Ejemplo n.º 1
0
/* serial_master()
 * The serial version of hmmsearch.
 * For each query HMM in <hmmdb> search the database for hits.
 * 
 * A master can only return if it's successful. All errors are handled
 * immediately and fatally with p7_Fail().
 */
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
  FILE            *ofp      = stdout;	         /* output file for results (default stdout)        */
  FILE            *tblfp    = NULL;		 /* output stream for tabular per-seq (--tblout)    */
  FILE            *dfamtblfp    = NULL;            /* output stream for tabular Dfam format (--dfamtblout)    */
  FILE            *aliscoresfp  = NULL;            /* output stream for alignment scores (--aliscoresout)    */

//  P7_HMM          *hmm        = NULL;              /* one HMM query                                   */
//  P7_SCOREDATA    *scoredata  = NULL;

  int              seqfmt   = eslSQFILE_UNKNOWN; /* format of seqfile                               */
  ESL_SQFILE      *sqfp     = NULL;              /* open seqfile                                    */
  P7_HMMFILE      *hfp      = NULL;		 /* open HMM database file                          */
  ESL_ALPHABET    *abc      = NULL;              /* sequence alphabet                               */
  P7_OPROFILE     *om       = NULL;		 /* target profile                                  */
  ESL_STOPWATCH   *w        = NULL;              /* timing                                          */
  ESL_SQ          *qsq      = NULL;		 /* query sequence                                  */
  int              nquery   = 0;
  int              textw;
  int              status   = eslOK;
  int              hstatus  = eslOK;
  int              sstatus  = eslOK;
  int              i;

  int              ncpus    = 0;

  int              infocnt  = 0;
  WORKER_INFO     *info     = NULL;
#ifdef HMMER_THREADS
  P7_OM_BLOCK     *block    = NULL;
  ESL_THREADS     *threadObj= NULL;
  ESL_WORK_QUEUE  *queue    = NULL;
#endif
  char             errbuf[eslERRBUFSIZE];

  double window_beta = -1.0 ;
  int window_length  = -1;
  if (esl_opt_IsUsed(go, "--w_beta")) { if (  ( window_beta   = esl_opt_GetReal(go, "--w_beta") )  < 0 || window_beta > 1  ) esl_fatal("Invalid window-length beta value\n"); }
  if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4  ) esl_fatal("Invalid window length value\n"); }


  w = esl_stopwatch_Create();

  if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
  else                                     textw = esl_opt_GetInteger(go, "--textw");

  /* If caller declared an input format, decode it */
  if (esl_opt_IsOn(go, "--qformat")) {
    seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
    if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
  }

  /* validate options if running as a daemon */
//  if (esl_opt_IsOn(go, "--daemon")) {
    /* running as a daemon, the input format must be type daemon */
//    if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
//      esl_fatal("Input format %s not supported.  Must be daemon\n", esl_opt_GetString(go, "--qformat"));
//    seqfmt = eslSQFILE_DAEMON;

//    if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
//  }

  /* Open the target profile database to get the sequence alphabet */
  status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem, trying to open HMM file %s.\n%s\n",                  cfg->hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",               status, cfg->hmmfile, errbuf);  
  if (! hfp->is_pressed)           p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n",             hfp->fname);

  hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
  if      (hstatus == eslEFORMAT)   p7_Fail("bad format, binary auxfiles, %s:\n%s",     cfg->hmmfile, hfp->errbuf);
  else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
  else if (hstatus != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile); 

  p7_oprofile_Destroy(om);
  p7_hmmfile_Close(hfp);

  /* Open the query sequence database */
  status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n",      cfg->seqfile);
  else if (status == eslEFORMAT)   p7_Fail("Sequence file %s is empty or misformatted\n",        cfg->seqfile);
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
  else if (status != eslOK)        p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
  if (sqfp->format > 100) // breaking the law!  That range is reserved for msa, for aligned formats
    p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n",   cfg->seqfile);
  qsq = esl_sq_CreateDigital(abc);


  /* Open the results output files */
  if (esl_opt_IsOn(go, "-o"))          { if ((ofp      = fopen(esl_opt_GetString(go, "-o"),          "w")) == NULL)  esl_fatal("Failed to open output file %s for writing\n",                 esl_opt_GetString(go, "-o")); }
  if (esl_opt_IsOn(go, "--tblout"))    { if ((tblfp    = fopen(esl_opt_GetString(go, "--tblout"),    "w")) == NULL)  esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
  if (esl_opt_IsOn(go, "--dfamtblout"))    { if ((dfamtblfp    = fopen(esl_opt_GetString(go, "--dfamtblout"),"w"))    == NULL)  esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
  if (esl_opt_IsOn(go, "--aliscoresout"))  { if ((aliscoresfp  = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL)  esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
 
  output_header(ofp, go, cfg->hmmfile, cfg->seqfile);

#ifdef HMMER_THREADS
  /* initialize thread data */
  if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
  else                           esl_threads_CPUCount(&ncpus);

  if (ncpus > 0)
    {
      threadObj = esl_threads_Create(&pipeline_thread);
      queue = esl_workqueue_Create(ncpus * 2);
    }
#endif

  infocnt = (ncpus == 0) ? 1 : ncpus;
  ESL_ALLOC(info, sizeof(*info) * infocnt);

  for (i = 0; i < infocnt; ++i)
    {
      info[i].bg    = p7_bg_Create(abc);
#ifdef HMMER_THREADS
      info[i].queue = queue;
#endif
    }

#ifdef HMMER_THREADS
  for (i = 0; i < ncpus * 2; ++i)
    {
      block = p7_oprofile_CreateBlock(BLOCK_SIZE);
      if (block == NULL)    esl_fatal("Failed to allocate sequence block");

      status = esl_workqueue_Init(queue, block);
      if (status != eslOK)  esl_fatal("Failed to add block to work queue");
    }
#endif

  /* Outside loop: over each query sequence in <seqfile>. */
  while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
  {
      if (sstatus == eslEMEM)                 p7_Fail("Memory allocation error reading sequence file\n", status);
      if (sstatus == eslEINCONCEIVABLE)       p7_Fail("Unexpected error %d reading sequence file\n", status);
     // if (qsq->L > NHMMER_MAX_RESIDUE_COUNT)  p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n",  qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);

      nquery++;
      esl_stopwatch_Start(w);	                          

      /* Open the target profile database */
      status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
      if (status != eslOK)        p7_Fail("Unexpected error %d in opening hmm file %s.\n",           status, cfg->hmmfile);  
  
#ifdef HMMER_THREADS
      /* if we are threaded, create a lock to prevent multiple readers */
      if (ncpus > 0)
      {
        status = p7_hmmfile_CreateLock(hfp);
        if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
      }
#endif

      if (fprintf(ofp, "Query:       %s  [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      if (qsq->acc[0]  != 0 && fprintf(ofp, "Accession:   %s\n", qsq->acc)     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc)    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

      for (i = 0; i < infocnt; ++i)
      {
        /* Create processing pipeline and hit list */
        info[i].th  = p7_tophits_Create();
        info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
        info[i].pli->hfp = hfp;  /* for two-stage input, pipeline needs <hfp> */


        p7_pli_NewSeq(info[i].pli, qsq);
        info[i].qsq = qsq;

        if (  esl_opt_IsUsed(go, "--toponly") )
          info[i].pli->strand = p7_STRAND_TOPONLY;
        else if (  esl_opt_IsUsed(go, "--bottomonly") )
          info[i].pli->strand = p7_STRAND_BOTTOMONLY;
        else
          info[i].pli->strand = p7_STRAND_BOTH;


        #ifdef HMMER_THREADS
          if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
        #endif
      }

#ifdef HMMER_THREADS
      if (ncpus > 0)  hstatus = thread_loop(threadObj, queue, hfp);
      else	      hstatus = serial_loop(info, hfp);
#else
      hstatus = serial_loop(info, hfp);
#endif
      switch(hstatus)
      {
        case eslEFORMAT:   p7_Fail("bad file format in HMM file %s",             cfg->hmmfile);	  break;
        case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets",   cfg->hmmfile);	  break;
        case eslEOF:
        case eslOK:   /* do nothing */
          break;
        default: 	   p7_Fail("Unexpected error in reading HMMs from %s",   cfg->hmmfile);
      }



      /* merge the results of the search results */
      for (i = 1; i < infocnt; ++i)
      {
        p7_tophits_Merge(info[0].th, info[i].th);
        p7_pipeline_Merge(info[0].pli, info[i].pli);

        p7_pipeline_Destroy(info[i].pli);
        p7_tophits_Destroy(info[i].th);
      }


      /* modify e-value to account for number of models */
      for (i = 0; i < info->th->N ; i++)
      {
        info->th->unsrt[i].lnP         += log((float)info->pli->nmodels);
        info->th->unsrt[i].dcl[0].lnP   = info->th->unsrt[i].lnP;
        info->th->unsrt[i].sortkey      = -1.0 * info->th->unsrt[i].lnP;
      }


      /* it's possible to have duplicates based on how viterbi ranges can overlap */
      p7_tophits_SortByModelnameAndAlipos(info->th);
      p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);

      /* Print results */
      p7_tophits_SortBySortkey(info->th);
      p7_tophits_Threshold(info->th, info->pli);

      //tally up total number of hits and target coverage
      info->pli->n_output = info->pli->pos_output = 0;
      for (i = 0; i < info->th->N; i++) {
          if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
              info->pli->n_output++;
              info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
          }
      }




      p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

      if (tblfp)     p7_tophits_TabularTargets(tblfp,    qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
      if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp,   qsq->name, NULL, info->th, info->pli);
      if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );


      esl_stopwatch_Stop(w);
      info->pli->nseqs = 1;
      p7_pli_Statistics(ofp, info->pli, w);
      if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
      fflush(ofp);

      p7_hmmfile_Close(hfp);
      p7_pipeline_Destroy(info->pli);
      p7_tophits_Destroy(info->th);
      esl_sq_Reuse(qsq);
  }



  if      (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
					    sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
  else if (sstatus != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					    sstatus, sqfp->filename);

  /* Terminate outputs - any last words?
   */
  if (tblfp)    p7_tophits_TabularTail(tblfp,    "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
  if (ofp)      { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }

  /* Cleanup - prepare for successful exit
   */
  for (i = 0; i < infocnt; ++i)
    p7_bg_Destroy(info[i].bg);

#ifdef HMMER_THREADS
  if (ncpus > 0)
    {
      esl_workqueue_Reset(queue);
      while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
        p7_oprofile_DestroyBlock(block);
      esl_workqueue_Destroy(queue);
      esl_threads_Destroy(threadObj);
    }
#endif

  free(info);

  esl_sq_Destroy(qsq);
  esl_stopwatch_Destroy(w);
  esl_alphabet_Destroy(abc);
  esl_sqfile_Close(sqfp);

  if (ofp != stdout) fclose(ofp);
  if (tblfp)         fclose(tblfp);
  if (dfamtblfp)     fclose(dfamtblfp);
  if (aliscoresfp)   fclose(aliscoresfp);

  return eslOK;

 ERROR:

 if (ofp != stdout) fclose(ofp);
 if (tblfp)         fclose(tblfp);
 if (dfamtblfp)     fclose(dfamtblfp);
 if (aliscoresfp)   fclose(aliscoresfp);

 return status;
}
Ejemplo n.º 2
0
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;
  ESL_RANDOMNESS *rng     = esl_randomness_CreateFast(0);
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_TRACE       *tr      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
  float           vsc, fsc, tsc;
  char            errbuf[eslERRBUFSIZE];
  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);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");

  /* 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);

  if (esl_opt_GetBoolean(go, "-p")) p7_oprofile_Dump(stdout, om);  

  fwd = p7_omx_Create(gm->M, sq->n, sq->n);
  gx  = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_Create();

  if (esl_opt_GetBoolean(go, "-m") == TRUE) p7_omx_SetDumpMode(stdout, fwd, TRUE); 
  p7_GViterbi(sq->dsq, sq->n, gm, gx,  &vsc);
  p7_Forward (sq->dsq, sq->n, om, fwd, &fsc);

  for (i = 0; i < N; i++)
    {
      p7_StochasticTrace(rng, sq->dsq, sq->n, om, fwd, tr);
      p7_trace_Score(tr, sq->dsq, gm, &tsc);
  
      if (esl_opt_GetBoolean(go, "-t") == TRUE) p7_trace_Dump(stdout, tr, gm, sq->dsq);
      if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK)  p7_Die("trace %d fails validation:\n%s\n", i, errbuf);

      printf("Sampled trace:  %.4f nats\n", tsc);
      p7_trace_Reuse(tr);
    }
  printf("Forward score:  %.4f nats\n", fsc);
  printf("Viterbi score:  %.4f nats\n", vsc);

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_trace_Destroy(tr);
  p7_omx_Destroy(fwd);
  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_randomness_Destroy(rng);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 3
0
/* seq_shuffling()
 * SRE, Tue Jan 22 08:35:51 2008 [Market Street Cafe, Leesburg]
 *
 * Shuffling of input sequences.
 *
 * Fixed-length (L>0) vs. full-length (L=0) modes handled differently.
 * In fixed-length mode:
 *   <shuff->seq> only needs to be allocated once, for L
 *   <targ> is an allocated copy of a random subseq of length L
 *   sequences < L residues long can't be shuffled
 * In full-length mode:
 *   <shuff->seq> is grown to length <sq->n> for each input seq
 *   <targ> just points to <sq->seq>
 */
static int 
seq_shuffling(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
  char       *seqfile = esl_opt_GetArg(go, 1);
  int         infmt   = eslSQFILE_UNKNOWN;
  ESL_SQFILE *sqfp    = NULL;
  ESL_SQ     *sq      = esl_sq_Create();
  ESL_SQ     *shuff   = esl_sq_Create();
  char       *targ    = NULL;
  int         N       = esl_opt_GetInteger(go, "-N");
  int         L       = esl_opt_GetInteger(go, "-L"); /* L>0 means select random fixed-len subseqs */
  int         kmers   = 0;
  int         i;
  int         status;
  
  if (esl_opt_GetString(go, "--informat") != NULL) {
    infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
    if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat"); 
  }

  if (esl_opt_IsOn(go, "-k")) kmers = esl_opt_GetInteger(go, "-k");


  status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
  if      (status == eslENOTFOUND) esl_fatal("No such file %s", seqfile);
  else if (status == eslEFORMAT)   esl_fatal("Format of seqfile %s unrecognized.", seqfile);
  else if (status == eslEINVAL)    esl_fatal("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        esl_fatal("Open failed, code %d.", status);

  if (L>0) { 
    esl_sq_GrowTo(shuff, L);
    shuff->n = L;
    ESL_ALLOC(targ, sizeof(char) * (L+1));
  }

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      if (L == 0) {		     /* shuffling entire sequence   */
	esl_sq_GrowTo(shuff, sq->n); /* make sure shuff can hold sq */	  
	shuff->n = sq->n;
	targ = sq->seq;
      } else {
	if (sq->n < L) continue;     /* reject seqs < L long */
      }

      for (i = 0; i < N; i++)
	{
	  if (L > 0) {		/* fixed-len mode: copy a random subseq */
	    int pos = esl_rnd_Roll(r, sq->n - L + 1);
	    strncpy(targ, sq->seq + pos, L);
	    targ[L] = '\0';	    
	  }

	  /* Do the requested kind of shuffling */
	  if      (esl_opt_GetBoolean(go, "-m"))  esl_rsq_CShuffle     (r, targ,        shuff->seq);  /* monoresidue shuffling */
	  else if (esl_opt_GetBoolean(go, "-d"))  esl_rsq_CShuffleDP   (r, targ,        shuff->seq);  /* diresidue shuffling */
	  else if (esl_opt_IsOn      (go, "-k"))  esl_rsq_CShuffleKmers(r, targ, kmers, shuff->seq);  /* diresidue shuffling */
	  else if (esl_opt_GetBoolean(go, "-0"))  esl_rsq_CMarkov0     (r, targ,        shuff->seq);  /* 0th order Markov */
	  else if (esl_opt_GetBoolean(go, "-1"))  esl_rsq_CMarkov1     (r, targ,        shuff->seq);  /* 1st order Markov */
	  else if (esl_opt_GetBoolean(go, "-r"))  esl_rsq_CReverse     (   targ,        shuff->seq);  /* reverse */
	  else if (esl_opt_IsOn      (go, "-w")) { /* regionally shuffle */	
	    int W= esl_opt_GetInteger(go, "-w"); esl_rsq_CShuffleWindows(r, targ, W, shuff->seq);
	  }

	  /* Set the name of the shuffled sequence */
	  if (N > 1) esl_sq_FormatName(shuff, "%s-shuffled-%d", sq->name, i);
	  else       esl_sq_FormatName(shuff, "%s-shuffled", sq->name);

	  /* Output the resulting sequence */
	  esl_sqio_Write(ofp, shuff, outfmt, FALSE);

	  /* don't need to reuse the shuffled sequence: we will use exactly the same memory */
	}
      esl_sq_Reuse(sq);
    }
  if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
					   sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
  else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					    status, sqfp->filename);

  if (L>0) free(targ);
  esl_sq_Destroy(shuff);
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  return eslOK;

 ERROR:
  if (targ != NULL) free(targ);
  esl_sq_Destroy(shuff);
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  return status;
}
Ejemplo n.º 4
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_GMX         *fwd     = NULL;
  P7_GMX         *bck     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           fsc, bsc;
  float           nullsc;
  int             status;

  /* Initialize log-sum calculator */
  p7_FLogsumInit();

  /* Read in one HMM */
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);
 
  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
 
  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);

  /* Now reconfig the models however we were asked to */
  if      (esl_opt_GetBoolean(go, "--fs"))  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  else if (esl_opt_GetBoolean(go, "--sw"))  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
  else if (esl_opt_GetBoolean(go, "--ls"))  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_GLOCAL);
  else if (esl_opt_GetBoolean(go, "--s"))   p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNIGLOCAL);
  
  /* Allocate matrices */
  fwd = p7_gmx_Create(gm->M, sq->n);
  bck = p7_gmx_Create(gm->M, sq->n);

  printf("%-30s   %-10s %-10s   %-10s %-10s\n", "# seq name",      "fwd (raw)",   "bck (raw) ",  "fwd (bits)",  "bck (bits)");
  printf("%-30s   %10s %10s   %10s %10s\n",     "#--------------", "----------",  "----------",  "----------",  "----------");

  while ( (status = esl_sqio_Read(sqfp, sq)) != eslEOF)
    {
      if      (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));     
      else if (status != eslOK)      p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);

      /* Resize the DP matrices if necessary */
      p7_gmx_GrowTo(fwd, gm->M, sq->n);
      p7_gmx_GrowTo(bck, gm->M, sq->n);

      /* Set the profile and null model's target length models */
      p7_bg_SetLength(bg,   sq->n);
      p7_ReconfigLength(gm, sq->n);

      /* Run Forward, Backward */
      p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
      p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);

      p7_gmx_Dump(stdout, fwd, p7_DEFAULT);

      /* Those scores are partial log-odds likelihoods in nats.
       * Subtract off the rest of the null model, convert to bits.
       */
      p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);

      printf("%-30s   %10.4f %10.4f   %10.4f %10.4f\n", 
	     sq->name, 
	     fsc, bsc, 
	     (fsc - nullsc) / eslCONST_LOG2, (bsc - nullsc) / eslCONST_LOG2);

      p7_gmx_Reuse(fwd);
      p7_gmx_Reuse(bck);
      esl_sq_Reuse(sq);
    }

  /* Cleanup */
  esl_sqfile_Close(sqfp);
  esl_sq_Destroy(sq);
  p7_gmx_Destroy(fwd);
  p7_gmx_Destroy(bck);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 5
0
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;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  ESL_SQ         *sq      = NULL;
  float           nullsc, filtersc, H;
  int             status;
 
  /* Read one HMM from <hmmfile> */
  if (p7_hmmfile_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");
  p7_hmmfile_Close(hfp);

  /* Open <seqfile> for reading */
  status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) esl_fatal("No such file.");
  else if (status == eslEFORMAT)   esl_fatal("Format unrecognized.");
  else if (status != eslOK)        esl_fatal("Open failed, code %d.", status);

  sq = esl_sq_CreateDigital(abc);
  bg = p7_bg_Create(abc);
  p7_bg_SetFilterByHMM(bg, hmm);

  H = esl_vec_FEntropy(bg->f, bg->abc->K);
  printf("bg iid H = %.4f\n", H);

  H = esl_vec_FEntropy(bg->mcomp, bg->abc->K);
  printf("modelcomp H = %.4f\n", H);

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      p7_bg_SetLength(bg, sq->n);

      p7_bg_NullOne    (bg, sq->dsq, sq->n, &nullsc);
      p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);

      printf("%-20s %5d %8.5f %8.5f %8.5f\n", sq->name, (int) sq->n, nullsc, filtersc, filtersc-nullsc);

      esl_sq_Reuse(sq);
    }
  if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s line %" PRId64 "):\n%s\n",
					    sqfp->filename, sqfp->linenumber, sqfp->errbuf);     
  else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					    status, sqfp->filename);

  esl_sqfile_Close(sqfp);
  esl_sq_Destroy(sq);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 6
0
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_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           fraw, braw, nullsc, fsc;
  float           gfraw, gbraw, gfsc;
  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");

  /* Open sequence file for reading */
  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_UNILOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);

  /* p7_oprofile_Dump(stdout, om);  */

  /* allocate DP matrices for O(M+L) parsers */
  fwd = p7_omx_Create(gm->M, 0, sq->n);
  bck = p7_omx_Create(gm->M, 0, sq->n);
  gx  = p7_gmx_Create(gm->M,    sq->n);

  /* allocate DP matrices for O(ML) fills */
  /* fwd = p7_omx_Create(gm->M, sq->n, sq->n); */
  /* bck = p7_omx_Create(gm->M, sq->n, sq->n); */

  /* p7_omx_SetDumpMode(stdout, fwd, TRUE); */     /* makes the fast DP algorithms dump their matrices */
  /* p7_omx_SetDumpMode(stdout, bck, TRUE); */  

  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(fwd, om->M, 0,   sq->n); 
      p7_omx_GrowTo(bck, om->M, 0,   sq->n); 
      p7_gmx_GrowTo(gx,  gm->M,      sq->n); 

      p7_bg_NullOne  (bg, sq->dsq, sq->n, &nullsc);
    
      p7_ForwardParser (sq->dsq, sq->n, om,      fwd, &fraw);
      p7_BackwardParser(sq->dsq, sq->n, om, fwd, bck, &braw);

      /* p7_Forward (sq->dsq, sq->n, om,      fwd, &fsc);        printf("forward:              %.2f nats\n", fsc);  */
      /* p7_Backward(sq->dsq, sq->n, om, fwd, bck, &bsc);        printf("backward:             %.2f nats\n", bsc);  */

      /* Comparison to other F/B implementations */
      p7_GForward     (sq->dsq, sq->n, gm, gx,  &gfraw);
      p7_GBackward    (sq->dsq, sq->n, gm, gx,  &gbraw);

      /* p7_gmx_Dump(stdout, gx);  */

      fsc  =  (fraw-nullsc) / eslCONST_LOG2;
      gfsc = (gfraw-nullsc) / eslCONST_LOG2;
      P  = esl_exp_surv(fsc,   om->evparam[p7_FTAU],  om->evparam[p7_FLAMBDA]);
      gP = esl_exp_surv(gfsc,  gm->evparam[p7_FTAU],  gm->evparam[p7_FLAMBDA]);

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s\t%-20s\t%9.2g\t%6.1f\t%9.2g\t%6.1f\n", sq->name, hmm->name, P, fsc, gP, gfsc);
	}
      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, fsc, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("fwd filter raw score: %.2f nats\n", fraw);
	  printf("bck filter raw score: %.2f nats\n", braw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", fsc);
	  printf("P-value:              %g\n",        P);
	  printf("GForward raw score:   %.2f nats\n", gfraw);
	  printf("GBackward raw score:  %.2f nats\n", gbraw);
	  printf("GForward seq score:   %.2f bits\n", gfsc);
	  printf("GForward P-value:     %g\n",        gP);
	}

      esl_sq_Reuse(sq);
    }

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  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;
}
Ejemplo n.º 7
0
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_GMX         *fwd     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  P7_TRACE       *tr      = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  char            errbuf[eslERRBUFSIZE];
  float           sc;
  int             d;
  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");
  p7_hmmfile_Close(hfp);
 
  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
  esl_sqfile_Close(sqfp);
 
  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  
  /* Allocate matrix and a trace */
  fwd = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_Create();

  /* Run Viterbi; do traceback */
  p7_GViterbi (sq->dsq, sq->n, gm, fwd, &sc);
  p7_GTrace   (sq->dsq, sq->n, gm, fwd, tr);

  /* Dump and validate the trace. */
  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);

  /* Domain info in the trace. */
  p7_trace_Index(tr);
  printf("# Viterbi: %d domains : ", tr->ndom);
  for (d = 0; d < tr->ndom; d++) printf("%6d %6d %6d %6d  ", tr->sqfrom[d], tr->sqto[d], tr->hmmfrom[d], tr->hmmto[d]);
  printf("\n");

  /* Cleanup */
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(fwd);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_sq_Destroy(sq);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 8
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS  *go      = NULL;	/* application configuration       */
  char         *hmmfile = NULL;	/* HMM file name                   */
  char         *seqfile = NULL; /* sequence file name              */
  char         *mapfile = NULL; /* optional mapped MSA file name   */
  int           infmt   = eslSQFILE_UNKNOWN;
  int           outfmt  = eslMSAFILE_STOCKHOLM;
  P7_HMMFILE   *hfp     = NULL;	/* open HMM file                   */
  ESL_SQFILE   *sqfp    = NULL;	/* open sequence file              */
  char         *outfile = NULL;	  /* output filename               */
  FILE         *ofp     = stdout; /* output stream                 */
  ESL_SQ      **sq      = NULL;	/* array of sequences              */
  void         *p       = NULL;	/* tmp ptr for reallocation        */
  int           nseq    = 0;	/* # of sequences in <seqfile>     */
  int           mapseq  = 0;	/* # of sequences in mapped MSA    */
  int           totseq  = 0;	/* # of seqs in all sources        */
  ESL_ALPHABET *abc     = NULL;	/* alphabet (set from the HMM file)*/
  P7_HMM       *hmm     = NULL;
  P7_TRACE    **tr      = NULL;	/* array of tracebacks             */
  ESL_MSA      *msa     = NULL;	/* resulting multiple alignment    */
  int           msaopts = 0;	/* flags to p7_tracealign_Seqs()   */
  int           idx;		/* counter over seqs, traces       */
  int           status;		/* easel/hmmer return code         */
  char          errbuf[eslERRBUFSIZE];

  /* Parse the command line
   */
  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
  if (esl_opt_VerifyConfig(go)               != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n",       go->errbuf);
  if (esl_opt_GetBoolean(go, "-h") )                   cmdline_help   (argv[0], go);
  if (esl_opt_ArgNumber(go) != 2)                      cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");        

  hmmfile = esl_opt_GetArg(go, 1);
  seqfile = esl_opt_GetArg(go, 2);

  if (strcmp(hmmfile, "-") == 0 && strcmp(seqfile, "-") == 0) 
    cmdline_failure(argv[0], "Either <hmmfile> or <seqfile> may be '-' (to read from stdin), but not both.\n");

  msaopts |= p7_ALL_CONSENSUS_COLS; /* default as of 3.1 */
  if (esl_opt_GetBoolean(go, "--trim"))    msaopts |= p7_TRIM;

  /* If caller declared an input format, decode it 
   */
  if (esl_opt_IsOn(go, "--informat")) {
    infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
    if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--informat"));
  }

  /* Determine output alignment file format */
  outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
  if (outfmt == eslMSAFILE_UNKNOWN)    cmdline_failure(argv[0], "%s is not a recognized output MSA file format\n", esl_opt_GetString(go, "--outformat"));

  /* Open output stream */
  if ( (outfile = esl_opt_GetString(go, "-o")) != NULL) 
  {
    if ((ofp = fopen(outfile, "w")) == NULL)
      cmdline_failure(argv[0], "failed to open -o output file %s for writing\n", outfile);
  }


  /* If caller forced an alphabet on us, create the one the caller wants  
   */
  if      (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
  else if (esl_opt_GetBoolean(go, "--dna"))   abc = esl_alphabet_Create(eslDNA);
  else if (esl_opt_GetBoolean(go, "--rna"))   abc = esl_alphabet_Create(eslRNA);

  /* Read one HMM, and make sure there's only one.
   */
  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);  

  status = p7_hmmfile_Read(hfp, &abc, &hmm);
  if      (status == eslEFORMAT)   p7_Fail("Bad file format in HMM file %s:\n%s\n",          hfp->fname, hfp->errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
  else if (status == eslEOF)       p7_Fail("Empty HMM file %s? No HMM data found.\n",        hfp->fname);
  else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s\n",     hfp->fname);

  status = p7_hmmfile_Read(hfp, &abc, NULL);
  if      (status != eslEOF)       p7_Fail("HMM file %s does not contain just one HMM\n",    hfp->fname);
  p7_hmmfile_Close(hfp);


  /* We're going to build up two arrays: sequences and traces.
   * If --mapali option is chosen, the first set of sequences/traces is from the provided alignment
   */
  if ( (mapfile = esl_opt_GetString(go, "--mapali")) != NULL)
  {
    map_alignment(mapfile, hmm, &sq, &tr, &mapseq);
  }
  totseq = mapseq;

  /* Read digital sequences into an array (possibly concat'ed onto mapped seqs)
   */
  status = esl_sqfile_OpenDigital(abc, seqfile, infmt, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n",          seqfile);
  else if (status == eslEFORMAT)   p7_Fail("Sequence file %s is empty or misformatted\n",            seqfile);
  else if (status != eslOK)        p7_Fail("Unexpected error %d opening sequence file %s\n", status, seqfile);

  ESL_RALLOC(sq, p, sizeof(ESL_SQ *) * (totseq + 1));
  sq[totseq] = esl_sq_CreateDigital(abc);
  nseq = 0;
  while ((status = esl_sqio_Read(sqfp, sq[totseq+nseq])) == eslOK)
  {
    nseq++;
    ESL_RALLOC(sq, p, sizeof(ESL_SQ *) * (totseq+nseq+1));
    sq[totseq+nseq] = esl_sq_CreateDigital(abc);
  }
  if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n", 
					   sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
  else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename);
  esl_sqfile_Close(sqfp);
  totseq += nseq;


  /* Remaining initializations, including trace array allocation
   */
  ESL_RALLOC(tr, p, sizeof(P7_TRACE *) * totseq);
  for (idx = mapseq; idx < totseq; idx++)
    tr[idx] = p7_trace_CreateWithPP();

  p7_tracealign_computeTraces(hmm, sq, mapseq, totseq - mapseq, tr);

  p7_tracealign_Seqs(sq, tr, totseq, hmm->M, msaopts, hmm, &msa);

  eslx_msafile_Write(ofp, msa, outfmt);

  for (idx = 0; idx <= totseq; idx++) esl_sq_Destroy(sq[idx]);    /* including sq[nseq] because we overallocated */
  for (idx = 0; idx <  totseq; idx++) p7_trace_Destroy(tr[idx]); 
  free(sq);
  free(tr);
  esl_msa_Destroy(msa);
  p7_hmm_Destroy(hmm);
  if (ofp != stdout) fclose(ofp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return eslOK;

 ERROR:
  return status;
}
Ejemplo n.º 9
0
static int
serial_loop(WORKER_INFO *info, ESL_SQFILE *dbfp, int n_targetseqs, FILE *ofp)
{
  int      sstatus;
  ESL_SQ   *dbsq     = NULL;   /* one target sequence (digital)  */
  int seq_cnt = 0;

  dbsq = esl_sq_CreateDigital(info->om->abc);

  SEQ_INFO *sqinfo = (SEQ_INFO *)malloc(INFO_SIZE * sizeof(SEQ_INFO));
  size_t capacity = INFO_SIZE;

  FILE *ftmp = fopen("tmp.txt", "w+");

  /* Main loop: */
  while ( (n_targetseqs==-1 || seq_cnt<n_targetseqs) &&  (sstatus = esl_sqio_Read(dbfp, dbsq)) == eslOK)
  {
//      p7_pli_NewSeq(info->pli, dbsq);
//      p7_bg_SetLength(info->bg, dbsq->n);
//      p7_oprofile_ReconfigLength(info->om, dbsq->n);

//      p7_Pipeline(info->pli, info->om, info->bg, dbsq, info->th);
      if (seq_cnt > capacity) {
    	  capacity = capacity << 1;
    	  SEQ_INFO * newsq = (SEQ_INFO * )realloc(sqinfo, capacity * sizeof(SEQ_INFO));
    	  if (newsq) sqinfo = newsq;
    	  else {
    		  printf("Mem Error\n");
    		  exit(1);
    	  }
      }
      sqinfo[seq_cnt].index = seq_cnt;
      sqinfo[seq_cnt].length = dbsq->n;

      esl_sq_Textize(dbsq);

//      if (dbsq->seq) printf("Text -- %s\n", dbsq->seq);
//      if (dbsq->name) printf("Name -- %s\n", dbsq->name);
//      if (dbsq->ss) printf("%s\n", dbsq->ss);
//      if (dbsq->desc) printf("Desc -- %s\n", dbsq->desc);
//      printf("%s\n", dbsq->desc);


//      printf("Pos1 -- %d ", pos);
      sqinfo[seq_cnt].pos = ftell(ftmp);

      fprintf(ftmp, ">%s %s\n%s\n", dbsq->name, dbsq->desc, dbsq->seq);

//      printf(" %d\n", pos);

      sqinfo[seq_cnt].size = ftell(ftmp) - sqinfo[seq_cnt].pos; //strlen(dbsq->name) + strlen(dbsq->desc) + strlen(dbsq->seq) + 4;

      seq_cnt++;
      esl_sq_Reuse(dbsq);
//      p7_pipeline_Reuse(info->pli);
  }

  qsort(sqinfo, seq_cnt, sizeof(SEQ_INFO), seqSortByLength);


//  esl_sqfile_Position(dbfp, 0);

  char *buf = (char *)malloc(sqinfo[0].size + 1);
  buf[sqinfo[0].size] = '\0';

  for (int i = 0; i < seq_cnt; ++i) {
//      printf("index: %d length: %d \n", sqinfo[i].index, sqinfo[i].length);
//      int ret = esl_sqfile_Position(dbfp, i);// sqinfo[i].index);
//      printf("return: %d \n", ret);

	  fseek(ftmp, sqinfo[i].pos, SEEK_SET);

      fread(buf, 1, sqinfo[i].size, ftmp);

      if ( i == 0 ) printf("II %s", buf);

      fwrite(buf, 1, sqinfo[i].size, ofp);

      int ret = esl_sqio_Read(dbfp, dbsq);

//      printf("2return: %d \n", ret);

//      printf("i: %d length: %d \n", i, dbsq->n);
      esl_sq_Reuse(dbsq);
  }


  if (n_targetseqs!=-1 && seq_cnt==n_targetseqs)
    sstatus = eslEOF;

  free(sqinfo);
  fclose(ftmp);

  esl_sq_Destroy(dbsq);

  return sstatus;
}
Ejemplo n.º 10
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 11
0
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);
  float           nu      = esl_opt_GetReal(go, "--nu");
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_GMX         *fwd     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  P7_TRACE       *tr      = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           sc, nullsc, seqscore, P;
  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");
  p7_hmmfile_Close(hfp);
 
  /* Open sequence file */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);

  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);

  /* Allocate matrix */
  fwd = p7_gmx_Create(gm->M, sq->n);

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      p7_ReconfigLength(gm,  sq->n);
      p7_bg_SetLength(bg,    sq->n);
      p7_gmx_GrowTo(fwd, gm->M, sq->n); 

      /* Run MSV */
      p7_GMSV(sq->dsq, sq->n, gm, fwd, nu, &sc);

      /* Calculate bit score and P-value using standard null1 model*/
      p7_bg_NullOne  (bg, sq->dsq, sq->n, &nullsc);
      seqscore = (sc - nullsc) / eslCONST_LOG2;
      P        =  esl_gumbel_surv(seqscore,  gm->evparam[p7_MMU],  gm->evparam[p7_MLAMBDA]);

      /* output suitable for direct use in profmark benchmark postprocessors:
       * <Pvalue> <bitscore> <target name> <query name>
       */
      printf("%g\t%.2f\t%s\t%s\n", P, seqscore, sq->name, hmm->name);

      esl_sq_Reuse(sq);
    }
  if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
  else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename);

  /* Cleanup */
  esl_sqfile_Close(sqfp); 
  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(fwd);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 12
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;
}
Ejemplo n.º 13
0
int
p7_seqcache_Open(char *seqfile, P7_SEQCACHE **ret_cache, char *errbuf)
{
  int                i;
  int                inx;
  int                val;
  int                status;

  int32_t            seq_cnt;
  int32_t            db_cnt;
  int32_t            db_inx[32];
  uint32_t           db_key;

  uint64_t           res_cnt;
  uint64_t           res_size;
  uint64_t           hdr_size;

  char              *hdr_ptr;
  char              *res_ptr;
  char              *desc_ptr;
  char              *ptr;
  char               buffer[512];
  off_t              offset;

  uint64_t           total_mem;

  SEQ_DB            *db         = NULL;
  P7_SEQCACHE       *cache      = NULL;

  ESL_RANDOMNESS    *rnd        = NULL;
  ESL_SQFILE        *sqfp       = NULL;
  ESL_SQ            *sq         = NULL;
  ESL_ALPHABET      *abc        = NULL;
  ESL_SQASCII_DATA  *ascii      = NULL;

  if (errbuf) errbuf[0] = '\0';	/* CURRENTLY UNUSED. FIXME */

  /* Open the target sequence database */
  if ((status = esl_sqfile_Open(seqfile, eslSQFILE_FASTA, NULL, &sqfp)) != eslOK) return status;

  /* This is a bit of a hack.  The first line contains database information.
   *
   * #<res_count> <seq_count> <db_count> <db_sequences_1> <db_sequences_before_removing_duplicates_1> <db_sequences_2> <db_sequences_before_removing_duplicates_2>  ... <date_stamp>
   *
   * The rest of the file is a fasta format.  The fasta header is just
   * sequence number followed by a binary number indicating which
   * database this sequence occurs in.
   *
   * The header line will be read in, parsed and saved.  Then the
   * parser will be repositioned after the line and used normally.
   */
  ascii = &sqfp->data.ascii;
  fseek(ascii->fp, 0L, SEEK_SET);
  if (fgets(buffer, sizeof(buffer), ascii->fp) == NULL) return eslEFORMAT;
  if (buffer[0] != '#')                                 return eslEFORMAT;

  ptr = buffer + 1;
  res_cnt = strtoll(ptr, &ptr, 10);
  seq_cnt = strtol(ptr, &ptr, 10);
  db_cnt  = strtol(ptr, &ptr, 10);

  if (db_cnt > (sizeof(db_inx)/sizeof(db_inx[0])))      return eslEFORMAT;

  total_mem = sizeof(P7_SEQCACHE);
  ESL_ALLOC(cache, sizeof(P7_SEQCACHE));
  memset(cache, 0, sizeof(P7_SEQCACHE));

  if (esl_strdup(seqfile, -1, &cache->name) != eslOK)   goto ERROR;

  total_mem += (sizeof(HMMER_SEQ) * seq_cnt);
  ESL_ALLOC(cache->list, sizeof(HMMER_SEQ) * seq_cnt);
  memset(cache->list, 0, sizeof(HMMER_SEQ) * seq_cnt);

  total_mem += (sizeof(SEQ_DB) * db_cnt);
  ESL_ALLOC(db, sizeof(SEQ_DB) * db_cnt);
  for (i = 0; i < db_cnt; ++i) {
    db[i].count  = strtol(ptr, &ptr, 10);
    db[i].K      = strtol(ptr, &ptr, 10);
    total_mem   += (sizeof(HMMER_SEQ *) * db[i].count);
    ESL_ALLOC(db[i].list, sizeof(HMMER_SEQ *) * db[i].count);
    memset(db[i].list, 0, sizeof(HMMER_SEQ *) * db[i].count);
  }

  /* grab the unique identifier */
  while (*ptr && isspace(*ptr)) ++ptr;
  i = strlen(ptr);
  ESL_ALLOC(cache->id, i+1);
  strcpy(cache->id, ptr);
  while (--i > 0 && isspace(cache->id[i])) cache->id[i] = 0;

  res_size = res_cnt + seq_cnt + 1;
  hdr_size = seq_cnt * 10;

  total_mem += res_size + hdr_size;
  ESL_ALLOC(cache->residue_mem, res_size);
  ESL_ALLOC(cache->header_mem, hdr_size);

  /* position the sequence file to the start of the first sequence.
   * this will force any buffers associated with the file to be reset.
   */
  offset = ftell(ascii->fp);
  if ((status = esl_sqfile_Position(sqfp, offset)) != eslOK) goto ERROR;

  abc = esl_alphabet_Create(eslAMINO);
  sq  = esl_sq_CreateDigital(abc);

  cache->db_cnt      = db_cnt;
  cache->db          = db;
  cache->abc         = abc;
  cache->res_size    = res_size;
  cache->hdr_size    = hdr_size;
  cache->count       = seq_cnt;

  hdr_ptr = cache->header_mem;
  res_ptr = cache->residue_mem;
  for (i = 0; i < db_cnt; ++i) db_inx[i] = 0;

  strcpy(buffer, "000000001");
  
  inx = 0;
  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) {

    /* sanity checks */
    if (inx >= seq_cnt)       { printf("inx: %d\n", inx); return eslEFORMAT; }
    if (sq->n + 1 > res_size) { printf("inx: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; }
    if (hdr_size <= 0)        { printf("inx: %d hdr %d\n", inx, (int)hdr_size); return eslEFORMAT; }

    /* generate the database key - modified to take the first word in the desc line.
     * The remaining part of the desc is then cached as the description.  */

    ptr = sq->desc;;
    desc_ptr = strchr(sq->desc, ' ');
    if(desc_ptr != NULL) {
    	*desc_ptr= '\0';
    	++desc_ptr;
    }
    val = 1;
    db_key = 0;
    while (*ptr) {
      if (*ptr == '1') db_key += val;
      val <<= 1;
      ++ptr;
    }


    if (db_key >= (1 << (db_cnt + 1))) { printf("inx: %d db %d %s\n", inx, db_key, sq->desc); return eslEFORMAT; }

    cache->list[inx].name   = hdr_ptr;
    cache->list[inx].dsq    = (ESL_DSQ *)res_ptr;
    cache->list[inx].n      = sq->n;
    cache->list[inx].idx    = inx;
    cache->list[inx].db_key = db_key;
    if(desc_ptr != NULL) esl_strdup(desc_ptr, -1, &(cache->list[inx].desc));

    /* copy the digitized sequence */
    memcpy(res_ptr, sq->dsq, sq->n + 1);
    res_ptr  += (sq->n + 1);
    res_size -= (sq->n + 1);

    /* copy the index to the header */
    strcpy(hdr_ptr, buffer);
    hdr_ptr += 10;
    hdr_size -= 10;

    /* increment the buffer string */
    ++buffer[8];
    for (i = 8; i > 0; --i) {
      if (buffer[i] > '9') {
        buffer[i] = '0';
        buffer[i-1]++;
      }
    }

    esl_sq_Reuse(sq);
    ++inx;    
  }
  if (status != eslEOF) { printf("Unexpected error %d at %d\n", status, inx); return status; }

  if (inx != seq_cnt) { printf("inx:: %d %d\n", inx, seq_cnt); return eslEFORMAT; }
  if (hdr_size != 0)  { printf("inx:: %d hdr %d\n", inx, (int)hdr_size); return eslEFORMAT; }
  if (res_size != 1)  { printf("inx:: %d size %d %d\n", inx, (int)sq->n + 1, (int)res_size); return eslEFORMAT; }

  /* copy the final sentinel character */
  *res_ptr++ = eslDSQ_SENTINEL;
  --res_size;

  /* sort the order of the database sequences */
  rnd = esl_randomness_CreateFast(seq_cnt);
  for (i = 0 ; i < seq_cnt; ++i) {
    rnd->x = rnd->x * 69069 + 1;
    cache->list[i].idx = rnd->x;
  }
  esl_randomness_Destroy(rnd);
  qsort(cache->list, seq_cnt, sizeof(HMMER_SEQ), sort_seq);

  /* fill in the different databases and fix the index */
  for (i = 0 ; i < seq_cnt; ++i) {
    inx = 0;
    db_key = cache->list[i].db_key;
    while (db_key) {
      if (db_key & 1) {
        SEQ_DB *db = cache->db + inx;
        if (db_inx[inx] >= db->count) { printf("sort:: %d %d\n", db_inx[inx], db->count); return eslEFORMAT; }
        db->list[db_inx[inx]] = &cache->list[i];
        ++db_inx[inx];
      }
      db_key >>= 1;
      ++inx;
    }
    cache->list[i].idx = (cache->list[i].name - cache->header_mem) / 10 + 1;
  }

  for (i = 0; i < cache->db_cnt; ++i) {
    printf("sequence database (%d):: %d %d\n", i, cache->db[i].count, db_inx[i]);
  }

  printf("\nLoaded sequence db file %s; total memory %" PRId64 "\n", seqfile, total_mem);

  esl_sqfile_Close(sqfp);
  esl_sq_Destroy(sq);

  *ret_cache = cache;

  return eslOK;

 ERROR:
  if (sq    != NULL) esl_sq_Destroy(sq);
  if (abc   != NULL) esl_alphabet_Destroy(abc);
  if (cache != NULL) {
    if (cache->header_mem  != NULL) free(cache->header_mem);
    if (cache->residue_mem != NULL) free(cache->residue_mem);
    if (cache->name        != NULL) free(cache->name);
    if (cache->id          != NULL) free(cache->id);
    free(cache);
  }
  for (i = 0; i < db_cnt; ++i) {
    if (db[i].list != NULL) free(db[i].list);
  }
  return eslEMEM;
}
Ejemplo n.º 14
0
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_GMX         *fwd     = NULL;
  P7_GMX         *bck     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           fsc, bsc;
  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");
  p7_hmmfile_Close(hfp);
 
  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
  esl_sqfile_Close(sqfp);
 
  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
  
  /* Allocate matrices */
  fwd = p7_gmx_Create(gm->M, sq->n);
  bck = p7_gmx_Create(gm->M, sq->n);

  /* Run Forward, Backward */
  p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
  p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);

  printf("fwd = %.4f nats\n", fsc);
  printf("bck = %.4f nats\n", bsc);

  /* Cleanup */
  esl_sq_Destroy(sq);
  p7_gmx_Destroy(fwd);
  p7_gmx_Destroy(bck);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 15
0
int 
main(int argc, char **argv)
{
  char           *hmmfile = argv[1];
  char           *seqfile = argv[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           sc;
  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);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");

  /* 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);
  p7_oprofile_Logify(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
  */

  p7_ViterbiScore(sq->dsq, sq->n, om, ox, &sc);  printf("viterbi (non-optimized):  %.2f nats\n", sc);
  p7_GViterbi    (sq->dsq, sq->n, gm, gx, &sc);  printf("viterbi (generic):        %.2f nats\n", sc);

  /* now in a real app, you'd need to convert raw nat scores to final bit
   * scores, by subtracting the null model score and rescaling.
   */

  /* 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);
  return 0;
}
Ejemplo n.º 16
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           msvraw, nullsc, msvscore;
  float           graw, gscore;
  double          P, gP;
  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");

  /* Open sequence file for reading */
  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, 0); /* one row version */
  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(stdout, ox, TRUE);      makes the fast DP algorithms dump their matrices
     p7_gmx_Dump(stdout, gx, p7_DEFAULT);       dumps a generic DP matrix
     p7_oprofile_SameMSV(om, gm);
  */
  //p7_oprofile_Dump(stdout, om);
  //p7_omx_SetDumpMode(stdout, ox, TRUE);    

  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_MSVFilter   (sq->dsq, sq->n, om, ox, &msvraw);  
      p7_bg_NullOne  (bg, sq->dsq, sq->n, &nullsc);
      msvscore = (msvraw - nullsc) / eslCONST_LOG2;
      P        = esl_gumbel_surv(msvscore,  om->evparam[p7_MMU],  om->evparam[p7_MLAMBDA]);

      p7_GMSV(sq->dsq, sq->n, gm, gx, 2.0, &graw);
      gscore   = (graw - nullsc) / eslCONST_LOG2;
      gP       = esl_gumbel_surv(gscore,  gm->evparam[p7_MMU],  gm->evparam[p7_MLAMBDA]);

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s  %-20s  %9.2g  %7.2f  %9.2g  %7.2f\n", sq->name, hmm->name, P, msvscore, gP, gscore);
	}
      else if (esl_opt_GetBoolean(go, "-P"))
	{ /* output suitable for direct use in profmark benchmark postprocessors: */
	  printf("%g  %.2f  %s  %s\n", P, msvscore, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("msv filter raw score: %.2f nats\n", msvraw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", msvscore);
	  printf("P-value:              %g\n",        P);
	  printf("GMSV raw score:       %.2f nats\n", graw);
	  printf("GSMV per-seq score:   %.2f bits\n", gscore);
	  printf("GSMV 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;
}
Ejemplo n.º 17
0
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_STOPWATCH *w	= esl_stopwatch_Create();
	ESL_RANDOMNESS*r	= esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
	ESL_ALPHABET*abc	= NULL;
	P7_HMMFILE	*hfp	= NULL;
	P7_HMM		*hmm	= NULL;
	P7_BG		*bg		= NULL;
	P7_PROFILE	*gm1, *gm2;
	int			L		= esl_opt_GetInteger(go, "-L");
	int			N		= esl_opt_GetInteger(go, "-N") / SSE16_NVALS;
	int			MaxPart	= esl_opt_GetInteger(go, "-M");
	int			NROUNDS	= esl_opt_GetInteger(go, "-R");
   	int			check	= esl_opt_GetBoolean(go, "-c");
	__m128		resdata[10];
	int			i, j;
	float		*sc1 	= (float*) resdata;
	ESL_SQFILE   *sqfp	= NULL;
	DATA_COPS16 *dcops;
	struct timeb tbstart, tbend;
	int sumlengths = 0;
	float* results = NULL;

	srand(time(NULL));
	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);
	gm1 = p7_profile_Create(hmm->M, abc);
	gm2 = p7_profile_Create(hmm->M, abc);
	p7_ProfileConfig(hmm, bg, gm1, L, p7_UNILOCAL);
	p7_ProfileConfig(hmm, bg, gm2, L, p7_UNILOCAL);

	dcops = p7_ViterbiCOPSw_Create(gm1);
	p7_ViterbiCOPSW_Setup(dcops, L+100, MaxPart); // use max L
	dcops->L = L;

    int dbsize = SSE16_NVALS*N;
	SEQ **seqsdb= calloc(dbsize+1, sizeof(SEQ*));
	int equallength = 1;

	if (esl_sqfile_OpenDigital(abc, seqfile, eslSQFILE_FASTA, NULL, &sqfp) == eslOK)
	{	// Use Sequence file
		ESL_SQ* sq = esl_sq_CreateDigital(abc);
        int maxseqs, len=0;
        
        if (esl_opt_IsDefault(go, "-N"))    // N not specified in cmdline
            maxseqs = INT_MAX;   // no limit
        else
            maxseqs = SSE16_NVALS*N;      // use cmdline limit

		for (j = 0; j < maxseqs && esl_sqio_Read(sqfp, sq) == eslOK; j++)
		{
		 	if (equallength && sq->n != len && j > 0)
                equallength = 0;
               
			len = sq->n;
			if (j > dbsize)
			{	seqsdb = realloc(seqsdb, 2*(dbsize+1)*sizeof(SEQ*));
				dbsize *= 2;
			}
            
			ESL_DSQ* dsq = sq->dsq;
			seqsdb[j] = malloc(sizeof(SEQ));
			seqsdb[j]->length = len;
			seqsdb[j]->seq = malloc((len+4)*sizeof(ESL_DSQ));
			memcpy(seqsdb[j]->seq, dsq, len+2);
			sumlengths += len;
			esl_sq_Reuse(sq);
		}
		N = j/SSE16_NVALS;
	}
    else	// Not found database. Generate random sequences
        for (i = 0; i < N; i++)
			for (j = 0; j < SSE16_NVALS; j++)
			{
				int len = L; // - rand()%1000;
				seqsdb[i*SSE16_NVALS+j] = malloc(sizeof(SEQ));
				seqsdb[i*SSE16_NVALS+j]->seq = malloc(len+4);
				seqsdb[i*SSE16_NVALS+j]->length = len;
				esl_rsq_xfIID(r, bg->f, abc->K, len, seqsdb[i*SSE16_NVALS+j]->seq);
				sumlengths += len;
			}

   	printf("Viterbi COPS Word with %d threads, model %s. ModelLen: %d, #Segms: %d, SeqL.: %d, #seqs: %d, Partition: %d, #parts: %d\n",
			NTHREADS, hmmfile, gm1->M, (int) ceil(gm1->M/SSE16_NVALS), L, SSE16_NVALS*N*NROUNDS, dcops->partition, dcops->Npartitions);
            
/*	// No. of partitions computed without full parallelism ( == no. of threads active while some are idle)
	int Niters_part	= dcops->Npartitions % NTHREADS;
	// No. of Model lines that could be computed but are wasted by idle threads waiting on the end
	int Nwasted_threads	= dcops->partition * ((NTHREADS-Niters_part) % NTHREADS);
	// No. of lines in the last partition that go beyond M. It's wasted comp time by a single thread
	int Nwasted_leftover= (dcops->partition - gm1->M % dcops->partition) % dcops->partition;
	// Total number of wasted lines
	int wastedcomp = Nwasted_threads + Nwasted_leftover;
	// Total number of lines computed and waited for
	int totalcomp = wastedcomp + gm1->M; // same as: roundtop(gm1->M, dcops->partition * NTHREADS);
	printf("Total Comp Lines: %d | Wasted Comp Lines: %d\n", totalcomp, wastedcomp);
*/

   	if (check) results = (float*) alloc_m128_aligned64((N+1)*2);

	ftime(&tbstart);
    
	if (!equallength)
	{	// Sort sequences by length
		qsort(seqsdb, N*SSE16_NVALS, sizeof(SEQ*), compare_seqs);
	}

	for (j = 0; j < NROUNDS; j++) 
        for (i = 0; i < N; i++)
        {
        //	if (i % 1000 == 0) printf("Seq %d\n", i);

            p7_ViterbiCOPSw_run(dcops, seqsdb+i*SSE16_NVALS, sc1);

         	if (check) memcpy(results+i*SSE16_NVALS, sc1, 32);	// 32 bytes indeed! SSE16_NVALS floats
        }
        
	ftime(&tbend);

	double secs = TIMEDIFF(tbstart,tbend);
	w->elapsed = w->user = secs;
	esl_stopwatch_Display(stdout, w, "# Opt CPU time: ");
	double compmillioncells = NROUNDS * (double) sumlengths * (double) hmm->M * 1e-6;
	printf("# %.0fM cells in %.1f Mc/s\n", compmillioncells, compmillioncells / secs);

	if (check)
    {   P7_OPROFILE *om = p7_oprofile_Create(hmm->M, gm1->abc);
		p7_oprofile_Convert(gm1, om);
		P7_OMX		*ox	= p7_omx_Create(hmm->M, 0, 0);
		printf("Compare results against base version\n");

        for (i = 0; i < N; i++)
        {
            int maxll = 0; float sc2;
            for (j = 0; j < SSE16_NVALS; j++)
                if (maxll < seqsdb[i*SSE16_NVALS+j]->length)
                    maxll = seqsdb[i*SSE16_NVALS+j]->length;

            p7_oprofile_ReconfigRestLength(om, maxll);
    //      p7_ReconfigLength(gm2, maxll);	// emulate the lock-step inter-sequence reconfigs

            for (j = 0; j < SSE16_NVALS; j++)
            {
    //			p7_ReconfigLength(gm2, seqsdb[i*SSE16_NVALS+j]->length);
    //			p7_Viterbi_unilocal(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc3);
    //			p7_Viterbi_unilocal_word(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, gm2, &sc2);

    //			p7_oprofile_ReconfigLength(om, seqsdb[i*SSE16_NVALS+j]->length);
                p7_ViterbiFilter(seqsdb[i*SSE16_NVALS+j]->seq, seqsdb[i*SSE16_NVALS+j]->length, om, ox, &sc2);
   				sc2 += 1.0;	// -2.0nat optimization, Local to Unilocal mode		
  
                if (fabs(results[i*SSE16_NVALS+j] - sc2) > 0.0001)
                {	printf("Seq %d Len %4d: %f - %f\tdiff: %f\n", i*SSE16_NVALS+j, seqsdb[i*SSE16_NVALS+j]->length, 
							results[i*SSE16_NVALS+j], sc2, fabs(results[i*SSE16_NVALS+j] - sc2));
                }
            }
        }
    }
    
	return 0;
}
Ejemplo n.º 18
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng     = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  P7_ANCHORS    *anch     = p7_anchors_Create();
  P7_ANCHORHASH  *ah      = p7_anchorhash_Create();
  P7_ENVELOPES   *env     = p7_envelopes_Create();
  P7_REFMX       *rxf     = NULL;
  P7_REFMX       *rxd     = NULL;
  P7_REFMX       *afu     = NULL;
  P7_REFMX       *afd     = NULL;
  P7_REFMX       *apu     = NULL;
  P7_REFMX       *apd     = NULL;
  P7_TRACE       *tr      = NULL;
  float          *wrk     = NULL;
  P7_MPAS_PARAMS  prm;
  P7_MPAS_STATS   stats;
  float           fsc, vsc, asc, asc_b;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);
 
  /* Open sequence file */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
 
  /* Read one sequence */
  status = esl_sqio_Read(sqfp, sq);
  if      (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));     
  else if (status != eslOK)      p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);
  esl_sqfile_Close(sqfp);

  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);
  p7_profile_Config(gm, hmm, bg);

  /* Set the profile and null model's target length models */
  p7_bg_SetLength     (bg, sq->n);
  p7_profile_SetLength(gm, sq->n);

  /* Allocate DP matrices and tracebacks */
  rxf = p7_refmx_Create(gm->M, sq->n);
  rxd = p7_refmx_Create(gm->M, sq->n);
  tr  = p7_trace_Create();
  afu = p7_refmx_Create(gm->M, sq->n);
  afd = p7_refmx_Create(gm->M, sq->n);

  /* First pass analysis */
  p7_ReferenceViterbi (sq->dsq, sq->n, gm, rxf,  tr, &vsc);
  p7_ReferenceForward (sq->dsq, sq->n, gm, rxf,      &fsc);
  p7_ReferenceBackward(sq->dsq, sq->n, gm, rxd, NULL);   
  p7_ReferenceDecoding(sq->dsq, sq->n, gm, rxf, rxd, rxd);   

  /* Customize MPAS parameters if you want; these are the defaults. */
  prm.max_iterations = 1000;
  prm.loss_threshold = 0.001;
  prm.nmax_sampling  = FALSE;
  prm.be_verbose     = FALSE;

  /* MPAS algorithm gets us an anchor set */
  p7_reference_Anchors(rng, sq->dsq, sq->n, gm, rxf, rxd, tr, &wrk, ah,
		       afu, afd, anch, &asc, &prm, &stats);

  
  //printf("# ASC Forward UP:\n");    p7_refmx_Dump(stdout, afu);
  //printf("# ASC Forward DOWN:\n"); p7_refmx_Dump(stdout, afd);

  /* We no longer need rxf and rxd. 
   * Use their space for apu/apd pair, which will briefly
   * hold ASC Backward matrices, then get used for ASC Decoding.
   */
  apu = rxf; p7_refmx_Reuse(apu);
  apd = rxd; p7_refmx_Reuse(apd);

  p7_ReferenceASCBackward(sq->dsq, sq->n, gm, anch->a, anch->D, apu, apd, &asc_b);
  
  //printf("# Backward score (raw, nats): %.2f\n", asc_b);
  //printf("# ASC Backward UP:\n");   p7_refmx_Dump(stdout, apu);
  //printf("# ASC Backward DOWN:\n"); p7_refmx_Dump(stdout, apd);

  /* ASC Decoding takes afu/afd and abu/abd as input;
   * overwrites abu/abd with decoding matrices
   */
  p7_ReferenceASCDecoding(sq->dsq, sq->n, gm, anch->a, anch->D, afu, afd, apu, apd, apu, apd);

  //printf("# ASC Decoding UP matrix:\n");  p7_refmx_Dump(stdout, apu);
  //printf("# ASC Decoding DOWN:\n");       p7_refmx_Dump(stdout, apu);


  /* Envelope calculation needs to get four matrices:
   * ASC Decoding pair, apu/apd, and it will leave these constant;
   * ASC Forward pair,  afu/afd, and it will overwrite these.
   */
  p7_reference_Envelopes(sq->dsq, sq->n, gm, anch->a, anch->D, apu, apd, afu, afd, env);

  p7_envelopes_Dump(stdout, env);

  p7_envelopes_Destroy(env);
  p7_anchorhash_Destroy(ah);
  p7_anchors_Destroy(anch);
  if (wrk) free(wrk);
  p7_trace_Destroy(tr);
  p7_refmx_Destroy(afd);
  p7_refmx_Destroy(afu);
  p7_refmx_Destroy(rxd);
  p7_refmx_Destroy(rxf);
  esl_sq_Destroy(sq);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 19
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go       = NULL;	                /* application configuration       */
  char           *seqfile  = NULL;	                /* sequence file name              */
  char           *maskfile = NULL;	                /* mask coordinate file name       */
  int             infmt    = eslSQFILE_UNKNOWN;         /* format code for seqfile         */
  int             outfmt   = eslSQFILE_FASTA;           /* format code for output seqs     */
  ESL_SQFILE     *sqfp     = NULL;                      /* open sequence file              */
  ESL_FILEPARSER *maskefp  = NULL;	                /* open mask coord file            */
  FILE           *ofp      = NULL;	                /* output stream for masked seqs   */
  char           *source   = NULL;			/* name of current seq to mask     */
  char           *p1, *p2;				/* pointers used in parsing        */
  int64_t         start, end;				/* start, end coord for masking    */
  int64_t         i, j, pos;				/* coords in a sequence            */
  int64_t         overmask;				/* # of extra residues to mask     */
  ESL_SQ         *sq       = esl_sq_Create();		/* current sequence                */
  int             do_fetching;
  int             do_lowercase;
  int             maskchar;
  int             status;		                /* easel return code               */


  /****************************************************************************
   * Parse command line
   ****************************************************************************/

  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
  if (esl_opt_VerifyConfig(go)               != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n",       go->errbuf);
  if (esl_opt_GetBoolean(go, "-h") )                   cmdline_help   (argv[0], go);
  if (esl_opt_ArgNumber(go) != 2)                      cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");        

  do_fetching  = esl_opt_GetBoolean(go, "-R");
  do_lowercase = esl_opt_GetBoolean(go, "-l");
  overmask     = (esl_opt_IsOn(go, "-x") ? esl_opt_GetInteger(go, "-x") : 0);
  maskchar     = (esl_opt_IsOn(go, "-m") ? esl_opt_GetChar(go, "-m")    : 'X');

  seqfile  = esl_opt_GetArg(go, 1);
  maskfile = esl_opt_GetArg(go, 2);

  /* Open the <seqfile>: text mode, not digital */
  if (esl_opt_GetString(go, "--informat") != NULL) {
    infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
    if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a valid input sequence file format for --informat"); 
  }
  status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
  if      (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n",     seqfile);
  else if (status == eslEFORMAT)   cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
  else if (status == eslEINVAL)    cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
  else if (status != eslOK)        cmdline_failure(argv[0], "Open failed, code %d.\n", status);

  if(do_fetching)
  {
    status = esl_sqfile_OpenSSI(sqfp, NULL);
    if      (status == eslEFORMAT)   cmdline_failure(argv[0], "SSI index is in incorrect format\n");
    else if (status == eslERANGE)    cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
    else if (status != eslOK)        cmdline_failure(argv[0], "Failed to open SSI index\n");
  }

  /* Open the <maskfile> */
  if (esl_fileparser_Open(maskfile, NULL, &maskefp) != eslOK) 
    cmdline_failure(argv[0], "Failed to open mask coordinate file %s\n", maskfile);
  esl_fileparser_SetCommentChar(maskefp, '#');

  /* Open the output file, if any */
  if (esl_opt_GetString(go, "-o") != NULL)
    {
      if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
	cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
    }
  else ofp = stdout;

  
  /****************************************************************************
   * Main loop over lines in <maskfile>
   ****************************************************************************/

  /* Read one data line at a time from the <maskfile>; 
   * parse into data fields <seqname> <start> <end> 
   */
  while (esl_fileparser_NextLine(maskefp) == eslOK)
    {
      /* First field is sequence name */
      if (esl_fileparser_GetTokenOnLine(maskefp, &source,  NULL) != eslOK)
	esl_fatal("Failed to read source seq name on line %d of file %s\n", maskefp->linenumber, maskfile);

      /* Get the sequence */
      if (do_fetching)
	{  /* If the <seqfile> is SSI indexed, try to reposition it and read <source> seq by random access */
	  status = esl_sqio_Fetch(sqfp, source, sq);
	  if      (status == eslENOTFOUND) esl_fatal("seq %s not found in SSI index for file %s\n", source, sqfp->filename);
	  else if (status == eslEINVAL)    esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->filename);
	  else if (status == eslEFORMAT)   esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));     
	  else if (status != eslOK)        esl_fatal("Unexpected failure in fetching %s from file %s\n", source, sqfp->filename);
	}
      else 
	{ /* else, assume we're reading sequentially; <sqfile> and <maskfile> have seqs in same order */
	  status = esl_sqio_Read(sqfp, sq);
	  if      (status == eslEOF)      esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->filename, source);
	  else if (status == eslEFORMAT)  esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
	  else if (status != eslOK)       esl_fatal("Unexpected error reading sequence file %s\n", sqfp->filename);
	  
	  if ((strcmp(sq->name, source) != 0) && (strcmp(sq->acc, source) != 0))
	    esl_fatal("Sequences in <sqfile> and <maskfile> aren't in same order; try -R");
	}
      
      /* If we're masking by lowercase, first make sure everything's uppercase */
      if (do_lowercase)
	for (pos = 0; pos < sq->n; pos++)
	  if (isalpha(sq->seq[pos]))
	    sq->seq[pos] = toupper(sq->seq[pos]);

      /* Next two fields are <start>, <end> for the masking  */
      /* possible future extension: wrap loop around this, enable multiple masked regions */
      if (esl_fileparser_GetTokenOnLine(maskefp, &p1, NULL) != eslOK)
	esl_fatal("Failed to read start coord on line %d of file %s\n", maskefp->linenumber, maskfile);
      start = strtoll(p1, &p2, 0) - 1;

      if (esl_fileparser_GetTokenOnLine(maskefp, &p2, NULL) != eslOK) 
	esl_fatal("Failed to read end coord on line %d of file %s\n", maskefp->linenumber, maskfile);
      end   = strtoll(p2, &p1, 0) - 1;

      /* Do the masking */
      if (esl_opt_GetBoolean(go, "-r")) /* Reverse masking */
	{ /* leave start..end unmasked; mask prefix 0..start-1, end+1..L-1 */
	  i = 0;
	  j = ESL_MIN(sq->n-1, start - 1 + overmask);
	  for (pos = i; pos <= j; pos++)
	    if (isalpha(sq->seq[pos])) 
	      sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
	  
	  i = ESL_MAX(0, end + 1 - overmask);
	  j = sq->n-1;
	  for (pos = i; pos <= j; pos++)
	    if (isalpha(sq->seq[pos])) 
	      sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
	}
      else
	{  /* normal: mask start..end */
	  i = ESL_MAX(0,       start - overmask);
	  j = ESL_MIN(sq->n-1, end   + overmask);
	  for (pos = i; pos <= j; pos++)
	    if (isalpha(sq->seq[pos])) 
	      sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
	}

      esl_sqio_Write(ofp, sq, outfmt, FALSE);
      esl_sq_Reuse(sq);
    }

  esl_sq_Destroy(sq);
  esl_fileparser_Close(maskefp);
  esl_sqfile_Close(sqfp);
  esl_getopts_Destroy(go);
  if (ofp != stdout) fclose(ofp);
  return 0;
}
Ejemplo n.º 20
0
int
main(int argc, char **argv)
{
    char          *cmfile;
    ESL_ALPHABET  *abc;
    char          *seqfile;
    ESL_SQFILE    *sqfp;
    int            format;
    CM_FILE       *cmfp;
    CM_t          *cm;
    ESL_SQ        *seq;
    float          sc, rev_sc;
    Parsetree_t   *tr;
    Fancyali_t    *fali;
    Fancyali_t    *rev_fali;

    int do_local;

    /* int status;    */
    /* char *optname; */
    /* char *optarg; */
    int   optind;

    int status;
    char errbuf[eslERRBUFSIZE];

    cmfile = seqfile = NULL;
    abc = NULL;
    sqfp = NULL;
    cmfp = NULL;
    cm = NULL;
    seq = NULL;
    tr = NULL;
    fali = NULL;
    rev_fali = NULL;
    format = eslSQFILE_UNKNOWN;
    do_local = TRUE;

    /* Should process options, but for now assume none and set optind */
    optind = 1;

    if ( argc - optind != 2 ) cm_Die("Incorrect number of arguments\n");
    cmfile = argv[optind++];
    seqfile = argv[optind++];

    if((status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf)) != eslOK)
        cm_Die("Failed to open covariance model save file\n");
    if ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK)
        cm_Die("Failed to read a CM from cm file\n");
    if (cm == NULL)
        cm_Die("CM file empty?\n");
    cm_file_Close(cmfp);

    if ( esl_sqfile_Open(seqfile, format, NULL, &sqfp) != eslOK )
        cm_Die("Failed to open sequence database file\n");

    if (do_local) cm->config_opts |= CM_CONFIG_LOCAL;

    if((status = cm_Configure(cm, errbuf, -1)) != eslOK) cm_Die(errbuf);
    /*SetMarginalScores_reproduce_bug_i27(cm);*/

    seq = esl_sq_Create();
    while ( esl_sqio_Read(sqfp, seq) == eslOK )
    {
        if (seq->n == 0) continue;

        int i0 = 1;
        int j0 = seq->n;

        if (seq->dsq == NULL)
            esl_sq_Digitize(abc, seq);
        sc = TrCYK_DnC(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
        /* sc = TrCYK_Inside(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, FALSE, &tr); */
        fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons, seq->dsq, FALSE, NULL);
        /* float sc, struct_sc;
         * ParsetreeScore(cm, NULL, NULL, tr, seq->dsq, FALSE, &sc, &struct_sc, NULL, NULL, NULL);
         * printf("Parsetree score: %.4f\n", sc);
         * ParsetreeDump(stdout, tr, cm, seq->dsq);
         */
        FreeParsetree(tr);

        revcomp(abc, seq, seq);
        rev_sc = TrCYK_DnC(cm,seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
        rev_fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons,seq->dsq, FALSE, NULL);
        /*ParsetreeDump(stdout, tr, cm, seq->dsq);*/
        FreeParsetree(tr);

        if (sc > rev_sc)
        {
            printf("sequence: %s\n", seq->name);
            printf("score:    %.2f\n",sc);
            PrintFancyAli(stdout, fali, 0, FALSE, FALSE, 60);
        }
        else
        {
            printf("sequence: %s (reversed)\n", seq->name);
            printf("score:    %.2f\n",rev_sc);
            PrintFancyAli(stdout, fali, seq->n, TRUE, FALSE, 60);
        }

        FreeFancyAli(fali);
        FreeFancyAli(rev_fali);

        esl_sq_Destroy(seq);
        seq = esl_sq_Create();

    }
    esl_sq_Destroy(seq);

    FreeCM(cm);
    esl_sqfile_Close(sqfp);

    return EXIT_SUCCESS;
}
Ejemplo n.º 21
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  P7_TRACE       *tr      = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  char            errbuf[eslERRBUFSIZE];
  float           fsc, bsc, vsc;
  float           accscore;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);
 
  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
  esl_sqfile_Close(sqfp);
 
  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL); /* multihit local: H3 default */
  
  /* Allocations */
  gx1 = p7_gmx_Create(gm->M, sq->n);
  gx2 = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_CreateWithPP();
  p7_FLogsumInit();

  /* Run Forward, Backward; do OA fill and trace */
  p7_GForward (sq->dsq, sq->n, gm, gx1, &fsc);
  p7_GBackward(sq->dsq, sq->n, gm, gx2, &bsc);
  p7_GDecoding(gm, gx1, gx2, gx2);                   /* <gx2> is now the posterior decoding matrix */
  p7_GOptimalAccuracy(gm, gx2, gx1, &accscore);	     /* <gx1> is now the OA matrix */
  p7_GOATrace(gm, gx2, gx1, tr);

  if (esl_opt_GetBoolean(go, "-d")) p7_gmx_Dump(stdout, gx2, p7_DEFAULT);
  if (esl_opt_GetBoolean(go, "-m")) p7_gmx_Dump(stdout, gx1, p7_DEFAULT);

  p7_trace_Dump(stdout, tr, gm, sq->dsq);
  if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace fails validation:\n%s\n", errbuf);

  printf("fwd = %.4f nats\n", fsc);
  printf("bck = %.4f nats\n", bsc);
  printf("acc = %.4f (%.2f%%)\n", accscore, accscore * 100. / (float) sq->n);

  p7_trace_Reuse(tr);

  p7_GViterbi(sq->dsq, sq->n, gm, gx1, &vsc);
  p7_GTrace  (sq->dsq, sq->n, gm, gx1, tr);
  p7_trace_SetPP(tr, gx2);
  p7_trace_Dump(stdout, tr, gm, sq->dsq);

  printf("vit = %.4f nats\n", vsc);
  printf("acc = %.4f\n", p7_trace_GetExpectedAccuracy(tr));

  /* Cleanup */
  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx1);
  p7_gmx_Destroy(gx2);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 22
0
/* multifetch:
 * given a file containing lines with one name or key per line;
 * parse the file line-by-line;
 * if we have an SSI index available, retrieve the seqs by key
 * as we see each line;
 * else, without an SSI index, store the keys in a hash, then
 * read the entire seq file in a single pass, outputting seqs
 * that are in our keylist. 
 * 
 * Note that with an SSI index, you get the seqs in the order they
 * appear in the <keyfile>, but without an SSI index, you get seqs in
 * the order they occur in the seq file.
 */
static void
multifetch(ESL_GETOPTS *go, FILE *ofp, char *keyfile, ESL_SQFILE *sqfp)
{
  ESL_KEYHASH    *keys   = esl_keyhash_Create();
  ESL_FILEPARSER *efp    = NULL;
  int             nseq   = 0;
  int             nkeys  = 0;
  char           *key;
  int             keylen;
  int             keyidx;
  int             status;

  
  if (esl_fileparser_Open(keyfile, NULL, &efp) != eslOK)  esl_fatal("Failed to open key file %s\n", keyfile);
  esl_fileparser_SetCommentChar(efp, '#');

  while (esl_fileparser_NextLine(efp) == eslOK)
    {
      if (esl_fileparser_GetTokenOnLine(efp, &key, &keylen) != eslOK)
	esl_fatal("Failed to read seq name on line %d of file %s\n", efp->linenumber, keyfile);
      
      status = esl_keyhash_Store(keys, key, keylen, &keyidx);
      if (status == eslEDUP) esl_fatal("seq key %s occurs more than once in file %s\n", key, keyfile);
	
      /* if we have an SSI index, just fetch them as we go. */
      if (sqfp->data.ascii.ssi != NULL) { onefetch(go, ofp, key, sqfp);  nseq++; }
      nkeys++;
    }

  /* If we don't have an SSI index, we haven't fetched anything yet; do it now. */
  if (sqfp->data.ascii.ssi == NULL) 
    {
      ESL_SQ *sq     = esl_sq_Create();

      while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
	{
	  if ( (sq->name[0] != '\0' && esl_keyhash_Lookup(keys, sq->name, -1, NULL) == eslOK) ||
	       (sq->acc[0]  != '\0' && esl_keyhash_Lookup(keys, sq->acc,  -1, NULL) == eslOK))
	    {
	      if (esl_opt_GetBoolean(go, "-r") )
		if (esl_sq_ReverseComplement(sq) != eslOK) 
		  esl_fatal("Failed to reverse complement %s\n", sq->name);
	      esl_sqio_Write(ofp, sq, eslSQFILE_FASTA, FALSE);
	      nseq++;
	    }
	  esl_sq_Reuse(sq);
	}
      if      (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
					       sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
      else if (status != eslEOF)     esl_fatal("Unexpected error %d reading sequence file %s",
					       status, sqfp->filename);
      esl_sq_Destroy(sq);
    }
  
  if (nkeys != nseq) esl_fatal("Tried to retrieve %d keys, but only retrieved %d sequences\n", nkeys, nseq);

  if (ofp != stdout) printf("\nRetrieved %d sequences.\n", nseq);

  esl_keyhash_Destroy(keys);
  esl_fileparser_Close(efp);
  return;
}