{

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;

{

typedef typename galosh::profile_traits<ProfileType>::ResidueType ResidueType;

int status;

uint32_t pos_i; // Position in profile. Corresponds to one less than match state pos in HMM.

uint32_t res_i;

ESL_DSQ hmmer_digitized_residue;

/* How many match states in the HMM? */

if( hmm->M == 0 ) { status = eslENORESULT; goto ERROR; }

profile.reinitialize( static_cast<uint32_t>( hmm->M ) );

profile.zero();

// NOTE that HMMER3 has a slightly different model, starting in

// Begin rather than in preAlign, and with 3 legal transitions out

// of Begin (one of these is to PreAlign). The galosh profile model

// begins in preAlign and transitions to Begin, and from there to

// either Match or Delete. One implication is that galosh profiles

// enforce t[ 0 ][ p7H_MI ] to be the same as t[ 0 ][ p7H_II ], but

// HMMER3 does not. Another way to say this is that H3 uses affine

// pre-aligns, and prohibits pre-align -to- delete transitions,

// whereas galosh / profillic uses non-affine pre-aligns and allows

// pre-align->delete.

// fromPreAlign

profile[ galosh::Transition::fromPreAlign ][ galosh::TransitionFromPreAlign::toPreAlign ] =

hmm->t[ 0 ][ p7H_II ];

profile[ galosh::Transition::fromPreAlign ][ galosh::TransitionFromPreAlign::toBegin ] =

hmm->t[ 0 ][ p7H_IM ];

for( res_i = 0; res_i < seqan::ValueSize<ResidueType>::VALUE; res_i++ ) {

hmmer_digitized_residue =

esl_abc_DigitizeSymbol( hmm->abc, static_cast<char>( ResidueType( res_i ) ) );

// See below where it says "TODO/NOTE"..

profile[ galosh::Emission::PreAlignInsertion ][ res_i ] =

hmm->ins[ 0 ][ hmmer_digitized_residue ];

}

// fromBegin

profile[ galosh::Transition::fromBegin ][ galosh::TransitionFromBegin::toMatch ] =

( hmm->t[ 0 ][ p7H_MM ] / ( 1.0 - hmm->t[ 0 ][ p7H_MI ] ) );

profile[ galosh::Transition::fromBegin ][ galosh::TransitionFromBegin::toDeletion ] =

( 1.0 - profile[ galosh::Transition::fromBegin ][ galosh::TransitionFromBegin::toMatch ] );

for( pos_i = 0; pos_i < profile.length(); pos_i++ ) {

// if( be_verbose ) {

// cout << '.';

// cout.flush();

// }

// TODO: If this is too slow, memoize the ResidueType( res_i )s.

for( res_i = 0; res_i < seqan::ValueSize<ResidueType>::VALUE; res_i++ ) {

hmmer_digitized_residue =

esl_abc_DigitizeSymbol( hmm->abc, static_cast<char>( ResidueType( res_i ) ) );

profile[ pos_i ][ galosh::Emission::Match ][ res_i ] =

hmm->mat[ pos_i + 1 ][ hmmer_digitized_residue ];

if( pos_i == ( profile.length() - 1 ) ) {

// Use post-align insertions

profile[ galosh::Emission::PostAlignInsertion ][ res_i ] =

hmm->ins[ pos_i + 1 ][ hmmer_digitized_residue ];

} else { // if this is the last position (use post-align insertions) .. else ..

profile[ galosh::Emission::Insertion ][ res_i ] +=

hmm->ins[ pos_i + 1 ][ hmmer_digitized_residue ];

} // End if this is the last position (use post-align insertions) .. else ..

} // End foreach res_i

if( pos_i == ( profile.length() - 1 ) ) {

// Use post-align insertions

profile[ galosh::Transition::fromPostAlign ][ galosh::TransitionFromPostAlign::toTerminal ] =

hmm->t[ pos_i + 1 ][ p7H_IM ];

profile[ galosh::Transition::fromPostAlign ][ galosh::TransitionFromPostAlign::toPostAlign ] =

( 1.0 - profile[ galosh::Transition::fromPostAlign ][ galosh::TransitionFromPostAlign::toTerminal ] );

} else { // if this is the last position (use post-align insertions) .. else ..

profile[ galosh::Transition::fromMatch ][ galosh::TransitionFromMatch::toMatch ] +=

hmm->t[ pos_i + 1 ][ p7H_MM ];

profile[ galosh::Transition::fromMatch ][ galosh::TransitionFromMatch::toInsertion ] +=

hmm->t[ pos_i + 1 ][ p7H_MI ];

profile[ galosh::Transition::fromMatch ][ galosh::TransitionFromMatch::toDeletion ] +=

hmm->t[ pos_i + 1 ][ p7H_MD ];

profile[ galosh::Transition::fromInsertion ][ galosh::TransitionFromInsertion::toMatch ] +=

hmm->t[ pos_i + 1 ][ p7H_IM ];

profile[ galosh::Transition::fromInsertion ][ galosh::TransitionFromInsertion::toInsertion ] +=

hmm->t[ pos_i + 1 ][ p7H_II ];

profile[ galosh::Transition::fromDeletion ][ galosh::TransitionFromDeletion::toMatch ] +=

hmm->t[ pos_i + 1 ][ p7H_DM ];

profile[ galosh::Transition::fromDeletion ][ galosh::TransitionFromDeletion::toDeletion ] +=

hmm->t[ pos_i + 1 ][ p7H_DD ];

} // End if this is the last position (use post-align insertions) .. else ..

} // End foreach pos_i

// Normalize with 0 as the minimum value we'll allow. Note that in

// profillic and profuse, it's generally 1E-5, so when the profile

// is read in by those programs, it might be slightly altered.

profile.normalize( 0 );

return eslOK;

ERROR:

return status;

{

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);