Ejemplo n.º 1
0
static void 
utest_normalization(ESL_GETOPTS *go)
{
  char         *msg     = "seqmodel normalization utest failed";
  ESL_ALPHABET *abc     = esl_alphabet_Create(eslAMINO);
  char         *seq     = "ACDEFGHIKLMNPQRSTVWYBJZOUX";
  int           L       = strlen(seq);
  ESL_DSQ      *dsq     = NULL;
  float         popen   = 0.1;
  float         pextend = 0.4;
  P7_BUILDER   *bld     = NULL;
  P7_BG        *bg      = p7_bg_Create(abc);
  P7_HMM       *hmm     = NULL;
  char          errbuf[eslERRBUFSIZE];

  if ( esl_abc_CreateDsq(abc, seq, &dsq)                                                 != eslOK) esl_fatal(msg);
  if ( (bld = p7_builder_Create(NULL, abc))                                              == NULL)  esl_fatal(msg);
  if ( p7_builder_LoadScoreSystem(bld, "BLOSUM62", popen, pextend, bg)                   != eslOK) esl_fatal(msg); 
  if ( p7_Seqmodel(abc, dsq, L, "aatest", bld->Q, bg->f, bld->popen, bld->pextend, &hmm) != eslOK) esl_fatal(msg);

  if (p7_hmm_Validate(hmm, errbuf, 0.0001) != eslOK) esl_fatal("normalization utest failed\n%s\n", errbuf);

  free(dsq);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_builder_Destroy(bld);
  esl_alphabet_Destroy(abc);
}
Ejemplo n.º 2
0
/* 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;
}
Ejemplo n.º 3
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_ALPHABET   *abc     = esl_alphabet_Create(eslAMINO);
  char           *qfile   = esl_opt_GetArg(go, 1);
  char           *tfile   = esl_opt_GetArg(go, 2);
  ESL_SQFILE     *qfp     = NULL;
  ESL_SQFILE     *tfp     = NULL;
  ESL_SQ         *qsq     = esl_sq_CreateDigital(abc);
  ESL_SQ         *tsq     = esl_sq_CreateDigital(abc);
  ESL_SCOREMATRIX *S      = esl_scorematrix_Create(abc);
  ESL_DMATRIX     *Q      = NULL;
  P7_BG           *bg     = p7_bg_Create(abc);
  P7_HMM          *hmm    = NULL;
  P7_PROFILE      *gm     = NULL;
  P7_REFMX        *vit    = p7_refmx_Create(200, 400); /* will grow as needed */
  double          *fa     = malloc(sizeof(double) * abc->K);
  double          popen   = 0.02;
  double          pextend = 0.4;
  double          lambda;
  float           vsc;
  float           nullsc;
  int             status;

  esl_composition_BL62(fa);
  esl_vec_D2F(fa, abc->K, bg->f);
  esl_scorematrix_Set("BLOSUM62", S);
  esl_scorematrix_ProbifyGivenBG(S, fa, fa, &lambda, &Q); 
  esl_scorematrix_JointToConditionalOnQuery(abc, Q);

  if (esl_sqfile_OpenDigital(abc, qfile, eslSQFILE_UNKNOWN, NULL, &qfp) != eslOK) esl_fatal("failed to open %s", qfile);
  if (esl_sqio_Read(qfp, qsq) != eslOK) esl_fatal("failed to read query seq");

  p7_Seqmodel(abc, qsq->dsq, qsq->n, qsq->name, Q, bg->f, popen, pextend, &hmm);  
  p7_hmm_SetComposition(hmm);
  p7_hmm_SetConsensus(hmm, qsq); 
  
  gm = p7_profile_Create(hmm->M, abc);
  p7_profile_ConfigUnilocal(gm, hmm, bg, 400);
  
  if (esl_sqfile_OpenDigital(abc, tfile, eslSQFILE_UNKNOWN, NULL, &tfp) != eslOK) esl_fatal("failed to open %s", tfile);
  while ((status = esl_sqio_Read(tfp, tsq)) == eslOK)
    {
      p7_bg_SetLength     (bg, tsq->n);
      p7_profile_SetLength(gm, tsq->n);
      
      p7_ReferenceViterbi(tsq->dsq, tsq->n, gm, vit, NULL, &vsc);    
      p7_bg_NullOne(bg, tsq->dsq, tsq->n, &nullsc);

      printf("%.4f %-25s %-25s\n", (vsc - nullsc) / eslCONST_LOG2, tsq->name, gm->name);
   
      esl_sq_Reuse(tsq);
      p7_refmx_Reuse(vit);
    }
  
  p7_refmx_Destroy(vit);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
  p7_bg_Destroy(bg);
  esl_dmatrix_Destroy(Q);
  esl_scorematrix_Destroy(S);
  free(fa);
  esl_sq_Destroy(qsq);
  esl_sq_Destroy(tsq);
  esl_sqfile_Close(qfp);
  esl_sqfile_Close(tfp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 4
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go    = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_ALPHABET   *abc   = esl_alphabet_Create(eslAMINO);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *qfile = esl_opt_GetArg(go, 2);
  ESL_SQ         *qsq   = esl_sq_CreateDigital(abc);
  ESL_SQFILE     *qfp   = NULL;
  FILE           *hmmfp = NULL;
  ESL_SCOREMATRIX *S    = esl_scorematrix_Create(abc);
  ESL_DMATRIX     *Q    = NULL;
  P7_BG           *bg   = p7_bg_Create(abc);		
  P7_HMM          *hmm  = NULL;
  double          *fa   = NULL;
  double          popen   = esl_opt_GetReal  (go, "-q");
  double          pextend = esl_opt_GetReal  (go, "-r");
  char            *mxfile = esl_opt_GetString(go, "-m");
  char            errbuf[eslERRBUFSIZE];
  double          slambda;
  int             a,b;
  int             status;

  /* Reverse engineer a scoring matrix to obtain conditional prob's
   * that we'll use for the single-seq query HMM. Because score mx is
   * symmetric, we can set up P[a][b] = P(b | a), so we can use the
   * matrix rows as HMM match emission vectors. This means dividing
   * the joint probs through by f_a.
   */
  if (mxfile == NULL) {
    if (esl_scorematrix_Set("BLOSUM62", S) != eslOK) esl_fatal("failed to set BLOSUM62 scores");
  } else {
    ESL_FILEPARSER *efp = NULL;

    if ( esl_fileparser_Open(mxfile, NULL,  &efp) != eslOK) esl_fatal("failed to open score file %s",  mxfile);
    if ( esl_scorematrix_Read(efp, abc, &S)               != eslOK) esl_fatal("failed to read matrix from %s", mxfile);
    esl_fileparser_Close(efp);
  }

  /* A wasteful conversion of the HMMER single-precision background probs to Easel double-prec */
  ESL_ALLOC(fa, sizeof(double) * bg->abc->K);
  esl_vec_F2D(bg->f, bg->abc->K, fa);

  /* Backcalculate joint probabilities Q, given score matrix S and background frequencies fa */
  status = esl_scorematrix_ProbifyGivenBG(S, fa, fa, &slambda, &Q); 
  if      (status == eslEINVAL)  esl_fatal("built-in score matrix %s has no valid solution for lambda", matrix);
  else if (status == eslENOHALT) esl_fatal("failed to solve score matrix %s for lambda", matrix);
  else if (status != eslOK)      esl_fatal("unexpected error in solving score matrix %s for probability parameters", matrix);

  esl_scorematrix_JointToConditionalOnQuery(abc, Q);

  /* Open the query sequence file in FASTA format */
  status = esl_sqfile_Open(qfile, eslSQFILE_FASTA, NULL, &qfp);
  if      (status == eslENOTFOUND) esl_fatal("No such file %s.", qfile);
  else if (status == eslEFORMAT)   esl_fatal("Format of %s unrecognized.", qfile);
  else if (status == eslEINVAL)    esl_fatal("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        esl_fatal("Open of %s failed, code %d.", qfile, status);

  /* Open the output HMM file */
  if ((hmmfp = fopen(hmmfile, "w")) == NULL) esl_fatal("Failed to open output HMM file %s", hmmfile);

  /* For each sequence, build a model and save it. 
   */
  while ((status = esl_sqio_Read(qfp, qsq)) == eslOK)
    {
      p7_Seqmodel(abc, qsq->dsq, qsq->n, qsq->name, Q, bg->f, popen, pextend, &hmm);
      if ( p7_hmm_Validate(hmm, errbuf, 1e-5)     != eslOK) esl_fatal("HMM validation failed: %s\n", errbuf);
      if ( p7_hmmfile_WriteASCII(hmmfp, -1, hmm)  != eslOK) esl_fatal("HMM save failed");

      p7_hmm_Destroy(hmm);
    }
  if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s line %" PRId64 "):\n%s\n",
					    qfp->filename, qfp->linenumber, qfp->errbuf);     
  else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					    status, qfp->filename);
  
  esl_dmatrix_Destroy(Q);
  esl_scorematrix_Destroy(S);
  free(fa);
  free(fb);
  esl_sq_Destroy(qsq);
  esl_sqfile_Close(qfp);
  fclose(hmmfp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}