int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
ESL_SQ *sq = esl_sq_CreateDigital(abc);
ESL_SQFILE *sqfp = NULL;
ESL_HMM *hmm = create_test_hmm(abc);
ESL_HMM *bg = create_null_hmm(abc);
ESL_HMX *hmx = esl_hmx_Create(400, hmm->M);
int format = eslSQFILE_UNKNOWN;
char *seqfile = esl_opt_GetArg(go, 1);
float fwdsc, nullsc;
int status;
status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file.");
else if (status == eslEFORMAT) esl_fatal("Format unrecognized.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
esl_hmx_GrowTo(hmx, sq->n, hmm->M);
esl_hmm_Forward(sq->dsq, sq->n, hmm, hmx, &fwdsc);
esl_hmm_Forward(sq->dsq, sq->n, bg, hmx, &nullsc);
printf("%-16s %5d %11.4f %8.4f %11.4f %8.4f %11.4f %8.4f\n", sq->name, (int) sq->n,
fwdsc * eslCONST_LOG2R, (fwdsc * eslCONST_LOG2R) / sq->n,
nullsc * eslCONST_LOG2R, (nullsc * eslCONST_LOG2R) / sq->n,
(fwdsc - nullsc) * eslCONST_LOG2R, (fwdsc-nullsc) * eslCONST_LOG2R / sq->n);
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s)\n%s\n",
sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
esl_hmm_Destroy(hmm);
esl_hmm_Destroy(bg);
esl_hmx_Destroy(hmx);
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_Create(esl_opt_GetInteger(go, "-s"));
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;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
P7_ANCHORS *anch = p7_anchors_Create();
P7_ANCHORHASH *ah = p7_anchorhash_Create();
P7_ENVELOPES *env = p7_envelopes_Create();
P7_REFMX *rxf = NULL;
P7_REFMX *rxd = NULL;
P7_REFMX *afu = NULL;
P7_REFMX *afd = NULL;
P7_REFMX *apu = NULL;
P7_REFMX *apd = NULL;
P7_TRACE *tr = NULL;
float *wrk = NULL;
P7_MPAS_PARAMS prm;
P7_MPAS_STATS stats;
float fsc, vsc, asc, asc_b;
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);
/* Open sequence file */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* Read one sequence */
status = esl_sqio_Read(sqfp, sq);
if (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslOK) p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);
esl_sqfile_Close(sqfp);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
p7_profile_Config(gm, hmm, bg);
/* Set the profile and null model's target length models */
p7_bg_SetLength (bg, sq->n);
p7_profile_SetLength(gm, sq->n);
/* Allocate DP matrices and tracebacks */
rxf = p7_refmx_Create(gm->M, sq->n);
rxd = p7_refmx_Create(gm->M, sq->n);
tr = p7_trace_Create();
afu = p7_refmx_Create(gm->M, sq->n);
afd = p7_refmx_Create(gm->M, sq->n);
/* First pass analysis */
p7_ReferenceViterbi (sq->dsq, sq->n, gm, rxf, tr, &vsc);
p7_ReferenceForward (sq->dsq, sq->n, gm, rxf, &fsc);
p7_ReferenceBackward(sq->dsq, sq->n, gm, rxd, NULL);
p7_ReferenceDecoding(sq->dsq, sq->n, gm, rxf, rxd, rxd);
/* Customize MPAS parameters if you want; these are the defaults. */
prm.max_iterations = 1000;
prm.loss_threshold = 0.001;
prm.nmax_sampling = FALSE;
prm.be_verbose = FALSE;
/* MPAS algorithm gets us an anchor set */
p7_reference_Anchors(rng, sq->dsq, sq->n, gm, rxf, rxd, tr, &wrk, ah,
afu, afd, anch, &asc, &prm, &stats);
//printf("# ASC Forward UP:\n"); p7_refmx_Dump(stdout, afu);
//printf("# ASC Forward DOWN:\n"); p7_refmx_Dump(stdout, afd);
/* We no longer need rxf and rxd.
* Use their space for apu/apd pair, which will briefly
* hold ASC Backward matrices, then get used for ASC Decoding.
*/
apu = rxf; p7_refmx_Reuse(apu);
apd = rxd; p7_refmx_Reuse(apd);
p7_ReferenceASCBackward(sq->dsq, sq->n, gm, anch->a, anch->D, apu, apd, &asc_b);
//printf("# Backward score (raw, nats): %.2f\n", asc_b);
//printf("# ASC Backward UP:\n"); p7_refmx_Dump(stdout, apu);
//printf("# ASC Backward DOWN:\n"); p7_refmx_Dump(stdout, apd);
/* ASC Decoding takes afu/afd and abu/abd as input;
* overwrites abu/abd with decoding matrices
*/
p7_ReferenceASCDecoding(sq->dsq, sq->n, gm, anch->a, anch->D, afu, afd, apu, apd, apu, apd);
//printf("# ASC Decoding UP matrix:\n"); p7_refmx_Dump(stdout, apu);
//printf("# ASC Decoding DOWN:\n"); p7_refmx_Dump(stdout, apu);
/* Envelope calculation needs to get four matrices:
* ASC Decoding pair, apu/apd, and it will leave these constant;
* ASC Forward pair, afu/afd, and it will overwrite these.
*/
p7_reference_Envelopes(sq->dsq, sq->n, gm, anch->a, anch->D, apu, apd, afu, afd, env);
p7_envelopes_Dump(stdout, env);
p7_envelopes_Destroy(env);
p7_anchorhash_Destroy(ah);
p7_anchors_Destroy(anch);
if (wrk) free(wrk);
p7_trace_Destroy(tr);
p7_refmx_Destroy(afd);
p7_refmx_Destroy(afu);
p7_refmx_Destroy(rxd);
p7_refmx_Destroy(rxf);
esl_sq_Destroy(sq);
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;
}
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;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
ESL_SQ *sq = NULL;
float nullsc, filtersc, H;
int status;
/* Read one HMM from <hmmfile> */
if (p7_hmmfile_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);
/* Open <seqfile> for reading */
status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file.");
else if (status == eslEFORMAT) esl_fatal("Format unrecognized.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
p7_bg_SetFilter(bg, hmm->M, hmm->compo);
H = esl_vec_FEntropy(bg->f, bg->abc->K);
printf("bg iid H = %.4f\n", H);
H = esl_vec_FEntropy(hmm->compo, bg->abc->K);
printf("modelcomp H = %.4f\n", H);
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
p7_bg_SetLength(bg, sq->n);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
printf("%-20s %5d %8.5f %8.5f %8.5f\n", sq->name, (int) sq->n, nullsc, filtersc, filtersc-nullsc);
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s)\n%s\n",
sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = 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 *fwd = NULL;
P7_GMX *bck = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float fsc, bsc;
float nullsc;
int status;
/* Initialize log-sum calculator */
p7_FLogsumInit();
/* 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_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
/* Now reconfig the models however we were asked to */
if (esl_opt_GetBoolean(go, "--fs")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
else if (esl_opt_GetBoolean(go, "--sw")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
else if (esl_opt_GetBoolean(go, "--ls")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_GLOCAL);
else if (esl_opt_GetBoolean(go, "--s")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNIGLOCAL);
/* Allocate matrices */
fwd = p7_gmx_Create(gm->M, sq->n);
bck = p7_gmx_Create(gm->M, sq->n);
printf("%-30s %-10s %-10s %-10s %-10s\n", "# seq name", "fwd (raw)", "bck (raw) ", "fwd (bits)", "bck (bits)");
printf("%-30s %10s %10s %10s %10s\n", "#--------------", "----------", "----------", "----------", "----------");
while ( (status = esl_sqio_Read(sqfp, sq)) != eslEOF)
{
if (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslOK) p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);
/* Resize the DP matrices if necessary */
p7_gmx_GrowTo(fwd, gm->M, sq->n);
p7_gmx_GrowTo(bck, gm->M, sq->n);
/* Set the profile and null model's target length models */
p7_bg_SetLength(bg, sq->n);
p7_ReconfigLength(gm, sq->n);
/* Run Forward, Backward */
p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);
p7_gmx_Dump(stdout, fwd, p7_DEFAULT);
/* Those scores are partial log-odds likelihoods in nats.
* Subtract off the rest of the null model, convert to bits.
*/
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
printf("%-30s %10.4f %10.4f %10.4f %10.4f\n",
sq->name,
fsc, bsc,
(fsc - nullsc) / eslCONST_LOG2, (bsc - nullsc) / eslCONST_LOG2);
p7_gmx_Reuse(fwd);
p7_gmx_Reuse(bck);
esl_sq_Reuse(sq);
}
/* Cleanup */
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
p7_gmx_Destroy(fwd);
p7_gmx_Destroy(bck);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}