profillic-hmmcopytransitions.cpp

/* hmmstat: display summary statistics for an HMM database.
 * 
 * Example:
 *  ./hmmstat Pfam
 *  
 * SRE, Thu May 24 11:18:20 2007
 * SVN $Id: hmmstat.c 3152 2010-02-07 22:55:22Z eddys $
 */
extern "C" {
#include "p7_config.h"
}

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>

extern "C" {
#include "easel.h"
#include "esl_getopts.h"
#include "esl_vectorops.h"

#include "hmmer.h"
}

/////////////// For profillic-hmmer //////////////////////////////////
#include "profillic-hmmer.hpp"
//#include "profillic-p7_builder.hpp"

/// Updated notices:
#define PROFILLIC_HMMER_VERSION "1.0a"
#define PROFILLIC_HMMER_DATE "July 2011"
#define PROFILLIC_HMMER_COPYRIGHT "Copyright (C) 2011 Paul T. Edlefsen, Fred Hutchinson Cancer Research Center."
#define PROFILLIC_HMMER_URL "http://galosh.org/"

/// Modified from hmmer.c p7_banner(..):
/* Version info - set once for whole package in configure.ac
 */
/*****************************************************************
 * 1. Miscellaneous functions for H3
 *****************************************************************/

/* Function:  p7_banner()
 * Synopsis:  print standard HMMER application output header
 * Incept:    SRE, Wed May 23 10:45:53 2007 [Janelia]
 *
 * Purpose:   Print the standard HMMER command line application banner
 *            to <fp>, constructing it from <progname> (the name of the
 *            program) and a short one-line description <banner>.
 *            For example, 
 *            <p7_banner(stdout, "hmmsim", "collect profile HMM score distributions");>
 *            might result in:
 *            
 *            \begin{cchunk}
 *            # hmmsim :: collect profile HMM score distributions
 *            # HMMER 3.0 (May 2007)
 *            # Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus
 *            # Freely licensed under the Janelia Software License.
 *            # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 *            \end{cchunk}
 *              
 *            <progname> would typically be an application's
 *            <argv[0]>, rather than a fixed string. This allows the
 *            program to be renamed, or called under different names
 *            via symlinks. Any path in the <progname> is discarded;
 *            for instance, if <progname> is "/usr/local/bin/hmmsim",
 *            "hmmsim" is used as the program name.
 *            
 * Note:    
 *    Needs to pick up preprocessor #define's from p7_config.h,
 *    as set by ./configure:
 *            
 *    symbol          example
 *    ------          ----------------
 *    HMMER_VERSION   "3.0"
 *    HMMER_DATE      "May 2007"
 *    HMMER_COPYRIGHT "Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus"
 *    HMMER_LICENSE   "Freely licensed under the Janelia Software License."
 *
 * Returns:   (void)
 */
void
profillic_p7_banner(FILE *fp, char *progname, char *banner)
{
  char *appname = NULL;

  if (esl_FileTail(progname, FALSE, &appname) != eslOK) appname = progname;

  fprintf(fp, "# %s :: %s\n", appname, banner);
  fprintf(fp, "# profillic-hmmer %s (%s); %s\n", PROFILLIC_HMMER_VERSION, PROFILLIC_HMMER_DATE, PROFILLIC_HMMER_URL);
  fprintf(fp, "# %s\n", PROFILLIC_HMMER_COPYRIGHT);
  fprintf(fp, "# HMMER %s (%s); %s\n", HMMER_VERSION, HMMER_DATE, HMMER_URL);
  fprintf(fp, "# %s\n", HMMER_COPYRIGHT);
  fprintf(fp, "# %s\n", HMMER_LICENSE);
  fprintf(fp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n");

  if (appname != NULL) free(appname);
  return;
}
/////////////// End profillic-hmmer //////////////////////////////////

static ESL_OPTIONS options[] = {
  /* name           type      default  env  range     toggles   reqs   incomp  help   docgroup*/
  { "-h",        eslARG_NONE,   FALSE, NULL, NULL,      NULL,  NULL, NULL, "show brief help on version and usage",            0 },
  {  0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
};

static char usage[]  = "[-options] <input hmmfile for emissions> <input hmmfile for transitions> <output hmmfile>";
static char banner[] = "create a hybrid of two HMMs with emissions from one, averaged transitions from the other";

int
main(int argc, char **argv)
{
  int status;
  ESL_GETOPTS     *go	   = NULL;      /* command line processing                   */
  ESL_ALPHABET    *abc     = NULL;
  char            *hmmfile = NULL;
  char            *transhmmfile = NULL;
  char            *outhmmfile = NULL;
  P7_HMMFILE      *hfp     = NULL;
  P7_HMMFILE      *transhfp     = NULL;
  FILE         *outhmmfp;          /* HMM output file handle                  */
  P7_HMM          *hmm     = NULL;
  P7_HMM          *transhmm     = NULL;
  P7_BG           *bg      = NULL;
  int              nhmm;	
  double           x;
  float            KL;

  float average_internal_transitions[ p7H_NTRANSITIONS ];
  int k;

  char        errmsg[eslERRBUFSIZE];

  /* Process the command line options.
   */
  go = esl_getopts_Create(options);
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK || 
      esl_opt_VerifyConfig(go)               != eslOK)
    {
      printf("Failed to parse command line: %s\n", go->errbuf);
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      profillic_p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      puts("\nwhere options are:");
      esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=docgroup, 2 = indentation; 80=textwidth*/
      exit(0);
    }
  if (esl_opt_ArgNumber(go) != 3) 
    {
      puts("Incorrect number of command line arguments.");
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  if ((hmmfile = esl_opt_GetArg(go, 1)) == NULL) 
    {
      puts("Failed to read <input hmmfile for emissions> argument from command line.");
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  if ((transhmmfile = esl_opt_GetArg(go, 2)) == NULL) 
    {
      puts("Failed to read <input hmmfile for transitions> argument from command line.");
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  if ((outhmmfile = esl_opt_GetArg(go, 3)) == NULL) 
    {
      puts("Failed to read <output hmmfile> argument from command line.");
      esl_usage(stdout, argv[0], usage);
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  profillic_p7_banner(stdout, argv[0], banner);
  
  /* Initializations: open the input HMM file (for emissions) for reading
   */
  status = p7_hmmfile_Open(hmmfile, NULL, &hfp);
  if      (status == eslENOTFOUND) p7_Fail("Failed to open HMM file %s for reading.\n",                   hmmfile);
  else if (status == eslEFORMAT)   p7_Fail("File %s does not appear to be in a recognized HMM format.\n", hmmfile);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n",       status, hmmfile);  

  /* Initializations: open the input HMM file (for transitions) for reading
   */
  status = p7_hmmfile_Open(transhmmfile, NULL, &transhfp);
  if      (status == eslENOTFOUND) p7_Fail("Failed to open HMM file %s for reading.\n",                   transhmmfile);
  else if (status == eslEFORMAT)   p7_Fail("File %s does not appear to be in a recognized HMM format.\n", transhmmfile);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n",       status, transhmmfile);  

  /* Initializations: open the output HMM file for writing
   */
  if ((outhmmfp = fopen(outhmmfile, "w")) == NULL) ESL_FAIL(status, errmsg, "Failed to open HMM file %s for writing", outhmmfile);

  /* Main body: read HMMs one at a time, print one line of stats
   */
  printf("#\n");
  printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s\n", "idx",  "name",                 "accession",    "nseq",     "eff_nseq", "M",      "relent", "info",   "p relE", "compKL");
  printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s\n", "----", "--------------------", "------------", "--------", "--------", "------", "------", "------", "------", "------");

  nhmm = 0;
  if ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF) 
    {
      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 if (status != eslOK)        esl_fatal("Unexpected error in reading HMMs from %s",   hmmfile);
      nhmm++;

      status = p7_hmmfile_Read(transhfp, &abc, &transhmm);

      if      (status == eslEOD)       esl_fatal("read failed, HMM file %s may be truncated?", transhmmfile);
      else if (status == eslEFORMAT)   esl_fatal("bad file format in HMM file %s",             transhmmfile);
      else if (status == eslEINCOMPAT) esl_fatal("HMM file %s contains different alphabets",   transhmmfile);
      else if (status == eslEOF)       esl_fatal("read failed, no HMM in file %s may be truncated?", transhmmfile);
      else if (status != eslOK)        esl_fatal("Unexpected error in reading HMMs from %s",   transhmmfile);

      if (bg == NULL) bg = p7_bg_Create(abc);

      // First get the average of the transitions from transhmm.
      esl_vec_FSet(average_internal_transitions, p7H_NTRANSITIONS, 0.);
      for( k = 1; k < transhmm->M; k++ ) {
        esl_vec_FAdd(average_internal_transitions, transhmm->t[k], p7H_NTRANSITIONS);
      }
      // Match transitions
      esl_vec_FNorm(average_internal_transitions, 3);
      // Insert transitions
      esl_vec_FNorm(average_internal_transitions + 3, 2);
      // Delete transitions
      esl_vec_FNorm(average_internal_transitions + 5, 2);

      // Ok now set them in the other hmm.
      for( k = 1; k < hmm->M; k++ ) {
        esl_vec_FCopy( average_internal_transitions, p7H_NTRANSITIONS, hmm->t[k] );
      }

      // Also copy the transitions from the first and last positions (which are non-internal so don't get averaged).
        esl_vec_FCopy( transhmm->t[0], p7H_NTRANSITIONS, hmm->t[0] );
        esl_vec_FCopy( transhmm->t[ transhmm->M ], p7H_NTRANSITIONS, hmm->t[ hmm->M ] );

      if ((status = p7_hmm_Validate(hmm, errmsg, 0.0001))       != eslOK) return status;
      if ((status = p7_hmmfile_WriteASCII(outhmmfp, -1, hmm)) != eslOK) ESL_FAIL(status, errmsg, "HMM save failed");
  
      p7_MeanPositionRelativeEntropy(hmm, bg, &x); 
      p7_hmm_CompositionKLDist(hmm, bg, &KL, NULL);

      printf("%-6d %-20s %-12s %8d %8.2f %6d %6.2f %6.2f %6.2f %6.2f\n",
	     nhmm,
	     hmm->name,
	     hmm->acc == NULL ? "-" : hmm->acc,
	     hmm->nseq,
	     hmm->eff_nseq,
	     hmm->M,
	     p7_MeanMatchRelativeEntropy(hmm, bg),
	     p7_MeanMatchInfo(hmm, bg),
	     x,
	     KL);

	     /*	     p7_MeanForwardScore(hmm, bg)); */

      p7_hmm_Destroy(hmm);
    }

  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  p7_hmmfile_Close(hfp);
  p7_hmmfile_Close(transhfp);
  if (outhmmfp != NULL) fclose(outhmmfp);
 esl_getopts_Destroy(go);
  exit(0);
}