示例#1
0
/* Function:  p7_CreateDefaultApp()
 * Synopsis:  Initialize a small/simple/standard HMMER application
 * Incept:    SRE, Thu Oct 28 15:03:21 2010 [Janelia]
 *
 * Purpose:   Identical to <esl_getopts_CreateDefaultApp()>, but 
 *            specialized for HMMER. See documentation in 
 *            <easel/esl_getopts.c>.
 *
 * Args:      options - array of <ESL_OPTIONS> structures for getopts
 *            nargs   - number of cmd line arguments expected (excl. of cmdname)
 *            argc    - <argc> from main()
 *            argv    - <argv> from main()
 *            banner  - optional one-line description of program (or NULL)
 *            usage   - optional one-line usage hint (or NULL)
 *
 * Returns:   ptr to new <ESL_GETOPTS> object.
 * 
 *            On command line errors, this routine prints an error
 *            message to <stderr> then calls <exit(1)> to halt
 *            execution with abnormal (1) status.
 *            
 *            If the standard <-h> option is seen, the routine prints
 *            the help page (using the data in the <options> structure),
 *            then calls <exit(0)> to exit with normal (0) status.
 *            
 * Xref:      J7/3
 * 
 * Note:      The only difference between this and esl_getopts_CreateDefaultApp()
 *            is to call p7_banner() instead of esl_banner(), to get HMMER
 *            versioning info into the header. There ought to be a better way
 *            (perhaps using PACKAGE_* define's instead of HMMER_* vs. EASEL_*
 *            define's in esl_banner(), thus removing the need for p7_banner).
 */
ESL_GETOPTS *
p7_CreateDefaultApp(ESL_OPTIONS *options, int nargs, int argc, char **argv, char *banner, char *usage)
{
  ESL_GETOPTS *go = NULL;

  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);
      if (usage != NULL) 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) 
    {
      if (banner != NULL) p7_banner(stdout, argv[0], banner);
      if (usage  != NULL) esl_usage (stdout, argv[0], usage);
      puts("\nOptions:");
      esl_opt_DisplayHelp(stdout, go, 0, 2, 80);
      exit(0);
    }
  if (esl_opt_ArgNumber(go) != nargs) 
    {
      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);
    }
  return go;
}
示例#2
0
static int
output_header(FILE *ofp, const ESL_GETOPTS *go)
{
  p7_banner(ofp, go->argv[0], banner);


  if (esl_opt_IsUsed(go, "--eval2score"))  {
     if (  fprintf(ofp, "# show score required to reach E-value:      %.2g\n",        esl_opt_GetReal(go, "-E"))     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }
  if (esl_opt_IsUsed(go, "--score2eval"))  {
     if (  fprintf(ofp,   "# show E-value corresponding to score:     %.2g\n",        esl_opt_GetReal(go, "-S"))     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }

  if (esl_opt_IsUsed(go, "--eval2score") || esl_opt_IsUsed(go, "--score2eval"))  {
     if (esl_opt_IsUsed(go, "--baseZ") ) {
       if (  fprintf(ofp, "# using base count (search both strands):  %d Mb\n",     esl_opt_GetInteger(go, "--baseZ")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
     } else if (esl_opt_IsUsed(go, "--baseZ1") ) {
       if (  fprintf(ofp, "# using base count (search single strand): %d Mb\n",     esl_opt_GetInteger(go, "--baseZ1")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
     } else {
       if (  fprintf(ofp, "# using database sequence count:           %d\n",        esl_opt_GetInteger(go, "-Z")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
     }
  }

  if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n")               < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  return eslOK;
}
示例#3
0
static int
output_header(const ESL_GETOPTS *go, const struct cfg_s *cfg)
{
  if (cfg->my_rank > 0)  return eslOK;
  /*  if (! cfg->be_verbose) return eslOK; */
  p7_banner(cfg->ofp, go->argv[0], banner);
  
  fprintf(cfg->ofp, "# input alignment file:             %s\n", cfg->alifile);
  fprintf(cfg->ofp, "# output HMM file:                  %s\n", cfg->hmmfile);

  if (esl_opt_IsUsed(go, "-n"))          fprintf(cfg->ofp, "# name (the single) HMM:            %s\n",   esl_opt_GetString(go, "-n"));
  if (esl_opt_IsUsed(go, "-o"))          fprintf(cfg->ofp, "# output directed to file:          %s\n",   esl_opt_GetString(go, "-o"));
  if (esl_opt_IsUsed(go, "-O"))          fprintf(cfg->ofp, "# processed alignment resaved to:   %s\n",   esl_opt_GetString(go, "-O"));
  if (esl_opt_IsUsed(go, "--amino"))     fprintf(cfg->ofp, "# input alignment is asserted as:   protein\n");
  if (esl_opt_IsUsed(go, "--dna"))       fprintf(cfg->ofp, "# input alignment is asserted as:   DNA\n");
  if (esl_opt_IsUsed(go, "--rna"))       fprintf(cfg->ofp, "# input alignment is asserted as:   RNA\n");
  if (esl_opt_IsUsed(go, "--fast"))      fprintf(cfg->ofp, "# model architecture construction:  fast/heuristic\n");
  if (esl_opt_IsUsed(go, "--hand"))      fprintf(cfg->ofp, "# model architecture construction:  hand-specified by RF annotation\n");
  if (esl_opt_IsUsed(go, "--symfrac"))   fprintf(cfg->ofp, "# sym fraction for model structure: %.3f\n", esl_opt_GetReal(go, "--symfrac"));
  if (esl_opt_IsUsed(go, "--fragthresh"))fprintf(cfg->ofp, "# seq called fragment if < xL    :  %.3f\n", esl_opt_GetReal(go, "--fragthresh"));
  if (esl_opt_IsUsed(go, "--wpb"))       fprintf(cfg->ofp, "# relative weighting scheme:        Henikoff PB\n");
  if (esl_opt_IsUsed(go, "--wgsc"))      fprintf(cfg->ofp, "# relative weighting scheme:        G/S/C\n");
  if (esl_opt_IsUsed(go, "--wblosum"))   fprintf(cfg->ofp, "# relative weighting scheme:        BLOSUM filter\n");
  if (esl_opt_IsUsed(go, "--wnone"))     fprintf(cfg->ofp, "# relative weighting scheme:        none\n");
  if (esl_opt_IsUsed(go, "--wid"))       fprintf(cfg->ofp, "# frac id cutoff for BLOSUM wgts:   %f\n",   esl_opt_GetReal(go, "--wid"));
  if (esl_opt_IsUsed(go, "--eent"))      fprintf(cfg->ofp, "# effective seq number scheme:      entropy weighting\n");
  if (esl_opt_IsUsed(go, "--eclust"))    fprintf(cfg->ofp, "# effective seq number scheme:      single linkage clusters\n");
  if (esl_opt_IsUsed(go, "--enone"))     fprintf(cfg->ofp, "# effective seq number scheme:      none\n");
  if (esl_opt_IsUsed(go, "--eset"))      fprintf(cfg->ofp, "# effective seq number:             set to %f\n", esl_opt_GetReal(go, "--eset"));
  if (esl_opt_IsUsed(go, "--ere") )      fprintf(cfg->ofp, "# minimum rel entropy target:       %f bits\n",   esl_opt_GetReal(go, "--ere"));
  if (esl_opt_IsUsed(go, "--esigma") )   fprintf(cfg->ofp, "# entropy target sigma parameter:   %f bits\n",   esl_opt_GetReal(go, "--esigma"));
  if (esl_opt_IsUsed(go, "--eid") )      fprintf(cfg->ofp, "# frac id cutoff for --eclust:      %f\n",        esl_opt_GetReal(go, "--eid"));
  if (esl_opt_IsUsed(go, "--EmL") )      fprintf(cfg->ofp, "# seq length for MSV Gumbel mu fit: %d\n",        esl_opt_GetInteger(go, "--EmL"));
  if (esl_opt_IsUsed(go, "--EmN") )      fprintf(cfg->ofp, "# seq number for MSV Gumbel mu fit: %d\n",        esl_opt_GetInteger(go, "--EmN"));
  if (esl_opt_IsUsed(go, "--EvL") )      fprintf(cfg->ofp, "# seq length for Vit Gumbel mu fit: %d\n",        esl_opt_GetInteger(go, "--EvL"));
  if (esl_opt_IsUsed(go, "--EvN") )      fprintf(cfg->ofp, "# seq number for Vit Gumbel mu fit: %d\n",        esl_opt_GetInteger(go, "--EvN"));
  if (esl_opt_IsUsed(go, "--EfL") )      fprintf(cfg->ofp, "# seq length for Fwd exp tau fit:   %d\n",        esl_opt_GetInteger(go, "--EfL"));
  if (esl_opt_IsUsed(go, "--EfN") )      fprintf(cfg->ofp, "# seq number for Fwd exp tau fit:   %d\n",        esl_opt_GetInteger(go, "--EfN"));
  if (esl_opt_IsUsed(go, "--Eft") )      fprintf(cfg->ofp, "# tail mass for Fwd exp tau fit:    %f\n",        esl_opt_GetReal(go, "--Eft"));
#ifdef HMMER_THREADS
  if (esl_opt_IsUsed(go, "--cpu"))       fprintf(cfg->ofp, "# number of worker threads:         %d\n", esl_opt_GetInteger(go, "--cpu"));  
#endif
#ifdef HAVE_MPI
  if (esl_opt_IsUsed(go, "--mpi") )      fprintf(cfg->ofp, "# parallelization mode:             MPI\n");
#endif
  if (esl_opt_IsUsed(go, "--seed"))  {
    if (esl_opt_GetInteger(go, "--seed") == 0) fprintf(cfg->ofp,"# random number seed:               one-time arbitrary\n");
    else                                       fprintf(cfg->ofp,"# random number seed set to:        %d\n", esl_opt_GetInteger(go, "--seed"));
  }
  if (esl_opt_IsUsed(go, "--laplace") )  fprintf(cfg->ofp, "# prior:                            Laplace +1\n");
  fprintf(cfg->ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n");

  return eslOK;
}
示例#4
0
static int
output_header(FILE *ofp, ESL_GETOPTS *go, char *hmmfile, char *seqfile)
{
  p7_banner(ofp, go->argv[0], banner);
  
  if (fprintf(ofp, "# query sequence file:             %s\n", seqfile)                                                                              < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# target HMM database:             %s\n", hmmfile)                                                                              < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-o")          && fprintf(ofp, "# output directed to file:         %s\n",            esl_opt_GetString(go, "-o"))          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--tblout")    && fprintf(ofp, "# per-seq hits tabular output:     %s\n",            esl_opt_GetString(go, "--tblout"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--dfamtblout")    && fprintf(ofp, "# hits output in Dfam format:      %s\n",            esl_opt_GetString(go, "--dfamtblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--aliscoresout")  && fprintf(ofp, "# alignment scores output:         %s\n",            esl_opt_GetString(go, "--aliscoresout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "--acc")       && fprintf(ofp, "# prefer accessions over names:    yes\n")                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--noali")     && fprintf(ofp, "# show alignments in output:       no\n")                                                  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--notextw")   && fprintf(ofp, "# max ASCII text line length:      unlimited\n")                                           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--textw")     && fprintf(ofp, "# max ASCII text line length:      %d\n",            esl_opt_GetInteger(go, "--textw"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "-E")          && fprintf(ofp, "# profile reporting threshold:     E-value <= %g\n", esl_opt_GetReal(go, "-E"))            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-T")          && fprintf(ofp, "# profile reporting threshold:     score >= %g\n",   esl_opt_GetReal(go, "-T"))            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incE")      && fprintf(ofp, "# profile inclusion threshold:     E-value <= %g\n", esl_opt_GetReal(go, "--incE"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incT")      && fprintf(ofp, "# profile inclusion threshold:     score >= %g\n",   esl_opt_GetReal(go, "--incT"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_ga")    && fprintf(ofp, "# model-specific thresholding:     GA cutoffs\n")                                          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_nc")    && fprintf(ofp, "# model-specific thresholding:     NC cutoffs\n")                                          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_tc")    && fprintf(ofp, "# model-specific thresholding:     TC cutoffs\n")                                          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--max")       && fprintf(ofp, "# Max sensitivity mode:            on [all heuristic filters off]\n")                      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F1")        && fprintf(ofp, "# MSV filter P threshold:       <= %g\n",            esl_opt_GetReal(go, "--F1"))          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F2")        && fprintf(ofp, "# Vit filter P threshold:       <= %g\n",            esl_opt_GetReal(go, "--F2"))          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F3")        && fprintf(ofp, "# Fwd filter P threshold:       <= %g\n",            esl_opt_GetReal(go, "--F3"))          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--nobias")    && fprintf(ofp, "# biased composition HMM filter:   off\n")                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--B1")         && fprintf(ofp, "# biased comp MSV window len:      %d\n",             esl_opt_GetInteger(go, "--B1"))       < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--B2")         && fprintf(ofp, "# biased comp Viterbi window len:  %d\n",             esl_opt_GetInteger(go, "--B2"))       < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--B3")         && fprintf(ofp, "# biased comp Forward window len:  %d\n",             esl_opt_GetInteger(go, "--B3"))       < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");


  if (esl_opt_IsUsed(go, "--nonull2")   && fprintf(ofp, "# null2 bias corrections:          off\n")                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "--toponly")    && fprintf(ofp, "# search only top strand:          on\n")                                                  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--bottomonly") && fprintf(ofp, "# search only bottom strand:       on\n")                                                  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "-Z")          && fprintf(ofp, "# sequence search space set to:    %.0f\n",          esl_opt_GetReal(go, "-Z"))            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--seed"))  {
    if (esl_opt_GetInteger(go, "--seed")==0 && fprintf(ofp, "# random number seed:              one-time arbitrary\n")                              < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
    else if (                                  fprintf(ofp, "# random number seed set to:       %d\n",        esl_opt_GetInteger(go, "--seed"))     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }
  if (esl_opt_IsUsed(go, "--qformat")   && fprintf(ofp, "# input seqfile format asserted:   %s\n",            esl_opt_GetString(go, "--qformat"))   < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--w_beta")     && fprintf(ofp, "# window length beta value:        %g\n",             esl_opt_GetReal(go, "--w_beta"))      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--w_length")   && fprintf(ofp, "# window length :                  %d\n",             esl_opt_GetInteger(go, "--w_length")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
//  if (esl_opt_IsUsed(go, "--daemon")    && fprintf(ofp, "run as a daemon process\n")                                                                < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
#ifdef HMMER_THREADS
  if (esl_opt_IsUsed(go, "--cpu")       && fprintf(ofp, "# number of worker threads:        %d\n",            esl_opt_GetInteger(go, "--cpu"))      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");  
#endif
  if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n")                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  return eslOK;
}
示例#5
0
static void
cmdline_help(char *argv0, ESL_GETOPTS *go) 
{
  p7_banner (stdout, argv0, banner);
  esl_usage (stdout, argv0, usage);
  puts("\nBasic options:");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
  puts("\nLess common options:");
  esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
  puts("\nSequence input formats include:   FASTA, EMBL, GenBank, UniProt");
  puts("Alignment output formats include: Stockholm, Pfam, A2M, PSIBLAST\n");
  exit(0);
}
/* Function:  output_header()
 * Synopsis:  Print details of FM-index construction
 */
static int
output_header(FILE *ofp, const ESL_GETOPTS *go, char *seqfile, char *fmfile)
{
  p7_banner(ofp, go->argv[0], banner);

  if (fprintf(ofp, "# input sequence file:                     %s\n", seqfile)                                < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# output binary-formatted HMMER database:  %s\n", fmfile)                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# alphabet     :                           %s\n", esl_opt_GetString(go, "--alph"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# bin_length   :                           %d\n", esl_opt_GetInteger(go, "--bin_length")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# suffix array sample rate:                %d\n", esl_opt_GetInteger(go, "--sa_freq"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n")           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  return eslOK;
}
static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_seqfile, char **ret_fmfile)
{
  ESL_GETOPTS *go = esl_getopts_Create(options);
  int          status;

  if (esl_opt_ProcessEnvironment(go)         != eslOK)  { if (printf("Failed to process environment: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK)  { if (printf("Failed to parse command line: %s\n", go->errbuf)  < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_VerifyConfig(go)               != eslOK)  { if (printf("Failed to parse command line: %s\n", go->errbuf)  < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }

  /* help format: */
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);

      if (puts("\nBasic options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 120=textwidth*/

      if (puts("\nSpecial options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80); /* 2= group; 2 = indentation; 120=textwidth*/

      exit(0);
  }

  if (esl_opt_ArgNumber(go)                  != 2)     { if (puts("Incorrect number of command line arguments.")      < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if ((*ret_seqfile = esl_opt_GetArg(go, 1)) == NULL)  { if (puts("Failed to get <seqfile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if ((*ret_fmfile  = esl_opt_GetArg(go, 2)) == NULL)  { if (puts("Failed to get <fmfile> argument on command line")  < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }

  /* Validate any attempted use of stdin streams */
  if (esl_strcmp(*ret_seqfile, "-") == 0 && esl_strcmp(*ret_fmfile, "-") == 0) 
    { if (puts("Either <seqfile> or <fmfile> may be '-' (to read from stdin), but not both.") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }

  *ret_go = go;
  return eslOK;

 FAILURE:  /* all errors handled here are user errors, so be polite.  */
  esl_usage(stdout, argv[0], usage);
  puts("\nwhere basic options are:");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/
  printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
  esl_getopts_Destroy(go);
  exit(1);

 ERROR:
  if (go) esl_getopts_Destroy(go);
  exit(status);
}
示例#8
0
static int
output_header(FILE *ofp, const ESL_GETOPTS *go, char *hmmfile, char *seqfile)
{
  p7_banner(ofp, go->argv[0], banner);

  if (fprintf(ofp, "# query HMM file:                  %s\n", hmmfile)                                                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# target sequence database:        %s\n", seqfile)                                                                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-o")           && fprintf(ofp, "# output directed to file:         %s\n",             esl_opt_GetString(go, "-o"))           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-A")           && fprintf(ofp, "# MSA of all hits saved to file:   %s\n",             esl_opt_GetString(go, "-A"))           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--tblout")     && fprintf(ofp, "# per-seq hits tabular output:     %s\n",             esl_opt_GetString(go, "--tblout"))     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--domtblout")  && fprintf(ofp, "# per-dom hits tabular output:     %s\n",             esl_opt_GetString(go, "--domtblout"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--pfamtblout") && fprintf(ofp, "# pfam-style tabular hit output:   %s\n",             esl_opt_GetString(go, "--pfamtblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--acc")        && fprintf(ofp, "# prefer accessions over names:    yes\n")                                                   < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--noali")      && fprintf(ofp, "# show alignments in output:       no\n")                                                    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--notextw")    && fprintf(ofp, "# max ASCII text line length:      unlimited\n")                                             < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--textw")      && fprintf(ofp, "# max ASCII text line length:      %d\n",             esl_opt_GetInteger(go, "--textw"))     < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-E")           && fprintf(ofp, "# sequence reporting threshold:    E-value <= %g\n",  esl_opt_GetReal(go, "-E"))             < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-T")           && fprintf(ofp, "# sequence reporting threshold:    score >= %g\n",    esl_opt_GetReal(go, "-T"))             < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--domE")       && fprintf(ofp, "# domain reporting threshold:      E-value <= %g\n",  esl_opt_GetReal(go, "--domE"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--domT")       && fprintf(ofp, "# domain reporting threshold:      score >= %g\n",    esl_opt_GetReal(go, "--domT"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incE")       && fprintf(ofp, "# sequence inclusion threshold:    E-value <= %g\n",  esl_opt_GetReal(go, "--incE"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incT")       && fprintf(ofp, "# sequence inclusion threshold:    score >= %g\n",    esl_opt_GetReal(go, "--incT"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incdomE")    && fprintf(ofp, "# domain inclusion threshold:      E-value <= %g\n",  esl_opt_GetReal(go, "--incdomE"))      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--incdomT")    && fprintf(ofp, "# domain inclusion threshold:      score >= %g\n",    esl_opt_GetReal(go, "--incdomT"))      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_ga")     && fprintf(ofp, "# model-specific thresholding:     GA cutoffs\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_nc")     && fprintf(ofp, "# model-specific thresholding:     NC cutoffs\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--cut_tc")     && fprintf(ofp, "# model-specific thresholding:     TC cutoffs\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--max")        && fprintf(ofp, "# Max sensitivity mode:            on [all heuristic filters off]\n")                        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F1")         && fprintf(ofp, "# MSV filter P threshold:       <= %g\n",             esl_opt_GetReal(go, "--F1"))           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F2")         && fprintf(ofp, "# Vit filter P threshold:       <= %g\n",             esl_opt_GetReal(go, "--F2"))           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--F3")         && fprintf(ofp, "# Fwd filter P threshold:       <= %g\n",             esl_opt_GetReal(go, "--F3"))           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--nobias")     && fprintf(ofp, "# biased composition HMM filter:   off\n")                                                   < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--restrictdb_stkey") && fprintf(ofp, "# Restrict db to start at seq key: %s\n",            esl_opt_GetString(go, "--restrictdb_stkey"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--restrictdb_n")     && fprintf(ofp, "# Restrict db to # target seqs:    %d\n",            esl_opt_GetInteger(go, "--restrictdb_n")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--ssifile")          && fprintf(ofp, "# Override ssi file to:            %s\n",            esl_opt_GetString(go, "--ssifile"))       < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "--nonull2")    && fprintf(ofp, "# null2 bias corrections:          off\n")                                                   < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "-Z")           && fprintf(ofp, "# sequence search space set to:    %.0f\n",           esl_opt_GetReal(go, "-Z"))             < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--domZ")       && fprintf(ofp, "# domain search space set to:      %.0f\n",           esl_opt_GetReal(go, "--domZ"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--seed"))  {
    if (esl_opt_GetInteger(go, "--seed") == 0 && fprintf(ofp, "# random number seed:              one-time arbitrary\n")                               < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
    else if (                               fprintf(ofp, "# random number seed set to:       %d\n",             esl_opt_GetInteger(go, "--seed"))      < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }
  if (esl_opt_IsUsed(go, "--tformat")    && fprintf(ofp, "# targ <seqfile> format asserted:  %s\n",             esl_opt_GetString(go, "--tformat"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n")                                                    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  return eslOK;
}
示例#9
0
static void
cmdline_help(char *argv0, ESL_GETOPTS *go) 
{
  p7_banner (stdout, argv0, banner);
  esl_usage (stdout, argv0, usage);
  puts("\nCommon options are:");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
  puts("\nOptions controlling what to emit:");
  esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
  puts("\nOptions controlling emission from profiles with -p:");
  esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
  puts("\nOptions controlling fancy consensus emission with -C:");
  esl_opt_DisplayHelp(stdout, go, 4, 2, 80);
  puts("\nOther options::");
  esl_opt_DisplayHelp(stdout, go, 5, 2, 80);
  exit(0);
}
示例#10
0
static void
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_hmmfile, char **ret_alifile)
{
  ESL_GETOPTS *go = NULL;

  if ((go = esl_getopts_Create(options))     == NULL)    p7_Die("problem with options structure");
  if (esl_opt_ProcessEnvironment(go)         != eslOK) { printf("Failed to process environment: %s\n", go->errbuf); goto ERROR; }
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { printf("Failed to parse command line: %s\n",  go->errbuf); goto ERROR; }
  if (esl_opt_VerifyConfig(go)               != eslOK) { printf("Failed to parse command line: %s\n",  go->errbuf); goto ERROR; }

  /* help format: */
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      puts("\nwhere basic options are:");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
      puts("\nOptions for selecting alphabet rather than guessing it:");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
      puts("\nAlternative model construction strategies:");
      esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
      puts("\nAlternative relative sequence weighting strategies:");
      esl_opt_DisplayHelp(stdout, go, 4, 2, 80);
      puts("\nAlternate effective sequence weighting strategies:");
      esl_opt_DisplayHelp(stdout, go, 5, 2, 80);
      puts("\nControl of E-value calibration:");
      esl_opt_DisplayHelp(stdout, go, 6, 2, 80);
      puts("\nOther options:");
      esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
      exit(0);
    }

  if (esl_opt_ArgNumber(go)                  != 2)    { puts("Incorrect number of command line arguments.");      goto ERROR; }
  if ((*ret_hmmfile = esl_opt_GetArg(go, 1)) == NULL) { puts("Failed to get <hmmfile> argument on command line"); goto ERROR; }
  if ((*ret_alifile = esl_opt_GetArg(go, 2)) == NULL) { puts("Failed to get <alifile> argument on command line"); goto ERROR; }
  *ret_go = go;
  return;
  
 ERROR:  /* all errors handled here are user errors, so be polite.  */
  esl_usage(stdout, argv[0], usage);
  puts("\nwhere basic options are:");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
  printf("\nTo see more help on other available options, do %s -h\n\n", argv[0]);
  exit(1);  
}
示例#11
0
static int
output_header(const ESL_GETOPTS *go, FILE *ofp, char *alifile, char *postmsafile)
{
  p7_banner(ofp, go->argv[0], banner);

  if (fprintf(ofp, "# input alignment file:             %s\n", alifile) < 0)     ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
    if (fprintf(ofp, "# output alignment file:            %s\n", postmsafile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }

  if (esl_opt_IsUsed(go, "--alirange")   && fprintf(ofp, "# alignment range:                  %s\n",        esl_opt_GetString(go, "--alirange"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--modelrange") && fprintf(ofp, "# model range:                      %s\n",        esl_opt_GetString(go, "--modelrange"))< 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--apendmask")  && fprintf(ofp, "# add to existing mask:             [on]\n"                                            )< 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");

  if (esl_opt_IsUsed(go, "--model2ali")   && fprintf(ofp, "# ali ranges for model range:      %s\n",        esl_opt_GetString(go, "--model2ali"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--ali2model")   && fprintf(ofp, "# model ranges for ali range:      %s\n",        esl_opt_GetString(go, "--ali2model"))  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");


  if (esl_opt_IsUsed(go, "-o")           && fprintf(ofp, "# output directed to file:          %s\n",        esl_opt_GetString(go, "-o"))         < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--amino")      && fprintf(ofp, "# input alignment is asserted as:   protein\n")                                        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--dna")        && fprintf(ofp, "# input alignment is asserted as:   DNA\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--rna")        && fprintf(ofp, "# input alignment is asserted as:   RNA\n")                                            < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--fast")       && fprintf(ofp, "# model architecture construction:  fast/heuristic\n")                                 < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--hand")       && fprintf(ofp, "# model architecture construction:  hand-specified by RF annotation\n")                < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--symfrac")    && fprintf(ofp, "# sym fraction for model structure: %.3f\n",      esl_opt_GetReal(go, "--symfrac"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--fragthresh") && fprintf(ofp, "# seq called frag if L <= x*alen:   %.3f\n",      esl_opt_GetReal(go, "--fragthresh")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--wpb")        && fprintf(ofp, "# relative weighting scheme:        Henikoff PB\n")                                    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--wgsc")       && fprintf(ofp, "# relative weighting scheme:        G/S/C\n")                                          < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--wblosum")    && fprintf(ofp, "# relative weighting scheme:        BLOSUM filter\n")                                  < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--wnone")      && fprintf(ofp, "# relative weighting scheme:        none\n")                                           < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--wid")        && fprintf(ofp, "# frac id cutoff for BLOSUM wgts:   %f\n",        esl_opt_GetReal(go, "--wid"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  if (esl_opt_IsUsed(go, "--seed"))  {
    if (esl_opt_GetInteger(go, "--seed") == 0  && fprintf(ofp,"# random number seed:               one-time arbitrary\n")                        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
    else if                              (  fprintf(ofp,"# random number seed set to:        %d\n",         esl_opt_GetInteger(go, "--seed"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  }

  if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
  return eslOK;
}
示例#12
0
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);


}
示例#13
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS     *go	   = NULL;      /* command line processing                   */
  ESL_ALPHABET    *abc     = NULL;
  char            *hmmfile = NULL;
  P7_HMMFILE      *hfp     = NULL;
  P7_HMM          *hmm     = NULL;
  P7_BG           *bg      = NULL;
  int              nhmm;	
  double           x;
  float            KL;
  int              status;
  char             errbuf[eslERRBUFSIZE];
  float            nseq;

  int              do_eval2score = 0;
  int              do_score2eval = 0;
  int              z_val;
  float            e_val;
  float            s_val;

  /* 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) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      puts("\nOptions:");
      esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=docgroup, 2 = indentation; 80=textwidth*/


      exit(0);
    }
  if (esl_opt_ArgNumber(go) != 1) 
    {
      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 <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);
    }

  output_header(stdout, go);

  if ( esl_opt_IsOn(go, "--eval2score") ) {
    do_eval2score = TRUE;
    e_val         =  esl_opt_GetReal(go, "-E");
  } else if ( esl_opt_IsOn(go, "--score2eval") ) {
    do_score2eval = TRUE;
    s_val         =  esl_opt_GetReal(go, "-S");
  } else if (  esl_opt_IsUsed(go, "--baseZ") || esl_opt_IsUsed(go, "--baseZ1") || esl_opt_IsUsed(go, "-Z") ) {
    puts("The flags -Z, --baseZ, and --baseZ1 are for use with --eval2score and --score2eval.");
    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_IsUsed(go, "--baseZ") ) {
    z_val    = 1000000 * 2 * (long)(esl_opt_GetInteger(go, "--baseZ"));
  } else if (esl_opt_IsUsed(go, "--baseZ1") ) {
    z_val    = 1000000 * (long)(esl_opt_GetInteger(go, "--baseZ1"));
  } else {
    z_val    =  esl_opt_GetInteger(go, "-Z");
  }

  /* Initializations: open the 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);  

  /* 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", "idx",  "name",                 "accession",    "nseq",     "eff_nseq", "M",      "relent", "info",   "p relE", "compKL");
  if (do_eval2score)
    printf (" %6s %6.2g", "sc for", e_val);
  if (do_score2eval)
    printf (" %6s %6.2f", "E-val for", s_val);

  printf("\n");
  printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s", "----", "--------------------", "------------", "--------", "--------", "------", "------", "------", "------", "------");
  if (do_eval2score)
    printf (" %13s", "-------------");
  if (do_score2eval)
    printf (" %13s", "-------------");
  printf("\n");


  nhmm = 0;
  while ((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++;

      if ( esl_opt_IsOn(go, "--eval2score") || esl_opt_IsOn(go, "--score2eval") ) {
        if (esl_opt_IsUsed(go, "--baseZ") || esl_opt_IsUsed(go, "--baseZ1" ) ) {
          if ( hmm->abc->type != eslRNA   && hmm->abc->type != eslDNA) {
            puts("The flags --baseZ and --baseZ1 can't be used with non-nucleotide models.");
            esl_usage(stdout, argv[0], usage);
            printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
            exit(1);
          }
        } else if ( hmm->abc->type != eslAMINO  && hmm->abc->type != eslRNA && hmm->abc->type != eslDNA) {
          puts("The flags --eval2score and --score2eval can't be used with non-sequence models.");
          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_IsUsed(go, "--baseZ") ) {
        nseq = (float)z_val / (float)(hmm->max_length);
      } else if (esl_opt_IsUsed(go, "--baseZ1") ) {
        nseq = (float)z_val / (float)(hmm->max_length);
      } else {
        nseq = z_val;
      }

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

      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",
	     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);



      if ( do_eval2score )
	{
	  float sc;
	  sc = esl_exp_invsurv( e_val / nseq ,  hmm->evparam[p7_FTAU],  hmm->evparam[p7_FLAMBDA]);
	  printf("%13.2f", sc);
	}
      else  if ( do_score2eval)  
	{
	  float e;
	  e = nseq * esl_exp_surv( s_val ,  hmm->evparam[p7_FTAU],  hmm->evparam[p7_FLAMBDA]);
	  printf("%13.2g", e);
	}
      printf("\n");

      /* p7_MeanForwardScore(hmm, bg)); */
      p7_hmm_Destroy(hmm);
    }

  p7_bg_Destroy(bg);
  esl_alphabet_Destroy(abc);
  p7_hmmfile_Close(hfp);
  esl_getopts_Destroy(go);
  exit(0);
}
示例#14
0
/* process_commandline()
 * 
 * Processes the commandline, filling in fields in <cfg> and creating and returning
 * an <ESL_GETOPTS> options structure. The help page (hmmsearch -h) is formatted
 * here.
 */
static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_hmmfile, char **ret_seqfile)
{
  ESL_GETOPTS *go = esl_getopts_Create(options);
  int          status;

  if (esl_opt_ProcessEnvironment(go)         != eslOK)  { if (printf("Failed to process environment: %s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK)  { if (printf("Failed to parse command line: %s\n",  go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_VerifyConfig(go)               != eslOK)  { if (printf("Failed to parse command line: %s\n",  go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
 
  /* help format: */
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      if (puts("\nBasic options:")                                           < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/

      if (puts("\nOptions controlling output:")                              < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80); 

      if (puts("\nOptions controlling reporting thresholds:")                < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 4, 2, 80); 

      if (puts("\nOptions controlling inclusion (significance) thresholds:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 5, 2, 80); 

      if (puts("\nOptions for model-specific thresholding:")                 < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 6, 2, 80); 

      if (puts("\nOptions controlling acceleration heuristics:")             < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 7, 2, 80); 

      if (puts("\nOther expert options:")                                    < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 12, 2, 80); 
      exit(0);
    }

  if (esl_opt_ArgNumber(go)                 != 2)      { if (puts("Incorrect number of command line arguments.")      < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if ((*ret_hmmfile = esl_opt_GetArg(go, 1)) == NULL)  { if (puts("Failed to get <hmmdb> argument on command line")   < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if ((*ret_seqfile = esl_opt_GetArg(go, 2)) == NULL)  { if (puts("Failed to get <seqfile> argument on command line") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }

  /* Validate any attempted use of stdin streams */
  if (strcmp(*ret_hmmfile, "-") == 0) 
    { if (puts("nhmmscan cannot read <hmm database> from stdin stream, because it must have hmmpress'ed auxfiles") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");   goto FAILURE;  }

  *ret_go = go;
  return eslOK;
  
 FAILURE:  /* all errors handled here are user errors, so be polite.  */
  esl_usage(stdout, argv[0], usage);
  if (puts("\nwhere most common options are:")                                 < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1= group; 2 = indentation; 80=textwidth*/
  if (printf("\nTo see more help on available options, do %s -h\n\n", argv[0]) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
  esl_getopts_Destroy(go);
  exit(1);  

 ERROR:
  if (go) esl_getopts_Destroy(go);
  exit(status);
}
示例#15
0
static int
process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_alifile, char **ret_postalifile)
{
  ESL_GETOPTS *go = esl_getopts_Create(options);
  int          status;

  if (esl_opt_ProcessEnvironment(go)         != eslOK) { if (printf("Failed to process environment:\n%s\n", go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) { if (printf("Failed to parse command line:\n%s\n",  go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_VerifyConfig(go)               != eslOK) { if (printf("Failed to parse command line:\n%s\n",  go->errbuf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }

  /* help format: */
  if (esl_opt_GetBoolean(go, "-h") == TRUE) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);

      if (puts("\nBasic options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80);

      if (puts("\nMask range options (format:  --xxx 10-20,30-40 ) :") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 5, 2, 80);

      if (puts("\nOptions for selecting alphabet rather than guessing it:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80);

      if (puts("\nAlternative model construction strategies:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 3, 2, 80);

      if (puts("\nAlternative relative sequence weighting strategies:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 4, 2, 80);

      if (puts("\nOther options:") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
      esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
      exit(0);
    }

  if (esl_opt_ArgNumber(go)                  > 2)    { if (puts("Incorrect number of command line arguments.")          < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if ((*ret_alifile     = esl_opt_GetArg(go, 1)) == NULL) { if (puts("Failed to get <msafile> argument on command line")     < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
    if ((*ret_postalifile = esl_opt_GetArg(go, 2)) == NULL) { if (puts("Failed to get <postmsafile> argument on command line")     < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }
  }

  if (strcmp(*ret_alifile, "-") == 0 && ! esl_opt_IsOn(go, "--informat"))
    { if (puts("Must specify --informat to read <alifile> from stdin ('-')") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto FAILURE; }


  *ret_go = go;
  return eslOK;
  
 FAILURE:  /* all errors handled here are user errors, so be polite.  */
  esl_usage(stdout, argv[0], usage);
  puts("\nwhere basic options are:");
  esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
  printf("\nTo see more help on other available options, do:\n  %s -h\n\n", argv[0]);
  esl_getopts_Destroy(go);
  exit(1);  

 ERROR:
  if (go) esl_getopts_Destroy(go);
  exit(status);
}
示例#16
0
int
main(int argc, char **argv)
{
  ESL_GETOPTS     *go	   = NULL;   
  ESL_STOPWATCH   *w       = esl_stopwatch_Create();
  struct cfg_s     cfg;

  p7_Init();

  /* Process 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) 
    {
      p7_banner(stdout, argv[0], banner);
      esl_usage(stdout, argv[0], usage);
      puts("\nCommon options:");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1=docgroup, 2 = indentation; 80=textwidth*/
      puts("\nChoice of score type :");
      esl_opt_DisplayHelp(stdout, go, 2, 2, 80); 
      puts("\nChoice of alignment mode :");
      esl_opt_DisplayHelp(stdout, go, 3, 2, 80); 
      puts("\nChoice of multi vs. unihit config :");
      esl_opt_DisplayHelp(stdout, go, 4, 2, 80); 
      puts("\nChoice of generic vs. vector DP implementation :");
      esl_opt_DisplayHelp(stdout, go, 5, 2, 80); 
      puts("\nOutput options (use only in serial mode, for single HMM input):");
      esl_opt_DisplayHelp(stdout, go, 6, 2, 80); 
      puts("\nControlling range of fitted tail masses :");
      esl_opt_DisplayHelp(stdout, go, 7, 2, 80);
      puts("\nRecalibrating E-values, and replacing HMM's existing parameters :");
      esl_opt_DisplayHelp(stdout, go, 8, 2, 80);
      puts("\nDebugging :");
      esl_opt_DisplayHelp(stdout, go, 9, 2, 80);
      puts("\nExperiments :");
      esl_opt_DisplayHelp(stdout, go, 10, 2, 80);
      exit(0);
    }
  if (esl_opt_ArgNumber(go) != 1) 
    {
      puts("Incorrect number of command line arguments.");
      esl_usage(stdout, argv[0], usage);
      puts("\nwhere general options are:");
      esl_opt_DisplayHelp(stdout, go, 1, 2, 80); /* 1=docgroup, 2 = indentation; 80=textwidth*/
      printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
      exit(1);
    }

  /* Validate combinations of score/config/implementation (4x3x2x2, score x mode x hit x DPimpl: 20 of 48 possible combos valid */
  if (esl_opt_GetBoolean(go, "--vector") && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("SIMD vector implementations only work for local alignment.");    /* -16/48 */
  if (esl_opt_GetBoolean(go, "--msv")    && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("MSV scoring is local by definition: use --local.");              /*  -4/48 */
  if (esl_opt_GetBoolean(go, "--vit")    && ! esl_opt_GetBoolean(go, "--local")) p7_Fail("no p7_GViterbiDual for new dual-mode profile implemented yet");  /*  -4/48 */

  /* Initialize configuration shared across all kinds of masters
   * and workers in this .c file.
   */
  cfg.hmmfile  = esl_opt_GetArg(go, 1);
  cfg.r        = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
//  cfg.abc      = esl_alphabet_Create(eslAMINO);


  cfg.my_rank  = 0;		/* MPI init will change this soon, if --mpi was set */
  cfg.nproc    = 0;		/* MPI init will change this soon, if --mpi was set */
  cfg.do_mpi   = FALSE;		/* --mpi will change this soon (below) if necessary */
  cfg.do_stall = esl_opt_GetBoolean(go, "--stall");
  cfg.N        = esl_opt_GetInteger(go, "-N");
  cfg.L        = esl_opt_GetInteger(go, "-L");
  cfg.hfp      = NULL;
  cfg.ofp      = NULL;
  cfg.survfp   = NULL;
  cfg.efp      = NULL;
  cfg.ffp      = NULL;
  cfg.xfp      = NULL;
  cfg.alfp     = NULL;
  cfg.bg       = NULL;


  /* This is our stall point, if we need to wait until we get a
   * debugger attached to this process for debugging (especially
   * useful for MPI):
   */
  while (cfg.do_stall); 

  /* Start timing. */
  esl_stopwatch_Start(w);

  /* Main body:
   * Handed off to serial version or MPI masters and workers as appropriate.
   */
#ifdef HAVE_MPI
  if (esl_opt_GetBoolean(go, "--mpi")) 
    {
      /* Initialize MPI, figure out who we are, and whether we're running
       * this show (proc 0) or working in it (procs >0).
       */
      cfg.do_mpi = TRUE;
      MPI_Init(&argc, &argv);
      MPI_Comm_rank(MPI_COMM_WORLD, &(cfg.my_rank));
      MPI_Comm_size(MPI_COMM_WORLD, &(cfg.nproc));
      if (cfg.my_rank == 0 && cfg.nproc < 2) p7_Fail("Need at least 2 MPI processes to run --mpi mode.");

      if (cfg.my_rank > 0)   mpi_worker(go, &cfg);
      else                   mpi_master(go, &cfg);

      esl_stopwatch_Stop(w);
      esl_stopwatch_MPIReduce(w, 0, MPI_COMM_WORLD);
      MPI_Finalize();		/* both workers and masters reach this line */
    }
  else
#endif /*HAVE_MPI*/
    {		
      /* No MPI? Then we're just the serial master. */
      serial_master(go, &cfg);
      esl_stopwatch_Stop(w);
    }      

  /* Stop timing. */
  if (cfg.my_rank == 0) esl_stopwatch_Display(stdout, w, "# CPU time: ");

  /* Clean up and exit. */
  if (cfg.my_rank == 0) {
    if (cfg.hfp    != NULL)      p7_hmmfile_Close(cfg.hfp);
    if (esl_opt_IsOn(go, "-o"))  fclose(cfg.ofp); 
    if (cfg.survfp != NULL)      fclose(cfg.survfp);
    if (cfg.efp    != NULL)      fclose(cfg.efp);
    if (cfg.ffp    != NULL)      fclose(cfg.ffp);
    if (cfg.xfp    != NULL)      fclose(cfg.xfp);
    if (cfg.alfp   != NULL)      fclose(cfg.alfp);
  }
  p7_bg_Destroy(cfg.bg);
  esl_alphabet_Destroy(cfg.abc);
  esl_randomness_Destroy(cfg.r);
  esl_getopts_Destroy(go);
  esl_stopwatch_Destroy(w);
  return eslOK;
}