Exemplo n.º 1
0
/* The "basic" utest is a minimal driver for making a small DNA profile and a small DNA sequence,
 * then running Viterbi and Forward. It's useful for dumping DP matrices and profiles for debugging.
 */
static void
utest_basic(ESL_GETOPTS *go)
{
  char           *query= "# STOCKHOLM 1.0\n\nseq1 GAATTC\nseq2 GAATTC\n//\n";
  int             fmt  = eslMSAFILE_STOCKHOLM;
  char           *targ = "GAATTC";
  ESL_ALPHABET   *abc  = NULL;
  ESL_MSA        *msa  = NULL;
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_BG          *bg   = NULL;
  P7_PRIOR       *pri  = NULL;	
  ESL_DSQ        *dsq  = NULL;
  P7_GMX         *gx   = NULL;
  P7_TRACE        *tr  = NULL;
  int             L    = strlen(targ);
  float           vsc, vsc2, fsc;

  if ((abc = esl_alphabet_Create(eslDNA))          == NULL)  esl_fatal("failed to create alphabet");
  if ((pri = p7_prior_CreateNucleic())             == NULL)  esl_fatal("failed to create prior");
  if ((msa = esl_msa_CreateFromString(query, fmt)) == NULL)  esl_fatal("failed to create MSA");
  if (esl_msa_Digitize(abc, msa, NULL)             != eslOK) esl_fatal("failed to digitize MSA");
  if (p7_Fastmodelmaker(msa, 0.5, NULL, &hmm, NULL) != eslOK) esl_fatal("failed to create GAATTC model");
  if (p7_ParameterEstimation(hmm, pri)             != eslOK) esl_fatal("failed to parameterize GAATTC model");
  if (p7_hmm_SetConsensus(hmm, NULL)               != eslOK) esl_fatal("failed to make consensus");
  if ((bg = p7_bg_Create(abc))                     == NULL)  esl_fatal("failed to create DNA null model");
  if ((gm = p7_profile_Create(hmm->M, abc))        == NULL)  esl_fatal("failed to create GAATTC profile");
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL)!= eslOK) esl_fatal("failed to config profile");
  if (p7_profile_Validate(gm, NULL, 0.0001)        != eslOK) esl_fatal("whoops, profile is bad!");
  if (esl_abc_CreateDsq(abc, targ, &dsq)           != eslOK) esl_fatal("failed to create GAATTC digital sequence");
  if ((gx = p7_gmx_Create(gm->M, L))               == NULL)  esl_fatal("failed to create DP matrix");
  if ((tr = p7_trace_Create())                     == NULL)  esl_fatal("trace creation failed");

  p7_GViterbi   (dsq, L, gm, gx, &vsc);
  if (esl_opt_GetBoolean(go, "-v")) printf("Viterbi score: %.4f\n", vsc);
  if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);

  p7_GTrace     (dsq, L, gm, gx, tr);
  p7_trace_Score(tr, dsq, gm, &vsc2);
  if (esl_opt_GetBoolean(go, "-v")) p7_trace_Dump(stdout, tr, gm, dsq);
  
  if (esl_FCompare(vsc, vsc2, 1e-5) != eslOK)  esl_fatal("trace score and Viterbi score don't agree.");

  p7_GForward   (dsq, L, gm, gx, &fsc);
  if (esl_opt_GetBoolean(go, "-v")) printf("Forward score: %.4f\n", fsc);
  if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);

  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx);
  free(dsq);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_msa_Destroy(msa);
  p7_prior_Destroy(pri);
  esl_alphabet_Destroy(abc);
  return;
}
Exemplo n.º 2
0
/* 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);
}
Exemplo n.º 3
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;
}
Exemplo n.º 4
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);
}
Exemplo n.º 5
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(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;
  P7_GMX         *fwd     = NULL;
  P7_TRACE       *tr      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  char            errbuf[eslERRBUFSIZE];
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
  float           vsc, fsc, tsc;
  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_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);

  fwd = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_Create();

  p7_GViterbi(sq->dsq, sq->n, gm, fwd,  &vsc);
  p7_GForward(sq->dsq, sq->n, gm, fwd, &fsc);
  if (esl_opt_GetBoolean(go, "-m") == TRUE)  p7_gmx_Dump(stdout, fwd, p7_DEFAULT);

  for (i = 0; i < N; i++)
    {
      p7_GStochasticTrace(r, sq->dsq, sq->n, gm, 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) esl_fatal("trace failed validation: %s\n", 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 */
  p7_gmx_Destroy(fwd);
  p7_trace_Destroy(tr);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Exemplo n.º 6
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;
}