コード例 #1
0
ファイル: evalues.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;

  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);

  esl_stopwatch_Start(w);
  while (N--)
    { /*                cfg   rng   bg    gm    om  */
      p7_Calibrate(hmm, NULL, NULL, NULL, NULL, NULL);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #2
0
int
main(int argc, char **argv)
{
    ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
    char           *hmmfile = esl_opt_GetArg(go, 1);
    ESL_STOPWATCH  *w       = esl_stopwatch_Create();
    ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
    ESL_ALPHABET   *abc     = NULL;
    P7_HMMFILE     *hfp     = NULL;
    P7_HMM         *hmm     = NULL;
    P7_BG          *bg      = NULL;
    P7_PROFILE     *gm      = NULL;
    P7_GMX         *gx1     = NULL;
    P7_GMX         *gx2     = NULL;
    int             L       = esl_opt_GetInteger(go, "-L");
    int             N       = esl_opt_GetInteger(go, "-N");
    ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
    float           null2[p7_MAXCODE];
    int             i;
    float           fsc, bsc;
    double          Mcs;

    if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
    if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

    bg = p7_bg_Create(abc);
    p7_bg_SetLength(bg, L);
    gm = p7_profile_Create(hmm->M, abc);
    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
    gx1 = p7_gmx_Create(gm->M, L);
    gx2 = p7_gmx_Create(gm->M, L);

    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
    p7_GForward (dsq, L, gm, gx1, &fsc);
    p7_GBackward(dsq, L, gm, gx2, &bsc);
    p7_GDecoding(gm, gx1, gx2, gx2);

    esl_stopwatch_Start(w);
    for (i = 0; i < N; i++)
        p7_GNull2_ByExpectation(gm, gx2, null2);
    esl_stopwatch_Stop(w);

    Mcs  = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
    esl_stopwatch_Display(stdout, w, "# CPU time: ");
    printf("# M    = %d\n", gm->M);
    printf("# %.1f Mc/s\n", Mcs);

    free(dsq);
    p7_gmx_Destroy(gx1);
    p7_gmx_Destroy(gx2);
    p7_profile_Destroy(gm);
    p7_bg_Destroy(bg);
    p7_hmm_Destroy(hmm);
    p7_hmmfile_Close(hfp);
    esl_alphabet_Destroy(abc);
    esl_stopwatch_Destroy(w);
    esl_randomness_Destroy(r);
    esl_getopts_Destroy(go);
    return 0;
}
コード例 #3
0
ファイル: p7_bg.c プロジェクト: TuftsBCB/SMURFBuild
int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
 
  /* 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);

  bg = p7_bg_Create(abc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_bg_SetFilterByHMM(bg, hmm);
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #4
0
ファイル: hmmfetch.c プロジェクト: Denis84/EPA-WorkBench
/* Create an SSI index file for open HMM file <hfp>.
 * Both name and accession of HMMs are stored as keys.
 */
static void
create_ssi_index(ESL_GETOPTS *go, P7_HMMFILE *hfp)
{
  ESL_NEWSSI   *ns      = NULL;
  ESL_ALPHABET *abc     = NULL;
  P7_HMM       *hmm     = NULL;
  int           nhmm    = 0;
  char         *ssifile = NULL;
  uint16_t      fh;
  int           status;

  if (esl_sprintf(&ssifile, "%s.ssi", hfp->fname) != eslOK) p7_Die("esl_sprintf() failed");

  status = esl_newssi_Open(ssifile, FALSE, &ns);
  if      (status == eslENOTFOUND)   esl_fatal("failed to open SSI index %s", ssifile);
  else if (status == eslEOVERWRITE)  esl_fatal("SSI index %s already exists; delete or rename it", ssifile);
  else if (status != eslOK)          esl_fatal("failed to create a new SSI index");

  if (esl_newssi_AddFile(ns, hfp->fname, 0, &fh) != eslOK) /* 0 = format code (HMMs don't have any yet) */
    esl_fatal("Failed to add HMM file %s to new SSI index\n", hfp->fname);

  printf("Working...    "); 
  fflush(stdout);
  
  while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
    {
      if      (status == eslEOD)       p7_Fail("read failed, HMM file %s may be truncated?", hfp->fname);
      else if (status == eslEFORMAT)   p7_Fail("bad file format in HMM file %s",             hfp->fname);
      else if (status == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets",   hfp->fname);
      else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s",   hfp->fname);
      nhmm++;

      if (hmm->name == NULL)           p7_Fail("Every HMM must have a name to be indexed. Failed to find name of HMM #%d\n", nhmm);

      if (esl_newssi_AddKey(ns, hmm->name, fh, hmm->offset, 0, 0) != eslOK)
	p7_Fail("Failed to add key %s to SSI index", hmm->name);

      if (hmm->acc) {
	if (esl_newssi_AddAlias(ns, hmm->acc, hmm->name) != eslOK)
	  p7_Fail("Failed to add secondary key %s to SSI index", hmm->acc);
      }
      p7_hmm_Destroy(hmm);
    }
  
  if (esl_newssi_Write(ns) != eslOK) 
    p7_Fail("Failed to write keys to ssi file %s\n", ssifile);

  printf("done.\n");
  if (ns->nsecondary > 0) 
    printf("Indexed %d HMMs (%ld names and %ld accessions).\n", nhmm, (long) ns->nprimary, (long) ns->nsecondary);
  else 
    printf("Indexed %d HMMs (%ld names).\n", nhmm, (long) ns->nprimary);
  printf("SSI index written to file %s\n", ssifile);

  free(ssifile);
  esl_alphabet_Destroy(abc);
  esl_newssi_Close(ns);
  return;
}  
コード例 #5
0
ファイル: emit.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng     = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_TRACE       *tr      = p7_trace_Create();
  ESL_SQ         *sq      = NULL;
  char            errbuf[eslERRBUFSIZE];
  int             i;
  int             status;

  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);

  p7_hmmfile_Close(hfp);

  bg = p7_bg_Create(abc);                p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);   p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  sq = esl_sq_CreateDigital(abc);

  for (i = 0; i < N; i++)
    {
      p7_ProfileEmit(rng, hmm, gm, bg, sq, tr);
      esl_sq_FormatName(sq, "%s-sample%d", hmm->name, i);
      esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);

      if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) esl_fatal(errbuf);

      esl_sq_Reuse(sq);
      p7_trace_Reuse(tr);
    }      

  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  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;
}
コード例 #6
0
ファイル: emit.c プロジェクト: ElofssonLab/TOPCONS2
int
main(int argc, char **argv)
{
  char            *hmmfile = argv[1];  /* name of HMM file to read one HMM from   */
  ESL_ALPHABET    *abc     = NULL;     /* sequence alphabet                       */
  ESL_RANDOMNESS  *r       = NULL;     /* source of randomness                    */
  P7_HMMFILE      *hfp     = NULL;     /* open hmmfile                            */
  P7_HMM          *hmm     = NULL;     /* HMM to emit from                        */
  P7_PROFILE      *gm      = NULL;     /* profile HMM (scores)                    */
  P7_BG           *bg      = NULL;     /* null model                              */
  P7_TRACE        *tr      = NULL;     /* sampled trace                           */
  ESL_SQ          *sq      = NULL;     /* sampled digital sequence                */
  int              n       = 1000;
  int              counts[p7T_NSTATETYPES];
  int              i;
  float            sc;
  float            nullsc;
  double           bitscore;

  r  = esl_randomness_CreateFast(0);
  tr = p7_trace_Create();
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("failed to open %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("failed to read HMM");
  sq = esl_sq_CreateDigital(abc);
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);

  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);

  for (i = 0; i < n; i++) 
    {
      p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
      p7_trace_GetStateUseCounts(tr, counts);

      p7_ReconfigLength(gm, sq->n);
      p7_bg_SetLength(bg, sq->n);
      p7_trace_Score(tr, sq->dsq, gm, &sc);
      p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
      bitscore = (sc - nullsc)/ eslCONST_LOG2;

      printf("%d  %8.4f\n",
	     counts[p7T_M] + (counts[p7T_I] + counts[p7T_D])/2,
	     bitscore);
    }

  p7_profile_Destroy(gm);
  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  esl_randomness_Destroy(r);
  esl_alphabet_Destroy(abc);
  p7_hmmfile_Close(hfp);
  p7_hmm_Destroy(hmm);
  return eslOK;
} 
コード例 #7
0
ファイル: hmmfetch.c プロジェクト: Denis84/EPA-WorkBench
/* 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 HMMs by key
 * as we see each line;
 * else, without an SSI index, store the keys in a hash, then
 * read the entire HMM file in a single pass, outputting HMMs
 * that are in our keylist. 
 * 
 * Note that with an SSI index, you get the HMMs in the order they
 * appear in the <keyfile>, but without an SSI index, you get HMMs in
 * the order they occur in the HMM file.
 */
static void
multifetch(ESL_GETOPTS *go, FILE *ofp, char *keyfile, P7_HMMFILE *hfp)
{
  ESL_KEYHASH    *keys   = esl_keyhash_Create();
  ESL_FILEPARSER *efp    = NULL;
  ESL_ALPHABET   *abc    = NULL;
  P7_HMM         *hmm    = NULL;
  int             nhmm   = 0;
  char           *key;
  int             keylen;
  int             keyidx;
  int             status;
  
  if (esl_fileparser_Open(keyfile, NULL, &efp) != eslOK)  p7_Fail("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)
	p7_Fail("Failed to read HMM name on line %d of file %s\n", efp->linenumber, keyfile);
      
      status = esl_key_Store(keys, key, &keyidx);
      if (status == eslEDUP) p7_Fail("HMM key %s occurs more than once in file %s\n", key, keyfile);
	
      if (hfp->ssi != NULL) { onefetch(go, ofp, key, hfp);  nhmm++; }
    }

  if (hfp->ssi == NULL) 
    {
      while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
	{
	  if      (status == eslEOD)       p7_Fail("read failed, HMM file %s may be truncated?", hfp->fname);
	  else if (status == eslEFORMAT)   p7_Fail("bad file format in HMM file %s",             hfp->fname);
	  else if (status == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets",   hfp->fname);
	  else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s",   hfp->fname);

	  if (esl_key_Lookup(keys, hmm->name, &keyidx) == eslOK || 
	      ((hmm->acc) && esl_key_Lookup(keys, hmm->acc, &keyidx) == eslOK))
	    {
	      p7_hmmfile_WriteASCII(ofp, -1, hmm);
	      nhmm++;
	    }

	  p7_hmm_Destroy(hmm);
	}
    }
  
  if (ofp != stdout) printf("\nRetrieved %d HMMs.\n", nhmm);
  if (abc != NULL) esl_alphabet_Destroy(abc);
  esl_keyhash_Destroy(keys);
  esl_fileparser_Close(efp);
  return;
}
コード例 #8
0
ファイル: p7_oprofile.c プロジェクト: Denis84/EPA-WorkBench
int
main(int argc, char **argv)
{
  char         *hmmfile = argv[1];
  ESL_ALPHABET *abc     = NULL;
  P7_HMMFILE   *hfp     = NULL;
  P7_HMM       *hmm     = NULL;
  P7_BG        *bg      = NULL;
  P7_PROFILE   *gm      = NULL;
  P7_OPROFILE  *om1     = NULL;
  P7_OPROFILE  *om2     = NULL;
  int           status;

  char          errmsg[512];

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

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

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

  p7_oprofile_Destroy(om1);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  return eslOK;
}
コード例 #9
0
ファイル: p7_oprofile.c プロジェクト: Denis84/EPA-WorkBench
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);

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

  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #10
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  float           ftol    = 1e-4;        /* floating-point tolerance for checking parameters against expected probs or summing to 1 */
  char            errbuf[eslERRBUFSIZE];

  /* Read in one HMM; sets alphabet to the HMM's alphabet */
  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);

  /* Set up a null model */
  bg = p7_bg_Create(abc);

  /* Allocate and configure a profile from HMM and null model */
  gm = p7_profile_Create(hmm->M, abc);
  p7_profile_Config(gm, hmm, bg);
  p7_profile_SetLength(gm, 400);    /* 400 is arbitrary here; this is whatever your target seq length L is */
  
  printf("profile memory consumed: %" PRId64 " bytes\n", (int64_t) p7_profile_Sizeof(gm));

  /* Debugging tools allow dumping, validating the object */
  if (p7_profile_Validate(gm, errbuf, ftol) != eslOK) p7_Fail("profile validation failed\n  %s\n", errbuf);
  
  if (esl_opt_GetBoolean(go, "--vv"))
    p7_profile_Dump(stdout, gm);

  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #11
0
ファイル: hmmsim.c プロジェクト: EddyRivasLab/hmmer
static void
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
  P7_HMM     *hmm = NULL;     
  double     *xv  = NULL;	/* results: array of N scores */
  int        *av  = NULL;	/* optional results: array of N alignment lengths */
  char        errbuf[eslERRBUFSIZE];
  int         status;


  if ((status = init_master_cfg(go, cfg, errbuf)) != eslOK) p7_Fail(errbuf);
  if ((xv = malloc(sizeof(double) * cfg->N)) == NULL)       p7_Fail("allocation failed");
  if (esl_opt_GetBoolean(go, "-a") && 
      (av = malloc(sizeof(int)    * cfg->N)) == NULL)       p7_Fail("allocation failed");

  while ((status = p7_hmmfile_Read(cfg->hfp, &(cfg->abc), &hmm)) != eslEOF) 
    {
      if      (status == eslEOD)       p7_Fail("read failed, HMM file %s may be truncated?", cfg->hmmfile);
      else if (status == eslEFORMAT)   p7_Fail("bad file format in HMM file %s",             cfg->hmmfile);
      else if (status == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets",   cfg->hmmfile);
      else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s",   cfg->hmmfile);

      if (cfg->bg == NULL) {
        if (esl_opt_GetBoolean(go, "--bgflat")) cfg->bg = p7_bg_CreateUniform(cfg->abc);
        else                                    cfg->bg = p7_bg_Create(cfg->abc);
        p7_bg_SetLength(cfg->bg, esl_opt_GetInteger(go, "-L"));  /* set the null model background length in both master and workers. */
      }


      if (esl_opt_GetBoolean(go, "--recal")) {
        if (recalibrate_model(go, cfg, errbuf, hmm)      != eslOK) p7_Fail(errbuf);
      }
      if (process_workunit(go, cfg, errbuf, hmm, xv, av) != eslOK) p7_Fail(errbuf);
      if (output_result   (go, cfg, errbuf, hmm, xv, av) != eslOK) p7_Fail(errbuf);

      p7_hmm_Destroy(hmm);      
    }
  free(xv);
  if (av != NULL) free(av);
}
コード例 #12
0
ファイル: hmmfetch.c プロジェクト: Denis84/EPA-WorkBench
/* onefetch():
 * Given one <key> (an HMM name or accession), retrieve the corresponding HMM.
 * In SSI mode, we can do this quickly by positioning the file, then reading
 * and writing the HMM that's at that position.
 * Without an SSI index, we have to parse the HMMs sequentially 'til we find
 * the one we're after.
 */
static void
onefetch(ESL_GETOPTS *go, FILE *ofp, char *key, P7_HMMFILE *hfp)
{
  ESL_ALPHABET *abc  = NULL;
  P7_HMM       *hmm  = NULL;
  int           status;

  if (hfp->ssi != NULL)
    {
      status = p7_hmmfile_PositionByKey(hfp, key);
      if      (status == eslENOTFOUND) p7_Fail("HMM %s not found in SSI index for file %s\n", key, hfp->fname);
      else if (status == eslEFORMAT)   p7_Fail("Failed to parse SSI index for %s\n", hfp->fname);
      else if (status != eslOK)        p7_Fail("Failed to look up location of HMM %s in SSI index of file %s\n", key, hfp->fname);
    }

  while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
    {
      if      (status == eslEOD)       p7_Fail("read failed, HMM file %s may be truncated?", hfp->fname);
      else if (status == eslEFORMAT)   p7_Fail("bad file format in HMM file %s",             hfp->fname);
      else if (status == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets",   hfp->fname);
      else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s",   hfp->fname);

      if (strcmp(key, hmm->name) == 0 || (hmm->acc && strcmp(key, hmm->acc) == 0)) break;
      p7_hmm_Destroy(hmm);
      hmm = NULL;
    }
  
  if (status == eslOK) 
    {
      p7_hmmfile_WriteASCII(ofp, -1, hmm);
      p7_hmm_Destroy(hmm);
    }
  else p7_Fail("HMM %s not found in file %s\n", key, hfp->fname);

  esl_alphabet_Destroy(abc);
}
コード例 #13
0
SV* isaHMM (char *input){
  P7_HMMFILE      *hfp      = NULL;                 /* open input HMM file */
  P7_HMM          *hmm      = NULL;                 /* HMM object */
  ESL_ALPHABET    *abc      = NULL;                 /* alphabet (set from the HMM file)*/
  int             isaHMM = 1;
  int             status;
  int             cnt = 0;
  HV* hash        = newHV();
  hv_store(hash, "type", strlen("type"), newSVpv("UNK", 3), 0);

  /* read the hmm */
  if ((status = p7_hmmfile_OpenBuffer(input, strlen(input), &hfp)) != 0 ) {
    hv_store(hash, "error", strlen("error"), newSViv(status), 0);
  }else{
    hv_store(hash, "type", strlen("type"), newSVpv("HMM", 3), 0);
  }

  if(status == 0){
    /* double check that we can read the whole HMM */
    status = p7_hmmfile_Read(hfp, &abc, &hmm);
    cnt++;
    if (status != eslOK ){
      hv_store(hash, "error", strlen("error"), newSVpv("Error in HMM format",19 ), 0);
    }else{
      hv_store(hash, "alpha", strlen("alpha"), newSViv(abc->type), 0);
      hv_store(hash, "hmmpgmd", strlen("hmmpgmd"), newSVpv(input, strlen(input)), 0);
      hv_store(hash, "count", strlen("count"), newSViv(cnt), 0);
    }
  }


  if (abc != NULL) esl_alphabet_Destroy(abc);
  if(hfp != NULL) p7_hmmfile_Close(hfp);
  if(hmm != NULL) p7_hmm_Destroy(hmm);
  return newRV_noinc((SV*) hash);
}
コード例 #14
0
ファイル: hmmlogo.c プロジェクト: dboudour2002/musicHMMER
int
main(int argc, char **argv)
{
  ESL_GETOPTS  *go      = NULL;
  int i, j;
  int              status   = eslOK;
  P7_HMMFILE      *hfp      = NULL;              /* open input HMM file                             */
  P7_HMM          *hmm      = NULL;              /* one HMM query                                   */
  ESL_ALPHABET    *abc      = NULL;              /* digital alphabet                                */
  P7_BG           *bg       = NULL;

  char   errbuf[eslERRBUFSIZE];
  char* hmmfile;

  float *rel_ents  = NULL;
  float **heights  = NULL;
  float **probs    = NULL;
  float *ins_P     = NULL;
  float *ins_expL  = NULL;
  float *occupancy = NULL;


  int mode = HMMLOGO_RELENT_ALL;  //default


  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal(argv[0], "Failed to parse command line: %s\n", go->errbuf);
  if (esl_opt_VerifyConfig(go)               != eslOK) esl_fatal(argv[0], "Error in configuration: %s\n",       go->errbuf);

  if (esl_opt_GetBoolean(go, "-h") )  {
   p7_banner (stdout, argv[0], banner);
   esl_usage (stdout, argv[0], usage);
   puts("\nOptions:");
   esl_opt_DisplayHelp(stdout, go, 1, 2, 100);
   exit(0);
  }

  if (esl_opt_ArgNumber(go) != 1)                      esl_fatal(argv[0], "Incorrect number of command line arguments.\n");

  hmmfile = esl_opt_GetArg(go, 1);

  if (esl_opt_IsOn(go, "--height_relent_all"))
    mode = HMMLOGO_RELENT_ALL;
  else if (esl_opt_IsOn(go, "--height_relent_abovebg"))
    mode = HMMLOGO_RELENT_ABOVEBG;
  else if (esl_opt_IsOn(go, "--height_score"))
    mode = HMMLOGO_SCORE;
  else
    mode = HMMLOGO_RELENT_ALL;  //default

  /* Open the query profile HMM file */
  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);

  bg     = p7_bg_Create(abc);

  ESL_ALLOC(rel_ents, (hmm->M+1) * sizeof(float));
  ESL_ALLOC(heights,  (hmm->M+1) * sizeof(float*));
  ESL_ALLOC(probs,    (hmm->M+1) * sizeof(float*));

  for (i = 1; i <= hmm->M; i++) {
    ESL_ALLOC(heights[i], abc->K * sizeof(float));
    ESL_ALLOC(probs[i],   abc->K * sizeof(float));
  }

  /* residue heights */
  if (mode == HMMLOGO_RELENT_ALL) {
    printf ("max expected height = %.2f\n", hmmlogo_maxHeight(bg) );
    hmmlogo_RelativeEntropy_all(hmm, bg, rel_ents, probs, heights);
  } else if (mode == HMMLOGO_RELENT_ABOVEBG) {
    printf ("max expected height = %.2f\n", hmmlogo_maxHeight(bg) );
    hmmlogo_RelativeEntropy_above_bg(hmm, bg, rel_ents, probs, heights);
  } else if (mode == HMMLOGO_SCORE) {
    hmmlogo_ScoreHeights(hmm, bg, heights );
  }

  printf ("Residue heights\n");
  for (i = 1; i <= hmm->M; i++) {
    printf("%d: ", i);
    for (j=0; j<abc->K; j++)
      printf("%6.3f ", heights[i][j] );

    if (mode != HMMLOGO_SCORE)
      printf(" (%6.3f)", rel_ents[i]);

    printf("\n");

  }

  if (rel_ents != NULL) free(rel_ents);
  if (heights != NULL) {
    for (i = 1; i <= hmm->M; i++)
      if (heights[i] != NULL) free(heights[i]);
    free(heights);
  }


  /* indel values */
  if (! esl_opt_IsOn(go, "--no_indel")) {

    ESL_ALLOC(ins_P, (hmm->M+1) * sizeof(float));
    ESL_ALLOC(ins_expL, (hmm->M+1) * sizeof(float));
    ESL_ALLOC(occupancy, (hmm->M+1) * sizeof(float));

    hmmlogo_IndelValues(hmm, ins_P, ins_expL, occupancy);

    printf ("Indel values\n");
    for (i = 1; i <= hmm->M; i++)
      printf("%d: %6.3f %6.3f %6.3f\n", i, ins_P[i], ins_expL[i], occupancy[i] );

    free(ins_P);
    free(ins_expL);
    free(occupancy);

  }


  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  p7_bg_Destroy(bg);


  exit(0);


  ERROR:
  if (rel_ents != NULL) free(rel_ents);
  if (heights != NULL) {
    for (i = 1; i <= hmm->M; i++)
      if (heights[i] != NULL) free(heights[i]);
    free(heights);
  }
  if (hfp != NULL) p7_hmmfile_Close(hfp);
  if (abc != NULL) esl_alphabet_Destroy(abc);


  if (ins_P != NULL)     free(ins_P);
  if (ins_expL != NULL)  free(ins_expL);
  if (occupancy != NULL) free(occupancy);


}
コード例 #15
0
ファイル: optacc.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  P7_TRACE       *tr      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc, accscore;
  float           fsc_g, bsc_g, accscore_g;
  double          Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);
  tr  = p7_trace_CreateWithPP();

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);
  p7_Backward(dsq, L, om, ox1, ox2, &bsc);
  p7_Decoding(om, ox1, ox2, ox2);              

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_OptimalAccuracy(om, ox2, ox1, &accscore);

      if (! esl_opt_GetBoolean(go, "--notrace"))
	{
	  p7_OATrace(om, ox2, ox1, tr);
	  p7_trace_Reuse(tr);
	}
    }
  esl_stopwatch_Stop(w);

  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x") )
    {
      gx1 = p7_gmx_Create(gm->M, L);
      gx2 = p7_gmx_Create(gm->M, L);
      
      p7_GForward (dsq, L, gm, gx1, &fsc_g);
      p7_GBackward(dsq, L, gm, gx2, &bsc_g);
      p7_GDecoding(gm, gx1, gx2, gx2);             
      p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g);

      printf("generic:  fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc_g, bsc_g, accscore_g);
      printf("VMX:      fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc,   bsc,   accscore);

      p7_gmx_Destroy(gx1);
      p7_gmx_Destroy(gx2);
    }

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_trace_Destroy(tr);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #16
0
ファイル: evalues.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  double          lambda  = 0.0;
  double          mmu     = 0.0;
  double          vmu     = 0.0;
  double          ftau    = 0.0;
  int             Z       = esl_opt_GetInteger(go, "-Z");
  int             EmL     = esl_opt_GetInteger(go, "--EmL");
  int             EmN     = esl_opt_GetInteger(go, "--EmN");
  int             EvL     = esl_opt_GetInteger(go, "--EvL");
  int             EvN     = esl_opt_GetInteger(go, "--EvN");
  int             EfL     = esl_opt_GetInteger(go, "--EfL");
  int             EfN     = esl_opt_GetInteger(go, "--EfN");
  int             Eft     = esl_opt_GetReal   (go, "--Eft");
  int             iteration;
  int             do_msv, do_vit, do_fwd;
  int             status;

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

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

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

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

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

  p7_hmmfile_Close(hfp);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return eslOK;
}
コード例 #17
0
ファイル: viterbi_cops.c プロジェクト: ParaSky/cops
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;
}
コード例 #18
0
ファイル: vitfilter.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           sc1, sc2;
  double          base_time, bench_time, Mcs;

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsVF(om, gm);

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

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

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

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

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

  free(dsq);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #19
0
ファイル: vitfilter.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           vfraw, nullsc, vfscore;
  float           graw, gscore;
  double          P, gP;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);

  /* create default null model, then create and optimize profile */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);

  /* allocate DP matrices, both a generic and an optimized one */
  ox = p7_omx_Create(gm->M, 0, sq->n);
  gx = p7_gmx_Create(gm->M, sq->n);

  /* Useful to place and compile in for debugging: 
     p7_oprofile_Dump(stdout, om);      dumps the optimized profile
     p7_omx_SetDumpMode(ox, TRUE);      makes the fast DP algorithms dump their matrices
     p7_gmx_Dump(stdout, gx);           dumps a generic DP matrix
  */

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      p7_oprofile_ReconfigLength(om, sq->n);
      p7_ReconfigLength(gm,          sq->n);
      p7_bg_SetLength(bg,            sq->n);
      p7_omx_GrowTo(ox, om->M, 0,    sq->n); 
      p7_gmx_GrowTo(gx, gm->M,       sq->n); 

      p7_ViterbiFilter  (sq->dsq, sq->n, om, ox, &vfraw);
      p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
      vfscore = (vfraw - nullsc) / eslCONST_LOG2;
      P        = esl_gumbel_surv(vfscore,  om->evparam[p7_VMU],  om->evparam[p7_VLAMBDA]);

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

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s\t%-20s\t%9.2g\t%7.2f\t%9.2g\t%7.2f\n", sq->name, hmm->name, P, vfscore, gP, gscore);
	}
      else if (esl_opt_GetBoolean(go, "-P"))
	{ /* output suitable for direct use in profmark benchmark postprocessors: */
	  printf("%g\t%.2f\t%s\t%s\n", P, vfscore, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("vit filter raw score: %.2f nats\n", vfraw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", vfscore);
	  printf("P-value:              %g\n",        P);
	  printf("GViterbi raw score:   %.2f nats\n", graw);
	  printf("GViterbi seq score:   %.2f bits\n", gscore);
	  printf("GViterbi P-value:     %g\n",        gP);
	}
      
      esl_sq_Reuse(sq);
    }

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #20
0
ファイル: fwdback.c プロジェクト: Denis84/EPA-WorkBench
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;
}
コード例 #21
0
ファイル: modelconfig.c プロジェクト: dboudour2002/musicHMMER
int
main(int argc, char **argv)
{
  ESL_ALPHABET    *abc     = NULL;     /* sequence alphabet                       */
  ESL_GETOPTS     *go      = NULL;     /* command line processing                 */
  ESL_RANDOMNESS  *r       = NULL;     /* source of randomness                    */
  P7_HMM          *hmm     = NULL;     /* sampled HMM to emit from                */
  P7_HMM          *core    = NULL;     /* safe copy of the HMM, before config     */
  P7_BG           *bg      = NULL;     /* null model                              */
  ESL_SQ          *sq      = NULL;     /* sampled sequence                        */
  P7_TRACE        *tr      = NULL;     /* sampled trace                           */
  P7_PROFILE      *gm      = NULL;     /* profile                                 */
  int              i,j;
  int              i1,i2;
  int              k1,k2;
  int              iseq;
  FILE            *fp      = NULL;
  double           expected;

  int              do_ilocal;
  char            *hmmfile = NULL;
  int              nseq;
  int              do_swlike;
  int              do_ungapped;
  int              L;
  int              M;
  int              do_h2;
  char            *ipsfile = NULL;
  char            *kpsfile = NULL;
  ESL_DMATRIX     *imx     = NULL;
  ESL_DMATRIX     *kmx     = NULL;
  ESL_DMATRIX     *iref    = NULL; /* reference matrix: expected i distribution under ideality */
  int              Lbins;
  int              status;
  char             errbuf[eslERRBUFSIZE];
  
  /*****************************************************************
   * Parse the command line
   *****************************************************************/
  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
  if (esl_opt_VerifyConfig(go)               != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
  if (esl_opt_GetBoolean(go, "-h") == TRUE) {
    puts(usage);
    puts("\n  where options are:\n");
    esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2 = indentation; 80=textwidth*/
    return eslOK;
  }
  do_ilocal   = esl_opt_GetBoolean(go, "-i");
  hmmfile     = esl_opt_GetString (go, "-m");
  nseq        = esl_opt_GetInteger(go, "-n");
  do_swlike   = esl_opt_GetBoolean(go, "-s");
  do_ungapped = esl_opt_GetBoolean(go, "-u");
  L           = esl_opt_GetInteger(go, "-L");
  M           = esl_opt_GetInteger(go, "-M");
  do_h2       = esl_opt_GetBoolean(go, "-2");
  ipsfile     = esl_opt_GetString (go, "--ips");
  kpsfile     = esl_opt_GetString (go, "--kps");

  if (esl_opt_ArgNumber(go) != 0) {
    puts("Incorrect number of command line arguments.");
    printf("Usage: %s [options]\n", argv[0]);
    return eslFAIL;
  }

  r = esl_randomness_CreateFast(0);

  if (hmmfile != NULL)
    {	/* Read the HMM (and get alphabet from it) */
      P7_HMMFILE      *hfp     = NULL;

      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);  
    
      if ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslOK) {
	if      (status == eslEOD)       esl_fatal("read failed, HMM file %s may be truncated?", hmmfile);
	else if (status == eslEFORMAT)   esl_fatal("bad file format in HMM file %s", hmmfile);
	else if (status == eslEINCOMPAT) esl_fatal("HMM file %s contains different alphabets", hmmfile);
	else                             esl_fatal("Unexpected error in reading HMMs");
      }
      M = hmm->M;
      p7_hmmfile_Close(hfp);
    }
  else
    {			/* Or sample the HMM (create alphabet first) */
      abc = esl_alphabet_Create(eslAMINO);    
      if      (do_ungapped) p7_hmm_SampleUngapped(r, M, abc, &hmm);
      else if (do_swlike)   p7_hmm_SampleUniform (r, M, abc, 0.05, 0.5, 0.05, 0.2, &hmm); /* tmi, tii, tmd, tdd */
      else                  p7_hmm_Sample        (r, M, abc, &hmm);
    }

  Lbins = M;
  imx  = esl_dmatrix_Create(Lbins, Lbins);
  iref = esl_dmatrix_Create(Lbins, Lbins);
  kmx  = esl_dmatrix_Create(M, M);
  esl_dmatrix_SetZero(imx);
  esl_dmatrix_SetZero(iref);
  esl_dmatrix_SetZero(kmx);
  tr    = p7_trace_Create();
  sq    = esl_sq_CreateDigital(abc);
  bg    = p7_bg_Create(abc);
  core  = p7_hmm_Clone(hmm);

  if (do_h2) {
    gm = p7_profile_Create(hmm->M, abc);
    p7_H2_ProfileConfig(hmm, bg, gm, p7_UNILOCAL);
  } else {
    gm = p7_profile_Create(hmm->M, abc);
    p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
    if (p7_hmm_Validate    (hmm, NULL, 0.0001) != eslOK) esl_fatal("whoops, HMM is bad!");
    if (p7_profile_Validate(gm,  NULL, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!");
  }

  /* Sample endpoints.
   * Also sample an ideal reference distribution for i endpoints.  i
   * endpoints are prone to discretization artifacts, when emitted
   * sequences have varying lengths. Taking log odds w.r.t. an ideal
   * reference that is subject to the same discretization artifacts 
   * cancels out the effect.
   */
  for (iseq = 0; iseq < nseq; iseq++)
    {				
      if (do_ilocal) ideal_local_endpoints  (r, core,     sq, tr, Lbins, &i1, &i2, &k1, &k2);
      else           profile_local_endpoints(r, core, gm, sq, tr, Lbins, &i1, &i2, &k1, &k2);

      imx->mx[i1-1][i2-1] += 1.;
      kmx->mx[k1-1][k2-1] += 1.; 

      /* reference distribution for i */
      ideal_local_endpoints  (r, core, sq, tr, Lbins, &i1, &i2, &k1, &k2);
      iref->mx[i1-1][i2-1] += 1.;
    }


  /* Adjust both mx's to log_2(obs/exp) ratio */
  printf("Before normalization/log-odds:\n");
  printf("   i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
  printf("   k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));
  printf("iref matrix values range from %f to %f\n", dmx_upper_min(iref), dmx_upper_max(iref));

  expected = (double) nseq * 2. / (double) (M*(M+1));
  for (i = 0; i < kmx->m; i++)
    for (j = i; j < kmx->n; j++)
      kmx->mx[i][j] = log(kmx->mx[i][j] / expected) / log(2.0);

  for (i = 0; i < imx->m; i++)
    for (j = i; j < imx->m; j++)
      if (iref->mx[i][j] == 0. && imx->mx[i][j] == 0.) 
	imx->mx[i][j] = 0.;
      else if (iref->mx[i][j] == 0.)
	imx->mx[i][j] = eslINFINITY;
      else if (imx->mx[i][j] == 0.)
	imx->mx[i][j] = -eslINFINITY;
      else
	imx->mx[i][j] = log(imx->mx[i][j] / iref->mx[i][j]) / log(2.0);
  
  /* Print ps files */
  if (kpsfile != NULL) {
    if ((fp = fopen(kpsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", kpsfile);
    dmx_Visualize(fp, kmx, -4., 5.);
    fclose(fp);
  }
  if (ipsfile != NULL) {
    if ((fp = fopen(ipsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", ipsfile);
    dmx_Visualize(fp, imx, -4., 5.); 
    /* dmx_Visualize(fp, imx, dmx_upper_min(imx), dmx_upper_max(imx)); */
    fclose(fp);
  }

  printf("After normalization/log-odds:\n");
  printf("i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
  printf("k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));

  
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(core);
  p7_hmm_Destroy(hmm);
  p7_trace_Destroy(tr);
  esl_sq_Destroy(sq);
  esl_dmatrix_Destroy(imx);
  esl_dmatrix_Destroy(kmx);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return eslOK;
}
コード例 #22
0
ファイル: null2.c プロジェクト: dboudour2002/musicHMMER
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  float           null2[p7_MAXCODE];
  int             i,j,d,pos;
  int             nsamples = 200;
  float           fsc, bsc;
  double          Mcs;

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

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

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

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

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

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

      free(n2sc);
      p7_trace_Destroy(tr);
    }
  else
    {
      p7_Backward(dsq, L, om, ox1, ox2, &bsc);
      p7_Decoding(om, ox1, ox2, ox2);              

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	p7_Null2_ByExpectation(om, ox2, null2);
      esl_stopwatch_Stop(w);
    }


  Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #23
0
ファイル: generic_optacc.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_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;
}
コード例 #24
0
ファイル: fwdback.c プロジェクト: Denis84/EPA-WorkBench
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc;
  float           fsc2, bsc2;
  double          base_time, bench_time, Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  if (esl_opt_GetBoolean(go, "-P")) {
    fwd = p7_omx_Create(gm->M, 0, L);
    bck = p7_omx_Create(gm->M, 0, L);
  } else {
    fwd = p7_omx_Create(gm->M, L, L);
    bck = p7_omx_Create(gm->M, L, L);
  }
  gx  = p7_gmx_Create(gm->M, L);

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

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      if (esl_opt_GetBoolean(go, "-P")) {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_ForwardParser (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_BackwardParser(dsq, L, om, fwd, bck, &bsc);
      } else {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_Forward (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_Backward(dsq, L, om, fwd, bck, &bsc);
      }

      if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x"))
	{
	  p7_GForward (dsq, L, gm, gx, &fsc2); 
	  p7_GBackward(dsq, L, gm, gx, &bsc2); 
	  printf("%.4f %.4f %.4f %.4f\n", fsc, bsc, fsc2, bsc2);  
	}
    }
  esl_stopwatch_Stop(w);
  bench_time = w->user - base_time;
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(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_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #25
0
ファイル: generic_viterbi.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_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;
}
コード例 #26
0
ファイル: sim-alignment.c プロジェクト: EddyRivasLab/hmmer
int 
main(int argc, char **argv)
{
  ESL_GETOPTS      *go       = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  ESL_RANDOMNESS   *rng      = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET     *abc      = NULL;
  char             *ghmmfile = esl_opt_GetArg(go, 1); /* HMMs parameterized for sequence generation */
  char             *ahmmfile = esl_opt_GetArg(go, 2); /* HMMs parameterized for alignment */
  int               N        = esl_opt_GetInteger(go, "-N");
  P7_HMMFILE       *ghfp     = NULL;
  P7_HMMFILE       *ahfp     = NULL;
  P7_HMM           *ghmm     = NULL;
  P7_HMM           *ahmm     = NULL;
  P7_PROFILE       *ggm      = NULL;
  P7_PROFILE       *agm      = NULL;
  P7_OPROFILE      *aom      = NULL;
  P7_BG            *bg       = NULL;
  ESL_SQ           *sq       = NULL;
  P7_TRACE         *reftr    = p7_trace_Create();
  P7_TRACE         *testtr   = p7_trace_Create();
  P7_TRACE_METRICS *tmetrics = p7_trace_metrics_Create();
  P7_REFMX         *rmx      = p7_refmx_Create(100,100);
  //  P7_FILTERMX      *ox       = NULL;
   P7_HARDWARE *hw;
  if ((hw = p7_hardware_Create ()) == NULL)  p7_Fail("Couldn't get HW information data structure"); 
  P7_SPARSEMASK    *sm       = p7_sparsemask_Create(100, 100, hw->simd);
  P7_SPARSEMX      *sxv      = p7_sparsemx_Create(NULL);
  int               idx;
  char              errbuf[eslERRBUFSIZE];
  int               status;
  
  p7_Init();

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

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

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

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

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

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

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

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

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

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

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

	  p7_trace_metrics(reftr, testtr, tmetrics);

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

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

  p7_hmmfile_Close(ghfp);  
  p7_hmmfile_Close(ahfp);
  //  p7_filtermx_Destroy(ox);
  p7_sparsemask_Destroy(sm);
  p7_sparsemx_Destroy(sxv);
  p7_refmx_Destroy(rmx);
  p7_trace_metrics_Destroy(tmetrics);
  p7_trace_Destroy(testtr);
  p7_trace_Destroy(reftr);
  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
}
コード例 #27
0
ファイル: generic_viterbi.c プロジェクト: TuftsBCB/SMURFBuild
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_GMX         *gx      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           sc;
  double          base_time, bench_time, Mcs;

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
  gx = p7_gmx_Create(gm->M, L);

  /* Baseline time. */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  esl_stopwatch_Stop(w);
  base_time = w->user;

  /* Benchmark time. */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      p7_GViterbi     (dsq, L, gm, gx, &sc);
    }
  esl_stopwatch_Stop(w);
  bench_time = w->user - base_time;
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);


  free(dsq);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
コード例 #28
0
ファイル: hmmpgmd2msa.c プロジェクト: dboudour2002/musicHMMER
/* Test driver. As written, requires files that won't be released with
 * the distribution. So it should be replaced with a tighter test.
 */
int
main(int argc, char **argv) {
  ESL_MSA           *msa   = NULL;
  ESL_SQ            *qsq   = NULL;
  ESL_SQFILE        *qfp   = NULL;              /* open qfile                                      */
  P7_HMMFILE        *hfp   = NULL;              /* open input HMM file                             */
  P7_HMM            *hmm   = NULL;              /* one HMM query                                   */
  ESL_ALPHABET      *abc   = NULL;              /* digital alphabet                                */
  FILE              *fp    = NULL;              /* open file containing the HMMPGMD data */
  void              *data  = NULL;              /* pointer to the full data stream built as if from hmmdmstr */
  long size = 0;

  char   errbuf[eslERRBUFSIZE];
  int status;
  
  float* statsOut;
  int x;
  //char *badstring = "asdlfuhasdfuhasdfhasdfhaslidhflaishdfliasuhdfliasuhdfliasudfh";

  char *hmm_file = "esl_align.hmm";
  char *fa_file  = "esl_align.fa";
  char *dat_file = "esl_align.big.bin";

  if (argc > 1 ) {
    ESL_ALLOC(hmm_file, sizeof(char) * (strlen(argv[1])+1) );
    strcpy(hmm_file, argv[1]);
  }
  if (argc > 2 ) {
    ESL_ALLOC(dat_file, sizeof(char) * (strlen(argv[2])+1) );
    strcpy(dat_file, argv[2]);
  }
  if (argc > 3 ) {
    ESL_ALLOC(fa_file, sizeof(char) * (strlen(argv[3])+1) );
    strcpy(fa_file, argv[3]);
  }

  printf("hmmpgmd2msa:\nhmm: %s\nfa:  %s\ndat: %s\n", hmm_file, fa_file, dat_file);


  /* read the hmm */
  if ( (status = p7_hmmfile_OpenE(hmm_file, NULL, &hfp, errbuf)) != 0 ) goto ERROR;
  if ( (status = p7_hmmfile_Read(hfp, &abc, &hmm)) != 0 ) goto ERROR;

  /* read the query sequence */
  //if ( (status = esl_sqfile_OpenDigital(abc, fa_file, eslSQFILE_UNKNOWN, NULL, &qfp)) != 0) goto ERROR;
  //qsq = esl_sq_CreateDigital(abc);
  //if ( (status = esl_sqio_Read(qfp, qsq)) != eslOK)  goto ERROR;

  //printf("sequence length %d\n", qsq->n);

  /* get stats for the hmmd data */

  if ( (fp = fopen(dat_file, "rb")) == NULL ) goto ERROR;

  fseek (fp , 0 , SEEK_END);
  size = ftell (fp);
  rewind (fp);
  ESL_ALLOC(data, size);
  fread(data, size, 1, fp);

  status = hmmpgmd2stats(data, hmm, &statsOut);
  //status = hmmpgmd2msa(data, hmm, qsq, NULL,0, NULL, 0, &msa);

  for(x = 0; x < hmm->M*3; x++)
  {
    if(statsOut[x] > 1)
    {
      printf("problem x: %d %f\n", x, statsOut[x]);
    }
  }

  for(x = 0; x < hmm->M; x++)
  {
    printf("%d", ((int)(10*statsOut[x])>=10)?9:(int)(10*statsOut[x]));
  }
  printf("\n");
  for(x = hmm->M; x < hmm->M*2; x++)
  {
    printf("%d", ((int)(10*statsOut[x])>=10)?9:(int)(10*statsOut[x]));
  }
  printf("\n");
  for(x = hmm->M*2; x < hmm->M*3; x++)
  {
    printf("%d", ((int)(10*statsOut[x])>=10)?9:(int)(10*statsOut[x]));
  }
  printf("\n");

  if (status != eslOK) goto ERROR;

  //eslx_msafile_Write(stdout, msa, eslMSAFILE_STOCKHOLM);

  exit(0);

ERROR:
  printf ("fail!\n");
  exit(1);

}
コード例 #29
0
ファイル: viterbi_stream-counter.c プロジェクト: ParaSky/cops
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		= 2000;		// esl_opt_GetInteger(go, "-L");
	int			N		= esl_opt_GetInteger(go, "-N");
	int			MaxPart	= esl_opt_GetInteger(go, "-M");
	__m128		resdata[10];
	float		*sc1 	= (float*)	(resdata+0);	// uses 1 __m128s
	ESL_DSQ		*dsq	= NULL;
	int			i, j;
	ESL_SQFILE   *sqfp	= NULL;
	DATA_STREAM *dstream;
	struct timeb tbstart, tbend;
	int sumlengths = 0;

	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);

	dstream = p7_ViterbiStream_Create(gm1);
	p7_ViterbiStream_Setup(dstream, L+100, MaxPart); // use max L
	dstream->L = L;

	// No. of partitions computed without full parallelism ( == no. of threads active while some are idle)
	int Niters_part	= dstream->Npartitions % NTHREADS;
	// No. of Model lines that could be computed but are wasted by idle threads waiting on the end
	int Nwasted_threads	= dstream->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= (dstream->partition - gm1->M % dstream->partition) % dstream->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, dstream->partition * NTHREADS);

	printf("Viterbi Stream Word with %d Threads, model %s: Modelsize %d, #Segms: %d, SeqL: %d, Nseqs %d, Part %d, #Parts %d\n",
			NTHREADS, hmmfile, gm1->M, (int) ceil(gm1->M/8.0), L, 8*N, dstream->partition, dstream->Npartitions);
	printf("Total Comp Lines: %d | Wasted Comp Lines: %d\n", totalcomp, wastedcomp);

	// for ViterbiFilter
	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);

	dsq_cmp_t **seqsdb= calloc(8*N+64, sizeof(dsq_cmp_t*));
if(0)
{	ESL_SQ* sq = esl_sq_CreateDigital(abc);
	if (esl_sqfile_OpenDigital(abc, seqfile, eslSQFILE_FASTA, NULL, &sqfp) != eslOK)
	{	p7_Fail("Failed to open sequence file\n");	return -1; }

	for (j = 0; j < 8*N; j++)
	{
		int res = esl_sqio_Read(sqfp, sq);
		if (res != eslOK) { printf("ATENCAO: faltam sequencias\n"); break; }
		int len = sq->n;
		dsq = sq->dsq;
		seqsdb[j] = malloc(sizeof(dsq_cmp_t));
		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);
	}

	ftime(&tbstart);
	N = j/8;
	printf("N = %d\n", N);
		// Sort sequences by length
	qsort(seqsdb, N*8, sizeof(dsq_cmp_t*), compare_seqs);
}
else if(0)
	for (i = 0; i < N; i++)
	{
		for (j = 0; j < 8; j++)
		{
			int len = L - rand()%1000;
			seqsdb[i*8+j] = malloc(sizeof(dsq_cmp_t));
			seqsdb[i*8+j]->seq = malloc(len+4);
			seqsdb[i*8+j]->length = len;
		    esl_rsq_xfIID(r, bg->f, abc->K, len, seqsdb[i*8+j]->seq);
			sumlengths += len;
		}
	}

//	double sumerrors = 0;
	float* results = (float*) alloc_m128_aligned64(N*2+2);	
	ftime(&tbstart);

	for (j = 0; j < N; j++)
	for (i = 0; i < N; i++)
	{
	//	if (i % 10000 == 0) printf("START %d\n", i);

		p7_ViterbiStream(dstream, seqsdb+i*8, sc1);

	//	memcpy(results+i*8, sc1, 32);
	}
	ftime(&tbend);

	double secs = TIMEDIFF(tbstart,tbend);
//	printf("Qsort time: %6.3f | Viterbi time: %6.3f\n", TIMEDIFF(tbqsort,tbstart), secs);
	w->elapsed = w->user = secs;
	esl_stopwatch_Display(stdout, w, "# Opt CPU time: ");
	printf("# %.0fM cells in %.1f Mc/s\n", (sumlengths * (double) gm1->M) / 1e6, (sumlengths * (double) gm1->M * 1e-6) / secs);

if(0)	// compare results against base version
	for (i = 0; i < 1000 && i < N; i++)
	{
		int maxll = 0; float sc2;
		for (j = 0; j < 8; j++)
			if (maxll < seqsdb[i*8+j]->length)
				maxll = seqsdb[i*8+j]->length;

//		for (j = 0; j < 8; j++)	printf("%d ", seqsdb[i*8+j]->length); printf("\n");
//		if (i % 10 == 0) printf("i %d\n", i);

		p7_oprofile_ReconfigRestLength(om, maxll);
		p7_ReconfigLength(gm2, maxll);	// fazer Reconfig aqui para emular compl o VitStream

		for (j = 0; j < 8; j++)
		{
//			p7_ReconfigLength(gm2, seqsdb[i*8+j]->length);
//			p7_Viterbi_unilocal(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, gm2, &sc3);
//			p7_Viterbi_unilocal_word(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, gm2, &sc2);

//			p7_oprofile_ReconfigLength(om, seqsdb[i*8+j]->length);
			p7_ViterbiFilter(seqsdb[i*8+j]->seq, seqsdb[i*8+j]->length, om, ox, &sc2);
			
			//sumerrors += fabs(sc1[j]- sc2);
			if (fabs(results[i*8+j] - sc2) > 0.00001)
			{	printf("%3d-%d L %4d: VS %f d %f\t| Base SerI %f\n", i, j, seqsdb[i*8+j]->length, 
						results[i*8+j], fabs(results[i*8+j] - sc2), sc2);
				getc(stdin);
			}
		}
	}

	return 0;
}
コード例 #30
0
ファイル: generic_optacc.c プロジェクト: ElofssonLab/TOPCONS2
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  P7_TRACE       *tr      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc, accscore;
  double          Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
  gx1 = p7_gmx_Create(gm->M, L);
  gx2 = p7_gmx_Create(gm->M, L);
  tr  = p7_trace_CreateWithPP();

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_GForward (dsq, L, gm, gx1, &fsc);
  p7_GBackward(dsq, L, gm, gx2, &bsc);
  p7_GDecoding(gm, gx1, gx2, gx2);                   /* <gx2> is now the posterior decoding matrix */

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_GOptimalAccuracy(gm, gx2, gx1, &accscore);	     /* <gx1> is now the OA matrix */

      if (! esl_opt_GetBoolean(go, "--notrace"))
	{
	  p7_GOATrace(gm, gx2, gx1, tr);
	  p7_trace_Reuse(tr);
	}
    }
  esl_stopwatch_Stop(w);
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n", gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx1);
  p7_gmx_Destroy(gx2);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}