コード例 #1
0
ファイル: mpi.c プロジェクト: Janelia-Farm-Xfam/Bio-HMM-Logo
static void
utest_oprofileSendRecv(int my_rank, int nproc)
{
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(42);
  ESL_ALPHABET   *abc  = esl_alphabet_Create(eslAMINO);
  P7_HMM         *hmm  = NULL;
  P7_BG          *bg   = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_OPROFILE    *om   = NULL;
  P7_OPROFILE    *om2  = NULL;
  int             M    = 200;
  int             L    = 400;
  char           *wbuf = NULL;
  int             wn   = 0;
  int             i;
  char            errbuf[eslERRBUFSIZE];

  p7_hmm_Sample(r, M, abc, &hmm); /* master and worker's sampled profiles are identical */
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);
  om = p7_oprofile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  p7_oprofile_Convert(gm, om);
  p7_bg_SetLength  (bg, L);

  if (my_rank == 0)
    {
      for (i = 1; i < nproc; i++)
	{
	  ESL_DPRINTF1(("Master: receiving test profile\n"));
	  p7_oprofile_MPIRecv(MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &wbuf, &wn, &abc, &om2);
	  ESL_DPRINTF1(("Master: test profile received\n"));

	  if (p7_oprofile_Compare(om, om2, 0.001, errbuf) != eslOK) 
	    p7_Die("Received profile not identical to what was sent\n%s", errbuf);

	  p7_oprofile_Destroy(om2);
	}
    }
  else 
    {
      ESL_DPRINTF1(("Worker %d: sending test profile\n", my_rank));
      p7_oprofile_MPISend(om, 0, 0, MPI_COMM_WORLD, &wbuf, &wn);
      ESL_DPRINTF1(("Worker %d: test profile sent\n", my_rank));
    }

  free(wbuf);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  return;
}
コード例 #2
0
ファイル: io.c プロジェクト: TuftsBCB/SMURFBuild
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go   = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = NULL;
  P7_BG          *bg   = NULL;
  P7_HMM         *hmm  = NULL;
  P7_OPROFILE    *om   = NULL;
  int             M    = esl_opt_GetInteger(go, "-M");
  int             L    = esl_opt_GetInteger(go, "-L");
  
  /* Sample a random HMM and optimized profile, in amino acid alphabet.  */
  if ((abc = esl_alphabet_Create(eslAMINO))                    == NULL)  esl_fatal("failed to create alphabet");
  if ((bg = p7_bg_Create(abc))                                 == NULL)  esl_fatal("failed to create null model");
  if (( p7_oprofile_Sample(r, abc, bg, M, L, &hmm, NULL, &om)) != eslOK) esl_fatal("failed to sample HMM and profile");

  /* unit test(s) */
  utest_ReadWrite(hmm, om);

  p7_oprofile_Destroy(om);
  p7_hmm_Destroy(hmm);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return eslOK;
}
コード例 #3
0
ファイル: vitscore.c プロジェクト: Denis84/EPA-WorkBench
/* ViterbiScore() unit test
 * 
 * We can compare these scores to GViterbi() almost exactly; the only
 * differences should be negligible roundoff errors. Must convert
 * the optimized profile to lspace, though, rather than pspace.
 */
static void
utest_viterbi_score(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_oprofile_Logify(om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_ViterbiScore(dsq, L, om, ox, &sc1);
      p7_GViterbi    (dsq, L, gm, gx, &sc2);

      if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi score unit test failed: scores differ");
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}
コード例 #4
0
ファイル: mpi.c プロジェクト: Denis84/EPA-WorkBench
/* Function:  p7_oprofile_MPIRecv()
 * Synopsis:  Receives an OPROFILE as a work unit from an MPI sender.
 * Incept:    MSF, Wed Oct 21, 2009 [Janelia]
 *
 * Purpose:   Receive a work unit that consists of a single OPROFILE
 *            sent by MPI <source> (<0..nproc-1>, or
 *            <MPI_ANY_SOURCE>) tagged as <tag> for MPI communicator <comm>.
 *            
 *            Work units are prefixed by a status code. If the unit's
 *            code is <eslOK> and no errors are encountered, this
 *            routine will return <eslOK> and a non-<NULL> <*ret_om>.
 *            If the unit's code is <eslEOD> (a shutdown signal), 
 *            this routine returns <eslEOD> and <*ret_om> is <NULL>.
 *   
 *            Caller provides a working buffer <*buf> of size
 *            <*nalloc> characters. These are passed by reference, so
 *            that <*buf> can be reallocated and <*nalloc> increased
 *            if necessary. As a special case, if <*buf> is <NULL> and
 *            <*nalloc> is 0, the buffer will be allocated
 *            appropriately, but the caller is still responsible for
 *            free'ing it.
 *            
 *            Caller may or may not already know what alphabet the OPROFILE
 *            is expected to be in.  A reference to the current
 *            alphabet is passed in <abc>. If the alphabet is unknown,
 *            pass <*abc = NULL>, and when the OPROFILE is received, an
 *            appropriate new alphabet object is allocated and passed
 *            back to the caller via <*abc>.  If the alphabet is
 *            already known, <*ret_abc> is that alphabet, and the new
 *            OPROFILE's alphabet type is verified to agree with it. This
 *            mechanism allows an application to let the first OPROFILE
 *            determine the alphabet type for the application, while
 *            still keeping the alphabet under the application's scope
 *            of control.
 *
 * Returns:   <eslOK> on success. <*ret_om> contains the received OPROFILE;
 *            it is allocated here, and the caller is responsible for
 *            free'ing it.  <*buf> may have been reallocated to a
 *            larger size, and <*nalloc> may have been increased.  If
 *            <*abc> was passed as <NULL>, it now points to an
 *            <ESL_ALPHABET> object that was allocated here; caller is
 *            responsible for free'ing this.
 *            
 *            Returns <eslEOD> if an end-of-data signal was received.
 *            In this case, <*buf>, <*nalloc>, and <*abc> are left unchanged,
 *            and <*ret_om> is <NULL>.
 *            
 *            Returns <eslEINCOMPAT> if the OPROFILE is in a different alphabet
 *            than <*abc> said to expect. In this case, <*abc> is unchanged,
 *            <*buf> and <*nalloc> may have been changed, and <*ret_om> is
 *            <NULL>.
 *            
 * Throws:    <eslEMEM> on allocation error, in which case <*ret_om> is 
 *            <NULL>.           
 */
int
p7_oprofile_MPIRecv(int source, int tag, MPI_Comm comm, char **buf, int *nalloc, ESL_ALPHABET **abc, P7_OPROFILE **ret_om)
{
  int         status;
  int         code;
  P7_OPROFILE     *om     = NULL;
  int         n;
  int         pos;
  MPI_Status  mpistatus;

  /* Probe first, because we need to know if our buffer is big enough. */
  MPI_Probe(source, tag, comm, &mpistatus);
  MPI_Get_count(&mpistatus, MPI_PACKED, &n);

  /* Make sure the buffer is allocated appropriately */
  if (*buf == NULL || n > *nalloc) {
    void *tmp;
    ESL_RALLOC(*buf, tmp, sizeof(char) * n);
    *nalloc = n; 
  }

  /* Receive the packed work unit */
  MPI_Recv(*buf, n, MPI_PACKED, source, tag, comm, &mpistatus);

  /* Unpack it, looking at the status code prefix for EOD/EOK  */
  pos = 0;
  if (MPI_Unpack(*buf, n, &pos, &code, 1, MPI_INT, comm) != 0) ESL_XEXCEPTION(eslESYS, "mpi unpack failed");
  if (code == eslEOD)  { *ret_om = NULL;  return eslEOD; }

  return p7_oprofile_MPIUnpack(*buf, *nalloc, &pos, comm, abc, ret_om);

 ERROR:
  if (om != NULL) p7_oprofile_Destroy(om);
  return status;
}
コード例 #5
0
ファイル: p7_builder.c プロジェクト: dboudour2002/musicHMMER
/* Function:  p7_Builder()
 * Synopsis:  Build a new HMM from an MSA.
 *
 * Purpose:   Take the multiple sequence alignment <msa> and a build configuration <bld>,
 *            and build a new HMM. 
 * 
 *            Effective sequence number determination and calibration steps require
 *            additionally providing a null model <bg>.
 *
 * Args:      bld         - build configuration
 *            msa         - multiple sequence alignment
 *            bg          - null model
 *            opt_hmm     - optRETURN: new HMM
 *            opt_trarr   - optRETURN: array of faux tracebacks, <0..nseq-1>
 *            opt_gm      - optRETURN: profile corresponding to <hmm>
 *            opt_om      - optRETURN: optimized profile corresponding to <gm>
 *            opt_postmsa - optRETURN: RF-annotated, possibly modified MSA 
 *
 * Returns:   <eslOK> on success. The new HMM is optionally returned in
 *            <*opt_hmm>, along with optional returns of an array of faux tracebacks
 *            for each sequence in <*opt_trarr>, the annotated MSA used to construct
 *            the model in <*opt_postmsa>, a configured search profile in 
 *            <*opt_gm>, and an optimized search profile in <*opt_om>. These are
 *            all optional returns because the caller may, for example, be interested
 *            only in an optimized profile, or may only be interested in the HMM.
 *            
 *            Returns <eslENORESULT> if no consensus columns were annotated.
 *            Returns <eslEFORMAT> on MSA format problems, such as a missing RF annotation
 *            line in hand architecture construction. On any returned error,
 *            <bld->errbuf> contains an informative error message.
 *
 * Throws:    <eslEMEM> on allocation error.
 *            <eslEINVAL> if relative weights couldn't be calculated from <msa>.
 *
 * Xref:      J4/30.
 */
int
p7_Builder(P7_BUILDER *bld, ESL_MSA *msa, P7_BG *bg,
	   P7_HMM **opt_hmm, P7_TRACE ***opt_trarr, P7_PROFILE **opt_gm, P7_OPROFILE **opt_om,
	   ESL_MSA **opt_postmsa)
{
  int i,j;
  uint32_t    checksum = 0;	/* checksum calculated for the input MSA. hmmalign --mapali verifies against this. */
  P7_HMM     *hmm      = NULL;
  P7_TRACE  **tr       = NULL;
  P7_TRACE ***tr_ptr   = (opt_trarr != NULL || opt_postmsa != NULL) ? &tr : NULL;
  int         status;
  if ((status =  validate_msa         (bld, msa))                       != eslOK) goto ERROR;
  if ((status =  esl_msa_Checksum     (msa, &checksum))                 != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to calculate checksum"); 
  if ((status =  relative_weights     (bld, msa))                       != eslOK) goto ERROR;
  if ((status =  esl_msa_MarkFragments(msa, bld->fragthresh))           != eslOK) goto ERROR;
  if ((status =  build_model          (bld, msa, &hmm, tr_ptr))         != eslOK) goto ERROR;

  //Ensures that the weighted-average I->I count <=  bld->max_insert_len
  //(MI currently contains the number of observed insert-starts)
  if (bld->max_insert_len>0)
    for (i=1; i<hmm->M; i++ )
      hmm->t[i][p7H_II] = ESL_MIN(hmm->t[i][p7H_II], bld->max_insert_len*hmm->t[i][p7H_MI]);

  if ((status =  effective_seqnumber  (bld, msa, hmm, bg))              != eslOK) goto ERROR;
  if ((status =  parameterize         (bld, hmm))                       != eslOK) goto ERROR;
  if ((status =  annotate             (bld, msa, hmm))                  != eslOK) goto ERROR;
  if ((status =  calibrate            (bld, hmm, bg, opt_gm, opt_om))   != eslOK) goto ERROR;
  if ((status =  make_post_msa        (bld, msa, hmm, tr, opt_postmsa)) != eslOK) goto ERROR;

  //force masked positions to background  (it'll be close already, so no relevant impact on weighting)
  if (hmm->mm != NULL)
    for (i=1; i<hmm->M; i++ )
      if (hmm->mm[i] == 'm')
        for (j=0; j<hmm->abc->K; j++)
          hmm->mat[i][j] = bg->f[j];

  if ( bld->abc->type == eslDNA ||  bld->abc->type == eslRNA ) {
	  if (bld->w_len > 0)           hmm->max_length = bld->w_len;
	  else if (bld->w_beta == 0.0)  hmm->max_length = hmm->M *4;
	  else if ( (status =  p7_Builder_MaxLength(hmm, bld->w_beta)) != eslOK) goto ERROR;
  }

  hmm->checksum = checksum;
  hmm->flags   |= p7H_CHKSUM;

  if (opt_hmm   != NULL) *opt_hmm   = hmm; else p7_hmm_Destroy(hmm);
  if (opt_trarr != NULL) *opt_trarr = tr;  else p7_trace_DestroyArray(tr, msa->nseq);
  return eslOK;

 ERROR:
  p7_hmm_Destroy(hmm);
  p7_trace_DestroyArray(tr, msa->nseq);
  if (opt_gm    != NULL) p7_profile_Destroy(*opt_gm);
  if (opt_om    != NULL) p7_oprofile_Destroy(*opt_om);
  return status;
}
コード例 #6
0
ファイル: fwdback.c プロジェクト: Denis84/EPA-WorkBench
/* 
 * compare to GForward() scores.
 */
static void
utest_fwdback(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  char        *msg = "forward/backward 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, 0, L);
  P7_OMX      *bck = p7_omx_Create(M, 0, L);
  P7_OMX      *oxf = p7_omx_Create(M, L, L);
  P7_OMX      *oxb = p7_omx_Create(M, L, L);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float tolerance;
  float fsc1, fsc2;
  float bsc1, bsc2;
  float generic_sc;

  p7_FLogsumInit();
  if (p7_FLogsumError(-0.4, -0.5) > 0.0001) tolerance = 1.0;  /* weaker test against GForward()   */
  else tolerance = 0.0001;   /* stronger test: FLogsum() is in slow exact mode. */

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_Forward       (dsq, L, om, oxf,      &fsc1);
      p7_Backward      (dsq, L, om, oxf, oxb, &bsc1);
      p7_ForwardParser (dsq, L, om, fwd,      &fsc2);
      p7_BackwardParser(dsq, L, om, fwd, bck, &bsc2);
      p7_GForward      (dsq, L, gm, gx,  &generic_sc);

      /* Forward and Backward scores should agree with high tolerance */
      if (fabs(fsc1-bsc1) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc2-bsc2) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc1-fsc2) > 0.0001)    esl_fatal(msg);

      /* GForward scores should approximate Forward scores, 
       * with tolerance that depends on how logsum.c was compiled
       */
      if (fabs(fsc1-generic_sc) > tolerance) esl_fatal(msg);
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(oxb);
  p7_omx_Destroy(oxf);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}
コード例 #7
0
ファイル: null2.c プロジェクト: dboudour2002/musicHMMER
/* 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);
}
コード例 #8
0
ファイル: decoding.c プロジェクト: dboudour2002/musicHMMER
/* 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);
}
コード例 #9
0
ファイル: p7_builder.c プロジェクト: dboudour2002/musicHMMER
/* Function:  p7_SingleBuilder()
 * Synopsis:  Build a new HMM from a single sequence.
 *
 * Purpose:   Take the sequence <sq> and a build configuration <bld>, and
 *            build a new HMM.
 *            
 *            The single sequence scoring system in the <bld>
 *            configuration must have been previously initialized by
 *            <p7_builder_SetScoreSystem()>.
 *            
 * Args:      bld       - build configuration
 *            sq        - query sequence
 *            bg        - null model (needed to paramaterize insert emission probs)
 *            opt_hmm   - optRETURN: new HMM
 *            opt_gm    - optRETURN: profile corresponding to <hmm>
 *            opt_om    - optRETURN: optimized profile corresponding to <gm>
 *
 * Returns:   <eslOK> on success.
 *
 * Throws:    <eslEMEM> on allocation error.
 *            <eslEINVAL> if <bld> isn't properly configured somehow.
 */
int
p7_SingleBuilder(P7_BUILDER *bld, ESL_SQ *sq, P7_BG *bg, P7_HMM **opt_hmm,
		 P7_TRACE **opt_tr, P7_PROFILE **opt_gm, P7_OPROFILE **opt_om)
{
  P7_HMM   *hmm = NULL;
  P7_TRACE *tr  = NULL;
  int       k;
  int       status;
  
  bld->errbuf[0] = '\0';
  if (! bld->Q) ESL_XEXCEPTION(eslEINVAL, "score system not initialized");

  if ((status = p7_Seqmodel(bld->abc, sq->dsq, sq->n, sq->name, bld->Q, bg->f, bld->popen, bld->pextend, &hmm)) != eslOK) goto ERROR;
  if ((status = p7_hmm_SetComposition(hmm))                                                                     != eslOK) goto ERROR;
  if ((status = p7_hmm_SetConsensus(hmm, sq))                                                                   != eslOK) goto ERROR; 
  if ((status = calibrate(bld, hmm, bg, opt_gm, opt_om))                                                        != eslOK) goto ERROR;

  if ( bld->abc->type == eslDNA ||  bld->abc->type == eslRNA ) {
    if (bld->w_len > 0)           hmm->max_length = bld->w_len;
    else if (bld->w_beta == 0.0)  hmm->max_length = hmm->M *4;
    else if ( (status =  p7_Builder_MaxLength(hmm, bld->w_beta)) != eslOK) goto ERROR;
  }


  /* build a faux trace: relative to core model (B->M_1..M_L->E) */
  if (opt_tr != NULL) 
    {
      if ((tr = p7_trace_Create())                      == NULL)  goto ERROR;
      if ((status = p7_trace_Append(tr, p7T_B, 0, 0))   != eslOK) goto ERROR; 
      for (k = 1; k <= sq->n; k++)
        if ((status = p7_trace_Append(tr, p7T_M, k, k)) != eslOK) goto ERROR;
      if ((status = p7_trace_Append(tr, p7T_E, 0, 0))   != eslOK) goto ERROR; 
      tr->M = sq->n;
      tr->L = sq->n;
    }

  /* note that <opt_gm> and <opt_om> were already set by calibrate() call above. */
  if (opt_hmm   != NULL) *opt_hmm = hmm; else p7_hmm_Destroy(hmm);
  if (opt_tr    != NULL) *opt_tr  = tr;
  return eslOK;

 ERROR:
  p7_hmm_Destroy(hmm);
  if (tr        != NULL) p7_trace_Destroy(tr);
  if (opt_gm    != NULL) p7_profile_Destroy(*opt_gm);
  if (opt_om    != NULL) p7_oprofile_Destroy(*opt_om);
  return status;
}
コード例 #10
0
void destroy_hmmer_wrapper() {
  int index;
  if(models != NULL) {
    for(index = 0;index < num_models;index++) {
      p7_oprofile_Destroy(models[index]);
      p7_profile_Destroy(gmodels[index]);
    }
    free(models);
    free(gmodels);
  }

  if(wrapper_results != NULL) {
    for(index = 0;index < num_models;index++) {
      destroy_result(wrapper_results[index]);
    }
    free(wrapper_results);
  }
  
  if(bg != NULL) {
    p7_bg_Destroy(bg);
  }

  if(hmm_fp != NULL) {
    p7_hmmfile_Close(hmm_fp);
  }

  if(oxf) {
    p7_omx_Destroy(oxf);
  }
  if(oxb) {
    p7_omx_Destroy(oxb);
  }

  if(gxf) {
    p7_gmx_Destroy(gxf);
  }
  if(gxb) {
    p7_gmx_Destroy(gxb);
  }

  if(abc) {
    esl_alphabet_Destroy(abc);
  }
  if(tr) {
    p7_trace_Destroy(tr);
  }
}
コード例 #11
0
ファイル: stotrace.c プロジェクト: Denis84/EPA-WorkBench
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go     = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r      = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc    = NULL;
  P7_HMM         *hmm    = NULL;
  P7_PROFILE     *gm     = NULL;
  P7_OPROFILE    *om     = NULL;
  P7_BG          *bg     = NULL;
  ESL_DSQ        *dsq    = NULL;
  ESL_SQ         *sq     = NULL;
  int             M      = 6;
  int             L      = 10;
  int             ntrace = 1000;

  if ((abc = esl_alphabet_Create(eslAMINO))         == NULL)  esl_fatal("failed to create alphabet");
  if (p7_hmm_Sample(r, M, abc, &hmm)                != eslOK) esl_fatal("failed to sample an HMM");
  if ((bg = p7_bg_Create(abc))                      == NULL)  esl_fatal("failed to create null model");
  if ((gm = p7_profile_Create(hmm->M, abc))         == NULL)  esl_fatal("failed to create profile");
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL)    != eslOK) esl_fatal("failed to config profile");
  if ((om = p7_oprofile_Create(gm->M, abc))         == NULL)  esl_fatal("failed to create optimized profile");
  if (p7_oprofile_Convert(gm, om)                   != eslOK) esl_fatal("failed to convert profile");

  /* Test with randomly generated (iid) sequence */
  if ((dsq = malloc(sizeof(ESL_DSQ) *(L+2)))  == NULL)  esl_fatal("malloc failed");
  if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal("seq generation failed");
  utest_stotrace(go, r, abc, gm, om, dsq, L, ntrace);

  /* Test with seq sampled from profile */
  if ((sq = esl_sq_CreateDigital(abc))             == NULL) esl_fatal("sequence allocation failed");
  if (p7_ProfileEmit(r, hmm, gm, bg, sq, NULL)    != eslOK) esl_fatal("profile emission failed");
  utest_stotrace(go, r, abc, gm, om, sq->dsq, sq->n, ntrace);
   
  esl_sq_Destroy(sq);
  free(dsq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #12
0
ファイル: vitfilter.c プロジェクト: TuftsBCB/SMURFBuild
/* 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);
}
コード例 #13
0
ファイル: p7_oprofile.c プロジェクト: Denis84/EPA-WorkBench
int
main(int argc, char **argv)
{
  char         *hmmfile = argv[1];
  ESL_ALPHABET *abc     = NULL;
  P7_HMMFILE   *hfp     = NULL;
  P7_HMM       *hmm     = NULL;
  P7_BG        *bg      = NULL;
  P7_PROFILE   *gm      = NULL;
  P7_OPROFILE  *om1     = NULL;
  P7_OPROFILE  *om2     = NULL;
  int           status;

  char          errmsg[512];

  status = p7_hmmfile_Open(hmmfile, NULL, &hfp);
  if      (status == eslENOTFOUND) esl_fatal("Failed to open HMM file %s for reading.\n",                   hmmfile);
  else if (status == eslEFORMAT)   esl_fatal("File %s does not appear to be in a recognized HMM format.\n", hmmfile);
  else if (status != eslOK)        esl_fatal("Unexpected error %d in opening HMM file %s.\n",       status, hmmfile);  

  status = p7_hmmfile_Read(hfp, &abc, &hmm);
  if      (status == eslEFORMAT)   esl_fatal("Bad file format in HMM file %s:\n%s\n",          hfp->fname, hfp->errbuf);
  else if (status == eslEINCOMPAT) esl_fatal("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
  else if (status == eslEOF)       esl_fatal("Empty HMM file %s? No HMM data found.\n",        hfp->fname);
  else if (status != eslOK)        esl_fatal("Unexpected error in reading HMMs from %s\n",     hfp->fname);

  bg  = p7_bg_Create(abc);
  gm  = p7_profile_Create(hmm->M, abc);   
  om1 = p7_oprofile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, 400, p7_LOCAL);
  p7_oprofile_Convert(gm, om1);
  
  om2 = p7_oprofile_Copy(om1);
  if (p7_oprofile_Compare(om1, om2, 0.001f, errmsg) != eslOK) esl_fatal("Compare failed %s\n", errmsg);

  p7_oprofile_Destroy(om1);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  return eslOK;
}
コード例 #14
0
ファイル: p7_hmmcache.c プロジェクト: felipegb94/hmmer
/* Function:  p7_hmmcache_Close()
 * Synopsis:  Free a profile cache.
 */
void
p7_hmmcache_Close(P7_HMMCACHE *cache)
{
  int i;

  if (cache)
    {
      if (cache->name) free(cache->name);
      if (cache->abc)  esl_alphabet_Destroy(cache->abc);
      for (i = 0; i < cache->n; i++)
	{
	  if (cache->gmlist) p7_profile_Destroy (cache->gmlist[i]);
	  if (cache->omlist) p7_oprofile_Destroy(cache->omlist[i]);
	}
      if (cache->gmlist) free(cache->gmlist);
      if (cache->omlist) free(cache->omlist);
      free(cache);
    }
}
コード例 #15
0
ファイル: io.c プロジェクト: felipegb94/hmmer
int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  ESL_ALPHABET  *abc     = NULL;
  char          *hmmfile = esl_opt_GetArg(go, 1);
  P7_HMMFILE    *hfp     = NULL;
  P7_OPROFILE   *om      = NULL;
  int            nmodel  = 0;
  uint64_t       totM    = 0;
  int            status;
  char           errbuf[eslERRBUFSIZE];

  esl_stopwatch_Start(w);

  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);  

  while ((status = p7_oprofile_ReadMSV(hfp, &abc, &om)) == eslOK)
    {
      nmodel++;
      totM += om->M;

      p7_oprofile_Destroy(om);
    }
  if      (status == eslEFORMAT)   p7_Fail("bad file format in profile file %s",           hmmfile);
  else if (status == eslEINCOMPAT) p7_Fail("profile file %s contains different alphabets", hmmfile);
  else if (status != eslEOF)       p7_Fail("Unexpected error in reading profiles from %s", hmmfile);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# number of models: %d\n", nmodel);
  printf("# total M:          %" PRId64 "\n", totM);
  
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #16
0
ファイル: io.c プロジェクト: TuftsBCB/SMURFBuild
/* Function:  p7_oprofile_DestroyBlock()
 * Synopsis:  Frees an <P7_OM_BLOCK>.
 * Incept:    
 *
 * Purpose:   Free a Create()'d block of profiles.
 */
void
p7_oprofile_DestroyBlock(P7_OM_BLOCK *block)
{
  int i;

  if (block == NULL) return;

  if (block->list != NULL)
    {
      for (i = 0; i < block->listSize; ++i)
	{
	  if (block->list[i] != NULL) p7_oprofile_Destroy(block->list[i]);
	}
      free(block->list);
    }

  free(block);
  return;
}
コード例 #17
0
ファイル: p7_oprofile.c プロジェクト: Denis84/EPA-WorkBench
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;

  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");

  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);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_oprofile_Convert(gm, om);
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M = %d\n", gm->M);

  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_getopts_Destroy(go);
  return 0;
}
コード例 #18
0
ファイル: io.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS   *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH *w       = esl_stopwatch_Create();
  ESL_ALPHABET  *abc     = NULL;
  char          *msvfile = esl_opt_GetArg(go, 1);
  FILE          *msvfp   = NULL;
  P7_OPROFILE   *om      = NULL;
  int            nmodel  = 0;
  uint64_t       totM    = 0;
  int            status;

  esl_stopwatch_Start(w);

  if ((msvfp = fopen(msvfile, "r")) == NULL) p7_Fail("Failed to open MSV file %s for reading.\n", msvfile);

  while ((status = p7_oprofile_ReadMSV(msvfp, &abc, NULL, &om)) == eslOK)
    {
      nmodel++;
      totM += om->M;

      p7_oprofile_Destroy(om);
    }
  if      (status == eslEFORMAT)   p7_Fail("bad file format in profile file %s",           msvfile);
  else if (status == eslEINCOMPAT) p7_Fail("profile file %s contains different alphabets", msvfile);
  else if (status != eslEOF)       p7_Fail("Unexpected error in reading profiles from %s", msvfile);

  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# number of models: %d\n", nmodel);
  printf("# total M:          %" PRId64 "\n", totM);
  
  fclose(msvfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #19
0
ファイル: hmmsim.c プロジェクト: EddyRivasLab/hmmer
/* recalibrate_model()
 * 
 * Optionally, user can choose (with --recal) to replace the
 * statistical parameters of the HMM.  The calibrated params are used
 * to generate "expected" distributions in output plots.  see
 * p7_Calibrate(), which this is a partial copy of. (p7_Calibrate()
 * requires a P7_BUILDER object that we don't have.)
 * 
 * On success, returns <eslOK> and the statistical parameters of the
 * <hmm> have been recalibrated and replaced.
 */
static int
recalibrate_model(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf, P7_HMM *hmm)
{
  P7_PROFILE  *gm   = NULL;
  P7_OPROFILE *om   = NULL;
  int          EmL  = esl_opt_GetInteger(go, "--EmL");
  int          EmN  = esl_opt_GetInteger(go, "--EmN");
  int          EvL  = esl_opt_GetInteger(go, "--EvL");
  int          EvN  = esl_opt_GetInteger(go, "--EvN");
  int          EfL  = esl_opt_GetInteger(go, "--EfL");
  int          EfN  = esl_opt_GetInteger(go, "--EfN");
  double       Eft  = esl_opt_GetReal   (go, "--Eft");
  double       lambda, mmu, vmu, ftau;

  gm = p7_profile_Create(hmm->M, cfg->abc);
  p7_profile_Config(gm, hmm, cfg->bg);      /* dual-mode multihit; L=0 (no length model needed right now) */
   P7_HARDWARE *hw;
  if ((hw = p7_hardware_Create ()) == NULL)  p7_Fail("Couldn't get HW information data structure"); 
  om = p7_oprofile_Create(gm->M, cfg->abc, hw->simd);
  p7_oprofile_Convert(gm, om);	/* om is now *local* multihit */

  p7_Lambda(hmm, cfg->bg, &lambda);
  p7_MSVMu    (cfg->r, om, cfg->bg, EmL, EmN, lambda,      &mmu);
  p7_ViterbiMu(cfg->r, om, cfg->bg, EvL, EvN, lambda,      &vmu);
  p7_Tau      (cfg->r, om, cfg->bg, EfL, EfN, lambda, Eft, &ftau);

  hmm->evparam[p7_MLAMBDA] = lambda;
  hmm->evparam[p7_VLAMBDA] = lambda;
  hmm->evparam[p7_FLAMBDA] = lambda;
  hmm->evparam[p7_MMU]     = mmu;
  hmm->evparam[p7_VMU]     = vmu;
  hmm->evparam[p7_FTAU]    = ftau;
  hmm->flags              |= p7H_STATS;

  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
  return eslOK;
}
コード例 #20
0
ファイル: evalues.c プロジェクト: ElofssonLab/TOPCONS2
/* Function:  p7_Calibrate()
 * Synopsis:  Calibrate the E-value parameters of a model.
 * Incept:    SRE, Thu Dec 25 09:29:31 2008 [Magallon]
 *
 * Purpose:   Calibrate the E-value parameters of a model with 
 *            one calculation ($\lambda$) and two brief simulations
 *            (Viterbi $\mu$, Forward $\tau$).
 *            
 * Args:      hmm     - HMM to be calibrated
 *            cfg_b   - OPTCFG: ptr to optional build configuration;
 *                      if <NULL>, use default parameters.
 *            byp_rng - BYPASS optimization: pass ptr to <ESL_RANDOMNESS> generator
 *                      if already known; 
 *                      <*byp_rng> == NULL> if <rng> return is desired;
 *                      pass <NULL> to use and discard internal default.
 *            byp_bg  - BYPASS optimization: pass ptr to <P7_BG> if already known; 
 *                      <*byp_bg == NULL> if <bg> return is desired;
 *                      pass <NULL> to use and discard internal default.
 *            byp_gm  - BYPASS optimization: pass ptr to <gm> profile if already known;
 *                      pass <*byp_gm == NULL> if <gm> return desired;
 *                      pass <NULL> to use and discard internal default.
 *            byp_om  - BYPASS optimization: pass ptr to <om> profile if already known;
 *                      pass <*byp_om == NULL> if <om> return desired;
 *                      pass <NULL> to use and discard internal default.          
 *
 * Returns:   <eslOK> on success.
 *
 * Throws:    <eslEMEM> on allocation failure.
 *            <eslEINVAL> if <hmm>, <gm>, <om> aren't compatible somehow.
 *
 * Xref:      J4/41
 */
int
p7_Calibrate(P7_HMM *hmm, P7_BUILDER *cfg_b, ESL_RANDOMNESS **byp_rng, P7_BG **byp_bg, P7_PROFILE **byp_gm, P7_OPROFILE **byp_om)
{
  P7_BG          *bg     = (esl_byp_IsProvided(byp_bg)  ? *byp_bg  : NULL); 
  P7_PROFILE     *gm     = (esl_byp_IsProvided(byp_gm)  ? *byp_gm  : NULL); 
  P7_OPROFILE    *om     = (esl_byp_IsProvided(byp_om)  ? *byp_om  : NULL); 
  ESL_RANDOMNESS *r      = (esl_byp_IsProvided(byp_rng) ? *byp_rng : NULL);
  char           *errbuf = ((cfg_b != NULL) ? cfg_b->errbuf : NULL);
  int             EmL    = ((cfg_b != NULL) ? cfg_b->EmL    : 200);
  int             EmN    = ((cfg_b != NULL) ? cfg_b->EmN    : 200);
  int             EvL    = ((cfg_b != NULL) ? cfg_b->EvL    : 200);
  int             EvN    = ((cfg_b != NULL) ? cfg_b->EvN    : 200);
  int             EfL    = ((cfg_b != NULL) ? cfg_b->EfL    : 100);
  int             EfN    = ((cfg_b != NULL) ? cfg_b->EfN    : 200);
  double          Eft    = ((cfg_b != NULL) ? cfg_b->Eft    : 0.04);
  double          lambda, mmu, vmu, tau;
  int             status;
  
  /* Configure any objects we need
   * that weren't already passed to us as a bypass optimization 
   */
  if (r  == NULL) {
    if ((r = esl_randomness_CreateFast(42)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create RNG");
  } else if (cfg_b != NULL && cfg_b->do_reseeding) {
    esl_randomness_Init(r, esl_randomness_GetSeed(r));
  }

  if (bg == NULL) {
    if ((bg = p7_bg_Create(hmm->abc)) == NULL)  ESL_XFAIL(eslEMEM, errbuf, "failed to allocate background");
  }

  /* there's an odd case where the <om> is provided and a <gm> isn't going to be returned
   * where we don't need a <gm> at all, and <gm> stays <NULL> after the next block.
   * Note that the <EvL> length in the ProfileConfig doesn't matter; the individual
   * calibration routines MSVMu(), etc. contain their own length reconfig calls.
   */
  if ((esl_byp_IsInternal(byp_gm) && ! esl_byp_IsProvided(byp_om)) || esl_byp_IsReturned(byp_gm)) {
    if  ( (gm     = p7_profile_Create(hmm->M, hmm->abc))          == NULL)  ESL_XFAIL(eslEMEM, errbuf, "failed to allocate profile");
    if  ( (status = p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL)) != eslOK) ESL_XFAIL(status,  errbuf, "failed to configure profile");
  }

  if (om == NULL) {
    if ((om     = p7_oprofile_Create(hmm->M, hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create optimized profile");
    if ((status = p7_oprofile_Convert(gm, om))         != eslOK) ESL_XFAIL(status,  errbuf, "failed to convert to optimized profile");
  }

  /* The calibration steps themselves */
  if ((status = p7_Lambda(hmm, bg, &lambda))                          != eslOK) ESL_XFAIL(status,  errbuf, "failed to determine lambda");
  if ((status = p7_MSVMu    (r, om, bg, EmL, EmN, lambda, &mmu))      != eslOK) ESL_XFAIL(status,  errbuf, "failed to determine msv mu");
  if ((status = p7_ViterbiMu(r, om, bg, EvL, EvN, lambda, &vmu))      != eslOK) ESL_XFAIL(status,  errbuf, "failed to determine vit mu");
  if ((status = p7_Tau      (r, om, bg, EfL, EfN, lambda, Eft, &tau)) != eslOK) ESL_XFAIL(status,  errbuf, "failed to determine fwd tau");

  /* Store results */
  hmm->evparam[p7_MLAMBDA] = om->evparam[p7_MLAMBDA] = lambda;
  hmm->evparam[p7_VLAMBDA] = om->evparam[p7_VLAMBDA] = lambda;
  hmm->evparam[p7_FLAMBDA] = om->evparam[p7_FLAMBDA] = lambda;
  hmm->evparam[p7_MMU]     = om->evparam[p7_MMU]     = mmu;
  hmm->evparam[p7_VMU]     = om->evparam[p7_VMU]     = vmu;
  hmm->evparam[p7_FTAU]    = om->evparam[p7_FTAU]    = tau;
  hmm->flags              |= p7H_STATS;

  if (gm != NULL) {
    gm->evparam[p7_MLAMBDA] = lambda;
    gm->evparam[p7_VLAMBDA] = lambda;
    gm->evparam[p7_FLAMBDA] = lambda;
    gm->evparam[p7_MMU]     = mmu;
    gm->evparam[p7_VMU]     = vmu;
    gm->evparam[p7_FTAU]    = tau;
  }
    
  if (byp_rng != NULL) *byp_rng = r;  else esl_randomness_Destroy(r); /* bypass convention: no-op if rng was provided.*/
  if (byp_bg  != NULL) *byp_bg  = bg; else p7_bg_Destroy(bg);         /* bypass convention: no-op if bg was provided. */
  if (byp_gm  != NULL) *byp_gm  = gm; else p7_profile_Destroy(gm);    /* bypass convention: no-op if gm was provided. */
  if (byp_om  != NULL) *byp_om  = om; else p7_oprofile_Destroy(om);   /* bypass convention: no-op if om was provided. */
  return eslOK;

 ERROR:
  if (! esl_byp_IsProvided(byp_rng)) esl_randomness_Destroy(r);
  if (! esl_byp_IsProvided(byp_bg))  p7_bg_Destroy(bg);
  if (! esl_byp_IsProvided(byp_gm))  p7_profile_Destroy(gm);
  if (! esl_byp_IsProvided(byp_om))  p7_oprofile_Destroy(om);
  return status;
}
コード例 #21
0
ファイル: optacc.c プロジェクト: ElofssonLab/TOPCONS2
/* 
 * 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);
}
コード例 #22
0
ファイル: vitfilter.c プロジェクト: TuftsBCB/SMURFBuild
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_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           vfraw, nullsc, vfscore;
  float           graw, gscore;
  double          P, gP;
  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);

  /* 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, sq->n);
  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(ox, TRUE);      makes the fast DP algorithms dump their matrices
     p7_gmx_Dump(stdout, gx);           dumps a generic DP matrix
  */

  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_ViterbiFilter  (sq->dsq, sq->n, om, ox, &vfraw);
      p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
      vfscore = (vfraw - nullsc) / eslCONST_LOG2;
      P        = esl_gumbel_surv(vfscore,  om->evparam[p7_VMU],  om->evparam[p7_VLAMBDA]);

      p7_GViterbi       (sq->dsq, sq->n, gm, gx, &graw); 
      gscore   = (graw - nullsc) / eslCONST_LOG2;
      gP       = esl_gumbel_surv(gscore,  gm->evparam[p7_VMU],  gm->evparam[p7_VLAMBDA]);

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s\t%-20s\t%9.2g\t%7.2f\t%9.2g\t%7.2f\n", sq->name, hmm->name, P, vfscore, gP, gscore);
	}
      else if (esl_opt_GetBoolean(go, "-P"))
	{ /* output suitable for direct use in profmark benchmark postprocessors: */
	  printf("%g\t%.2f\t%s\t%s\n", P, vfscore, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("vit filter raw score: %.2f nats\n", vfraw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", vfscore);
	  printf("P-value:              %g\n",        P);
	  printf("GViterbi raw score:   %.2f nats\n", graw);
	  printf("GViterbi seq score:   %.2f bits\n", gscore);
	  printf("GViterbi 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;
}
コード例 #23
0
ファイル: evalues.c プロジェクト: ElofssonLab/TOPCONS2
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_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;
  double          lambda  = 0.0;
  double          mmu     = 0.0;
  double          vmu     = 0.0;
  double          ftau    = 0.0;
  int             Z       = esl_opt_GetInteger(go, "-Z");
  int             EmL     = esl_opt_GetInteger(go, "--EmL");
  int             EmN     = esl_opt_GetInteger(go, "--EmN");
  int             EvL     = esl_opt_GetInteger(go, "--EvL");
  int             EvN     = esl_opt_GetInteger(go, "--EvN");
  int             EfL     = esl_opt_GetInteger(go, "--EfL");
  int             EfN     = esl_opt_GetInteger(go, "--EfN");
  int             Eft     = esl_opt_GetReal   (go, "--Eft");
  int             iteration;
  int             do_msv, do_vit, do_fwd;
  int             status;

  if      (esl_opt_GetBoolean(go, "--msvonly") == TRUE) { do_msv =  TRUE; do_vit = FALSE; do_fwd = FALSE; }
  else if (esl_opt_GetBoolean(go, "--vitonly") == TRUE) { do_msv = FALSE; do_vit =  TRUE; do_fwd = FALSE; }
  else if (esl_opt_GetBoolean(go, "--fwdonly") == TRUE) { do_msv = FALSE; do_vit = FALSE; do_fwd =  TRUE; }
  else                                                  { do_msv =  TRUE; do_vit =  TRUE; do_fwd =  TRUE; }

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF) 
    {
      if (bg == NULL) bg = p7_bg_Create(abc);
      gm = p7_profile_Create(hmm->M, abc);
      p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL); /* the EvL doesn't matter */
      om = p7_oprofile_Create(hmm->M, abc);
      p7_oprofile_Convert(gm, om);

      if (esl_opt_IsOn(go, "--lambda"))	lambda = esl_opt_GetReal(go, "--lambda"); 
      else p7_Lambda(hmm, bg, &lambda);	  

      for (iteration = 0; iteration < Z; iteration++)
	{
	  if (do_msv) p7_MSVMu     (r, om, bg, EmL, EmN, lambda,       &mmu);
	  if (do_vit) p7_ViterbiMu (r, om, bg, EvL, EvN, lambda,       &vmu);
	  if (do_fwd) p7_Tau       (r, om, bg, EfL, EfN, lambda, Eft,  &ftau);
      
	  printf("%s %.4f %.4f %.4f %.4f\n", hmm->name, lambda, mmu, vmu, ftau);
	}

      p7_hmm_Destroy(hmm);      
      p7_profile_Destroy(gm);
      p7_oprofile_Destroy(om);
    }

  p7_hmmfile_Close(hfp);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return eslOK;
}
コード例 #24
0
ファイル: optacc.c プロジェクト: ElofssonLab/TOPCONS2
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;
}
コード例 #25
0
ファイル: vitfilter.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_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_OMX         *ox      = NULL;
  P7_GMX         *gx      = 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           sc1, sc2;
  double          base_time, bench_time, Mcs;

  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");

  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_profile_SameAsVF(om, gm);

  ox = p7_omx_Create(gm->M, 0, 0);
  gx = p7_gmx_Create(gm->M, L);

  /* Get a baseline time: how long it takes just to generate the sequences */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  esl_stopwatch_Stop(w);
  base_time = w->user;

  /* Run the benchmark */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      p7_ViterbiFilter(dsq, L, om, ox, &sc1);   

      if (esl_opt_GetBoolean(go, "-c")) 
	{
	  p7_GViterbi(dsq, L, gm, gx, &sc2); 
	  printf("%.4f %.4f\n", sc1, sc2);  
	}

      if (esl_opt_GetBoolean(go, "-x"))
	{
	  p7_GViterbi(dsq, L, gm, gx, &sc2); 
	  sc2 /= om->scale_w;
	  if (om->mode == p7_UNILOCAL)   sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
	  else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
	  printf("%.4f %.4f\n", sc1, sc2);  
	}
    }
  esl_stopwatch_Stop(w);
  bench_time = w->user - base_time;
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  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_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #26
0
ファイル: optacc.c プロジェクト: ElofssonLab/TOPCONS2
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         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  P7_TRACE       *tr      = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  char            errbuf[eslERRBUFSIZE];
  float           fsc, bsc;
  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 */
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);

  /* Allocations */
  ox1 = p7_omx_Create(gm->M, sq->n, sq->n);
  ox2 = p7_omx_Create(gm->M, sq->n, sq->n);
  gx  = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_CreateWithPP();
  p7_FLogsumInit();

  /* Run Forward, Backward; do OA fill and trace */
  p7_Forward (sq->dsq, sq->n, om, ox1,      &fsc);
  p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc);
  p7_Decoding(om, ox1, ox2, ox2);                   /* <gx2> is now the posterior decoding matrix */
  p7_OptimalAccuracy(om, ox2, ox1, &accscore);	    /* <gx1> is now the OA matrix */
  p7_OATrace(om, ox2, ox1, tr);
  
  if (esl_opt_GetBoolean(go, "-d")) { p7_omx_FDeconvert(ox2, gx);  p7_gmx_Dump(stdout, gx, p7_DEFAULT); }
  if (esl_opt_GetBoolean(go, "-m")) { p7_omx_FDeconvert(ox1, gx);  p7_gmx_Dump(stdout, gx, 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);

  /* Cleanup */
  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #27
0
ファイル: null2.c プロジェクト: dboudour2002/musicHMMER
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_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = 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,j,d,pos;
  int             nsamples = 200;
  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);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);

  if (esl_opt_GetBoolean(go, "-t"))
    {
      P7_TRACE *tr   = p7_trace_Create();
      float    *n2sc = malloc(sizeof(float) * (L+1));

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	{ /* This is approximately what p7_domaindef.c::region_trace_ensemble() is doing: */
	  for (j = 0; j < nsamples; j++)
	    {
	      p7_StochasticTrace(r, dsq, L, om, ox1, tr);
	      p7_trace_Index(tr);
	      pos = 1; 
	      for (d = 0; d < tr->ndom; d++)
		{
		  p7_Null2_ByTrace(om, tr, tr->tfrom[d], tr->tto[d], ox2, null2);
		  for (; pos <= tr->sqfrom[d]; pos++) n2sc[pos] += 1.0;
		  for (; pos < tr->sqto[d];    pos++) n2sc[pos] += null2[dsq[pos]];
		}
	      for (; pos <= L; pos++)  n2sc[pos] += 1.0;
	      p7_trace_Reuse(tr);
	    }

	  for (pos = 1; pos <= L; pos++)
	    n2sc[pos] = logf(n2sc[pos] / nsamples);
	}
      esl_stopwatch_Stop(w);

      free(n2sc);
      p7_trace_Destroy(tr);
    }
  else
    {
      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_Null2_ByExpectation(om, ox2, null2);
      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);

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  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;
}
コード例 #28
0
ファイル: hmmdwrkr.c プロジェクト: dboudour2002/musicHMMER
static void 
search_thread(void *arg)
{
  int               i;
  int               count;
  int               seed;
  int               status;
  int               workeridx;
  WORKER_INFO      *info;
  ESL_THREADS      *obj;
  ESL_SQ            dbsq;
  ESL_STOPWATCH    *w        = NULL;         /* timing stopwatch               */
  P7_BUILDER       *bld      = NULL;         /* HMM construction configuration */
  P7_BG            *bg       = NULL;         /* null model                     */
  P7_PIPELINE      *pli      = NULL;         /* work pipeline                  */
  P7_TOPHITS       *th       = NULL;         /* top hit results                */
  P7_PROFILE       *gm       = NULL;         /* generic model                  */
  P7_OPROFILE      *om       = NULL;         /* optimized query profile        */

  obj = (ESL_THREADS *) arg;
  esl_threads_Started(obj, &workeridx);

  info = (WORKER_INFO *) esl_threads_GetData(obj, workeridx);
  w    = esl_stopwatch_Create();
  bg   = p7_bg_Create(info->abc);
  esl_stopwatch_Start(w);

  /* set up the dummy description and accession fields */
  dbsq.desc = "";
  dbsq.acc  = "";

  /* process a query sequence or hmm */
  if (info->seq != NULL) {
    bld = p7_builder_Create(NULL, info->abc);
    if ((seed = esl_opt_GetInteger(info->opts, "--seed")) > 0) {
      esl_randomness_Init(bld->r, seed);
      bld->do_reseeding = TRUE;
    }
    bld->EmL = esl_opt_GetInteger(info->opts, "--EmL");
    bld->EmN = esl_opt_GetInteger(info->opts, "--EmN");
    bld->EvL = esl_opt_GetInteger(info->opts, "--EvL");
    bld->EvN = esl_opt_GetInteger(info->opts, "--EvN");
    bld->EfL = esl_opt_GetInteger(info->opts, "--EfL");
    bld->EfN = esl_opt_GetInteger(info->opts, "--EfN");
    bld->Eft = esl_opt_GetReal   (info->opts, "--Eft");

    if (esl_opt_IsOn(info->opts, "--mxfile")) status = p7_builder_SetScoreSystem (bld, esl_opt_GetString(info->opts, "--mxfile"), NULL, esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg);
    else                                      status = p7_builder_LoadScoreSystem(bld, esl_opt_GetString(info->opts, "--mx"),           esl_opt_GetReal(info->opts, "--popen"), esl_opt_GetReal(info->opts, "--pextend"), bg); 
    if (status != eslOK) {
      //client_error(info->sock, status, "hmmgpmd: failed to set single query sequence score system: %s", bld->errbuf);
      fprintf(stderr, "hmmpgmd: failed to set single query sequence score system: %s", bld->errbuf);
      pthread_exit(NULL);
      return;
    }
    p7_SingleBuilder(bld, info->seq, bg, NULL, NULL, NULL, &om); /* bypass HMM - only need model */
    p7_builder_Destroy(bld);
  } else {
    gm = p7_profile_Create (info->hmm->M, info->abc);
    om = p7_oprofile_Create(info->hmm->M, info->abc);
    p7_ProfileConfig(info->hmm, bg, gm, 100, p7_LOCAL);
    p7_oprofile_Convert(gm, om);
  }

  /* Create processing pipeline and hit list */
  th  = p7_tophits_Create(); 
  pli = p7_pipeline_Create(info->opts, om->M, 100, FALSE, p7_SEARCH_SEQS);
  p7_pli_NewModel(pli, om, bg);

  if (pli->Z_setby == p7_ZSETBY_NTARGETS) pli->Z = info->db_Z;

  /* loop until all sequences have been processed */
  count = 1;
  while (count > 0) {
    int          inx;
    int          blksz;
    HMMER_SEQ  **sq;

    /* grab the next block of sequences */
    if (pthread_mutex_lock(info->inx_mutex) != 0) p7_Fail("mutex lock failed");
    inx = *info->inx;
    blksz = *info->blk_size;
    if (inx > *info->limit) {
      blksz /= 5;
      if (blksz < 1000) {
        *info->limit = info->sq_cnt * 2;
      } else {
        *info->limit = inx + (info->sq_cnt - inx) * 2 / 3; 
      }
    }
    *info->blk_size = blksz;
    *info->inx += blksz;
    if (pthread_mutex_unlock(info->inx_mutex) != 0) p7_Fail("mutex unlock failed");

    sq = info->sq_list + inx;

    count = info->sq_cnt - inx;
    if (count > blksz) count = blksz;

    /* Main loop: */
    for (i = 0; i < count; ++i, ++sq) {
      if ( !(info->range_list) || hmmpgmd_IsWithinRanges ((*sq)->idx, info->range_list)) {
        dbsq.name  = (*sq)->name;
        dbsq.dsq   = (*sq)->dsq;
        dbsq.n     = (*sq)->n;
        dbsq.idx   = (*sq)->idx;
        if((*sq)->desc != NULL) dbsq.desc  = (*sq)->desc;

        p7_bg_SetLength(bg, dbsq.n);
        p7_oprofile_ReconfigLength(om, dbsq.n);

        p7_Pipeline(pli, om, bg, &dbsq, th);

        p7_pipeline_Reuse(pli);
      }
    }
  }

  /* make available the pipeline objects to the main thread */
  info->th = th;
  info->pli = pli;

  /* clean up */
  p7_bg_Destroy(bg);
  p7_oprofile_Destroy(om);

  if (gm != NULL)  p7_profile_Destroy(gm);

  esl_stopwatch_Stop(w);
  info->elapsed = w->elapsed;

  esl_stopwatch_Destroy(w);

  esl_threads_Finished(obj, workeridx);

  pthread_exit(NULL);
  return;
}
コード例 #29
0
ファイル: decoding.c プロジェクト: Denis84/EPA-WorkBench
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_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_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  P7_OMX         *pp      = 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;
  double          Mcs;

  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");

  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);

  fwd = p7_omx_Create(gm->M, L, L);
  bck = p7_omx_Create(gm->M, L, L);
  pp  = p7_omx_Create(gm->M, L, L);

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, fwd,      &fsc);
  p7_Backward(dsq, L, om, fwd, bck, &bsc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_Decoding(om, fwd, bck, pp);              
  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);

  free(dsq);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(pp);
  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 eslOK;
}
コード例 #30
0
ファイル: sim-alignment.c プロジェクト: EddyRivasLab/hmmer
int 
main(int argc, char **argv)
{
  ESL_GETOPTS      *go       = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_RANDOMNESS   *rng      = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET     *abc      = NULL;
  char             *ghmmfile = esl_opt_GetArg(go, 1); /* HMMs parameterized for sequence generation */
  char             *ahmmfile = esl_opt_GetArg(go, 2); /* HMMs parameterized for alignment */
  int               N        = esl_opt_GetInteger(go, "-N");
  P7_HMMFILE       *ghfp     = NULL;
  P7_HMMFILE       *ahfp     = NULL;
  P7_HMM           *ghmm     = NULL;
  P7_HMM           *ahmm     = NULL;
  P7_PROFILE       *ggm      = NULL;
  P7_PROFILE       *agm      = NULL;
  P7_OPROFILE      *aom      = NULL;
  P7_BG            *bg       = NULL;
  ESL_SQ           *sq       = NULL;
  P7_TRACE         *reftr    = p7_trace_Create();
  P7_TRACE         *testtr   = p7_trace_Create();
  P7_TRACE_METRICS *tmetrics = p7_trace_metrics_Create();
  P7_REFMX         *rmx      = p7_refmx_Create(100,100);
  //  P7_FILTERMX      *ox       = NULL;
   P7_HARDWARE *hw;
  if ((hw = p7_hardware_Create ()) == NULL)  p7_Fail("Couldn't get HW information data structure"); 
  P7_SPARSEMASK    *sm       = p7_sparsemask_Create(100, 100, hw->simd);
  P7_SPARSEMX      *sxv      = p7_sparsemx_Create(NULL);
  int               idx;
  char              errbuf[eslERRBUFSIZE];
  int               status;
  
  p7_Init();

  /* open HMM file containing models parameterized for generation (sampling) of seqs */
  status = p7_hmmfile_OpenE(ghmmfile, NULL, &ghfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", ghmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem in trying to open HMM file %s.\n%s\n",                ghmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",                       status, ghmmfile, errbuf);  

  /* open HMM file containing models parameterized for alignment (may be the same as ghmmfile) */
  status = p7_hmmfile_OpenE(ahmmfile, NULL, &ahfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", ahmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem in trying to open HMM file %s.\n%s\n",                ahmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",                       status, ahmmfile, errbuf);  
  
  while ( (status = p7_hmmfile_Read(ghfp, &abc, &ghmm)) == eslOK) /* <abc> gets set on first read  */
    {
      /* read the counterpart HMM from <ahfp> */
      status = p7_hmmfile_Read(ahfp, &abc, &ahmm);
      if      (status == eslEFORMAT)   p7_Fail("Bad file format in HMM file %s:\n%s\n",          ahfp->fname, ahfp->errbuf);
      else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", ahfp->fname, esl_abc_DecodeType(abc->type));
      else if (status == eslEOF)       p7_Fail("Empty HMM file %s? No HMM data found.\n",        ahfp->fname);
      else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s\n",     ahfp->fname);

      /* try to validate that they're the "same" */
      if (ahmm->M != ghmm->M || strcmp(ahmm->name, ghmm->name) != 0) p7_Fail("<gen-hmmfile>, <ali-hmmfile> contain different set or order of models");

      /* deferred one-time creation of structures that need to know the alphabet */
      if (!bg) bg = p7_bg_Create(abc);
      if (!sq) sq = esl_sq_CreateDigital(abc);

      ggm = p7_profile_Create(ghmm->M,  abc);
      agm = p7_profile_Create(ahmm->M,  abc);

      aom = p7_oprofile_Create(ahmm->M, abc, hw->simd);

      p7_profile_ConfigCustom(ggm, ghmm, bg, esl_opt_GetInteger(go, "--gL"), esl_opt_GetReal(go, "--gnj"), esl_opt_GetReal(go, "--gpglocal"));
      p7_profile_ConfigCustom(agm, ahmm, bg, 100,                            esl_opt_GetReal(go, "--anj"), esl_opt_GetReal(go, "--apglocal"));
      p7_oprofile_Convert(agm, aom);

      for (idx = 1; idx <= N; idx++)
	{
	  p7_ProfileEmit(rng, ghmm, ggm, bg, sq, reftr);

	  if (esl_opt_GetBoolean(go, "--dumpseqs")) {
	    esl_sq_FormatName(sq, "seq%d", idx);
	    esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);
	  }

	  p7_bg_SetLength(bg, sq->n);
	  p7_profile_SetLength(agm, sq->n);
	  p7_sparsemask_Reinit(sm, agm->M, sq->n);
	  p7_sparsemask_AddAll(sm);

	  if (esl_opt_GetBoolean(go, "--vit"))  p7_ReferenceViterbi(sq->dsq, sq->n, agm,     rmx, testtr, /*opt_vsc=*/NULL);
	  else                         	        p7_SparseViterbi   (sq->dsq, sq->n, agm, sm, sxv, testtr, /*opt_vsc=*/NULL);

	  p7_trace_metrics(reftr, testtr, tmetrics);

	  p7_sparsemask_Reuse(sm);
	  p7_sparsemx_Reuse(sxv);
	  //p7_filtermx_Reuse(ox);
	  p7_refmx_Reuse(rmx);
	  esl_sq_Reuse(sq);
	  p7_trace_Reuse(reftr);
	  p7_trace_Reuse(testtr);
	}

      p7_oprofile_Destroy(aom);
      p7_profile_Destroy(ggm);
      p7_profile_Destroy(agm);
      p7_hmm_Destroy(ghmm);
      p7_hmm_Destroy(ahmm);
    }
  /* we leave the loop with <status> set by a p7_hmmfile_Read() on ghfp; if all is well, status=eslEOF */
  if      (status == eslEFORMAT)   p7_Fail("Bad file format in HMM file %s:\n%s\n",          ghfp->fname, ghfp->errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", ghfp->fname, esl_abc_DecodeType(abc->type));
  else if (status != eslEOF)       p7_Fail("Unexpected error in reading HMMs from %s\n",     ghfp->fname);
  
  p7_trace_metrics_Dump(stdout, tmetrics);

  p7_hmmfile_Close(ghfp);  
  p7_hmmfile_Close(ahfp);
  //  p7_filtermx_Destroy(ox);
  p7_sparsemask_Destroy(sm);
  p7_sparsemx_Destroy(sxv);
  p7_refmx_Destroy(rmx);
  p7_trace_metrics_Destroy(tmetrics);
  p7_trace_Destroy(testtr);
  p7_trace_Destroy(reftr);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
}