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);
}
/* process_workunit()
*
* This is the routine that actually does the work.
*
* A work unit consists of one HMM, <hmm>.
* The result is the <scores> array, which contains an array of N scores;
* caller provides this memory.
* How those scores are generated is controlled by the application configuration in <cfg>.
*/
static int
process_workunit(ESL_GETOPTS *go, struct cfg_s *cfg, char *errbuf, P7_HMM *hmm, double *scores, int *alilens)
{
int L = esl_opt_GetInteger(go, "-L");
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_REFMX *rmx = NULL;
P7_CHECKPTMX *cx = NULL;
P7_FILTERMX *fx = NULL;
P7_TRACE *tr = NULL;
ESL_DSQ *dsq = NULL;
int i;
int scounts[p7T_NSTATETYPES]; /* state usage counts from a trace */
float sc;
float nullsc;
int status;
P7_HARDWARE *hw;
if ((hw = p7_hardware_Create ()) == NULL) p7_Fail("Couldn't get HW information data structure");
/* Optionally set a custom background, determined by model composition;
* an experimental hack.
*/
if (esl_opt_GetBoolean(go, "--bgcomp"))
{
float *p = NULL;
float KL;
p7_hmm_CompositionKLDist(hmm, cfg->bg, &KL, &p);
esl_vec_FCopy(p, cfg->abc->K, cfg->bg->f);
}
/* Create and configure our generic profile, as requested */
gm = p7_profile_Create(hmm->M, cfg->abc);
if (esl_opt_GetBoolean(go, "--multi"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_Config (gm, hmm, cfg->bg); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigLocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigGlocal(gm, hmm, cfg->bg, L); }
}
else if (esl_opt_GetBoolean(go, "--uni"))
{
if (esl_opt_GetBoolean(go, "--dual")) { p7_profile_ConfigCustom (gm, hmm, cfg->bg, L, 0.0, 0.5); }
else if (esl_opt_GetBoolean(go, "--local")) { p7_profile_ConfigUnilocal (gm, hmm, cfg->bg, L); }
else if (esl_opt_GetBoolean(go, "--glocal")) { p7_profile_ConfigUniglocal(gm, hmm, cfg->bg, L); }
}
p7_profile_SetLength(gm, L);
p7_bg_SetLength(cfg->bg, L);
if (esl_opt_GetBoolean(go, "--x-no-lengthmodel")) elide_length_model(gm, cfg->bg);
/* Allocate DP matrix for <gm>.
*/
rmx = p7_refmx_Create(gm->M, L);
/* Create and configure the vectorized profile, if needed;
* and allocate its DP matrix
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
om = p7_oprofile_Create(gm->M, cfg->abc, om->simd);
p7_oprofile_Convert(gm, om);
cx = p7_checkptmx_Create(gm->M, L, ESL_MBYTES(32), om->simd);
fx = p7_filtermx_Create(gm->M, om->simd);
}
/* Remaining allocation */
ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));
tr = p7_trace_Create();
/* Collect scores from N random sequences of length L */
for (i = 0; i < cfg->N; i++)
{
esl_rsq_xfIID(cfg->r, cfg->bg->f, cfg->abc->K, L, dsq);
sc = eslINFINITY;
/* Vectorized implementations of Viterbi, MSV may overflow.
* In this case, they'll leave sc=eslINFINITY.
* Then we fail over to the nonvector "generic" implementation.
* That's why this next block isn't an if/else.
*/
if (esl_opt_GetBoolean(go, "--vector"))
{
if (esl_opt_GetBoolean(go, "--vit")) p7_ViterbiFilter(dsq, L, om, fx, &sc);
else if (esl_opt_GetBoolean(go, "--fwd")) p7_ForwardFilter(dsq, L, om, cx, &sc);
else if (esl_opt_GetBoolean(go, "--msv")) p7_MSVFilter (dsq, L, om, fx, &sc);
}
/* If we tried a vector calculation above but it overflowed,
* or if we're to do --generic DP calculations, sc==eslINFINITY now;
* hence the if condition here:
*/
if (sc == eslINFINITY)
{
if (esl_opt_GetBoolean(go, "--fwd")) p7_ReferenceForward(dsq, L, gm, rmx, &sc); /* any mode: dual,local,glocal; gm's config takes care of this */
else if (esl_opt_GetBoolean(go, "--vit")) p7_ReferenceViterbi(dsq, L, gm, rmx, tr, &sc); /* local-only mode. cmdline opts processing has already assured that --local set */
else if (esl_opt_GetBoolean(go, "--msv")) p7_Die("We used to be able to do a generic MSV algorithm - but no longer");
}
/* Optional: get Viterbi alignment length too. */
if (esl_opt_GetBoolean(go, "-a")) /* -a only works with Viterbi; getopts has checked this already; <tr> must be valid */
{
p7_trace_GetStateUseCounts(tr, scounts);
/* there's various ways we could counts "alignment length".
* Here we'll use the total length of model used, in nodes: M+D states.
* score vs al would gives us relative entropy / model position.
*/
/* alilens[i] = scounts[p7T_D] + scounts[p7T_I]; SRE: temporarily testing this instead */
alilens[i] = scounts[p7T_ML] + scounts[p7T_DL] + scounts[p7T_IL] +
scounts[p7T_MG] + scounts[p7T_DG] + scounts[p7T_IG];
p7_trace_Reuse(tr);
}
p7_bg_NullOne(cfg->bg, dsq, L, &nullsc);
scores[i] = (sc - nullsc) / eslCONST_LOG2;
if (cx) p7_checkptmx_Reuse(cx);
if (fx) p7_filtermx_Reuse(fx);
p7_refmx_Reuse(rmx);
}
status = eslOK;
/* deliberate flowthru */
ERROR:
if (dsq != NULL) free(dsq);
p7_checkptmx_Destroy(cx);
p7_filtermx_Destroy(fx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_refmx_Destroy(rmx);
p7_trace_Destroy(tr);
if (status == eslEMEM) sprintf(errbuf, "allocation failure");
return status;
}
/**
* int main(int argc, char **argv)
* Main driver
*/
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_ALPHABET *abc = NULL;
char *hmmfile = NULL;
char *outhmmfile = NULL;
P7_HMMFILE *hfp = NULL;
FILE *outhmmfp; /* HMM output file handle */
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
int nhmm;
double x;
float KL;
int status;
char errbuf[eslERRBUFSIZE];
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("\nOptions:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=docgroup, 2 = indentation; 80=textwidth*/
exit(0);
}
if (esl_opt_ArgNumber(go) != 2)
{
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> 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, 2)) == 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 reading
*/
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);
/* 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;
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 (bg == NULL) bg = p7_bg_Create(abc);
esl_vec_FSet(average_internal_transitions, p7H_NTRANSITIONS, 0.);
for( k = 1; k < hmm->M; k++ ) {
esl_vec_FAdd(average_internal_transitions, hmm->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.
for( k = 1; k < hmm->M; k++ ) {
esl_vec_FCopy( average_internal_transitions, p7H_NTRANSITIONS, hmm->t[k] );
}
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);
if (outhmmfp != NULL) fclose(outhmmfp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
int status;
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_ALPHABET *abc = NULL;
char *hmmfile = NULL;
char *outhmmfile = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
int nhmm;
double x;
float KL;
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) != 2)
{
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> 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, 2)) == 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 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);
/* 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++;
if (bg == NULL) bg = p7_bg_Create(abc);
if( abc->type == eslDNA ) {
galosh::ProfileTreeRoot<seqan::Dna, floatrealspace> profile;
if( (status = convert_to_galosh_profile( hmm, profile )) != eslOK ) esl_fatal("Unexpected error in converting HMM from file %s to a dna galosh profile", hmmfile);
std::ofstream fs ( outhmmfile );
if( !fs.is_open() ) {
esl_fatal("Unexpected error in opening the file %s for writing", outhmmfile);
} else {
fs << profile;
fs.close();
}
} else if( abc->type == eslAMINO ) {
galosh::ProfileTreeRoot<seqan::AminoAcid20, floatrealspace> profile;
if( (status = convert_to_galosh_profile( hmm, profile )) != eslOK ) esl_fatal("Unexpected error in converting HMM from file %s to an amino galosh profile", hmmfile);
std::ofstream fs ( outhmmfile );
if( !fs.is_open() ) {
esl_fatal("Unexpected error in opening the file %s for writing", outhmmfile);
} else {
fs << profile;
fs.close();
}
} else {
ESL_EXCEPTION(eslEUNIMPLEMENTED, "Sorry, at present the profillic-hmmtoprofile software can only handle amino and dna.");
}
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);
esl_getopts_Destroy(go);
exit(0);
}
