it in isolation and obtain
* an alignment display for it.
*
* (Later, we can add up all the individual domain scores from this
* seq into a new per-seq score, to compare to the original per-seq
* score).
*
* The caller provides model <om> configured in unilocal mode; by
* using unilocal (as opposed to multilocal), we're going to force the
* identification of a single domain in this envelope now.
*
* The alignment is an optimal accuracy alignment (sensu IH Holmes),
* also obtained in unilocal mode.
*
* The caller provides DP matrices <ox1> and <ox2> with sufficient
* space to hold Forward and Backward calculations for this domain
* against the model. (The caller will typically already have matrices
* sufficient for the complete sequence lying around, and can just use
* those.) The caller also provides a <P7_DOMAINDEF> object which is
* (efficiently, we trust) managing any necessary temporary working
* space and heuristic thresholds.
*
* Returns <eslOK> if a domain was successfully identified, scored,
* and aligned in the envelope; if so, the per-domain information is
* registered in <ddef>, in <ddef->dcl>.
*
* And here's what's happened to our working memory:
*
* <ddef>: <ddef->tr> has been used, and possibly reallocated, for
* the OA trace of the domain. Before exit, we called
* <Reuse()> on it.
*
* <ox1> : happens to be holding OA score matrix for the domain
* upon return, but that's not part of the spec; officially
* its contents are "undefined".
*
* <ox2> : happens to be holding a posterior probability matrix
* for the domain upon return, but we're not making that
* part of the spec, so caller shouldn't rely on this;
* spec just makes its contents "undefined".
*/
static int
glocal_rescore_isolated_domain(P7_DOMAINDEF *ddef, const P7_PROFILE *gm, const ESL_SQ *sq,
P7_GMX *gx1, P7_GMX *gx2, int i, int j, int null2_is_done,
int do_null2, int do_aln)
{
P7_DOMAIN *dom = NULL;
int Ld = j-i+1;
float domcorrection = 0.0;
float envsc, oasc;
int z;
int pos;
float null2[p7_MAXCODE];
int status;
p7_GForward (sq->dsq + i-1, Ld, gm, gx1, &envsc);
oasc = 0.;
if(do_null2 || do_aln) {
p7_GBackward(sq->dsq + i-1, Ld, gm, gx2, NULL);
status = p7_GDecoding(gm, gx1, gx2, gx2); /* <ox2> is now overwritten with post probabilities */
if (status == eslERANGE) return eslFAIL; /* rare: numeric overflow; domain is assumed to be repetitive garbage [J3/119-212] */
/* Is null2 set already for this i..j? (It is, if we're in a domain that
* was defined by stochastic traceback clustering in a multidomain region;
* it isn't yet, if we're in a simple one-domain region). If it isn't,
* do it now, by the expectation (posterior decoding) method.
*/
if ((! null2_is_done) && do_null2) {
p7_GNull2_ByExpectation(gm, gx2, null2);
for (pos = i; pos <= j; pos++)
ddef->n2sc[pos] = logf(null2[sq->dsq[pos]]);
}
if(do_null2) {
for (pos = i; pos <= j; pos++)
domcorrection += ddef->n2sc[pos]; /* domcorrection is in units of NATS */
}
if(do_aln) {
/* Find an optimal accuracy alignment */
p7_GOptimalAccuracy(gm, gx2, gx1, &oasc); /* <ox1> is now overwritten with OA scores */
p7_GOATrace (gm, gx2, gx1, ddef->tr); /* <tr>'s seq coords are offset by i-1, rel to orig dsq */
/* hack the trace's sq coords to be correct w.r.t. original dsq */
for (z = 0; z < ddef->tr->N; z++)
if (ddef->tr->i[z] > 0) ddef->tr->i[z] += i-1;
}
/* get ptr to next empty domain structure in domaindef's results */
}
if (ddef->ndom == ddef->nalloc) {
void *p;
ESL_RALLOC(ddef->dcl, p, sizeof(P7_DOMAIN) * (ddef->nalloc*2));
ddef->nalloc *= 2;
}
dom = &(ddef->dcl[ddef->ndom]);
/* store the results in it */
dom->ienv = i;
dom->jenv = j;
dom->envsc = envsc; /* in units of NATS */
dom->domcorrection = domcorrection; /* in units of NATS, will be 0. if do_null2 == FALSE */
dom->oasc = oasc; /* in units of expected # of correctly aligned residues, will be 0. if do_aln == FALSE */
dom->dombias = 0.0; /* gets set later, using bg->omega and dombias */
dom->bitscore = 0.0; /* gets set later by caller, using envsc, null score, and dombias */
dom->lnP = 1.0; /* gets set later by caller, using bitscore */
dom->is_reported = FALSE; /* gets set later by caller */
dom->is_included = FALSE; /* gets set later by caller */
dom->ad = NULL;
dom->iali = i;
dom->jali = j;
ddef->ndom++;
if(do_aln) {
p7_trace_Reuse(ddef->tr);
}
return eslOK;
ERROR:
if(do_aln) {
p7_trace_Reuse(ddef->tr);
}
return status;
}
