/* cmconvert: converting covariance model files to Infernal-1.1 CM format. * * EPN, Fri Jul 1 05:11:15 2011 * SRE, Thu Oct 16 08:57:43 2008 [janelia] (hmmconvert.c) * SVN $Id$ */ #include "esl_config.h" #include "p7_config.h" #include #include #include #include "easel.h" #include "esl_alphabet.h" #include "esl_getopts.h" #include "hmmer.h" #include "infernal.h" #define OUTOPTS "-a,-b,-1,--mlhmm,--fhmm" 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 }, { "-a", eslARG_NONE,"default",NULL, NULL, OUTOPTS, NULL, NULL, "ascii: output models in INFERNAL 1.1 ASCII format", 0 }, { "-b", eslARG_NONE, FALSE, NULL, NULL, OUTOPTS, NULL, NULL, "binary: output models in INFERNAL 1.1 binary format", 0 }, { "-1", eslARG_NONE, FALSE, NULL, NULL, OUTOPTS, NULL, NULL, "output backward compatible Infernal v0.7-->v1.0.2 ASCII format", 0 }, { "-o", eslARG_OUTFILE,FALSE, NULL, NULL, NULL, NULL, NULL, "save CM file to file , not stdout", 0 }, { "--mlhmm", eslARG_NONE, FALSE, NULL, NULL, OUTOPTS, NULL, NULL, "output maximum likelihood HMM for CM in HMMER3 format", 0 }, { "--fhmm", eslARG_NONE, FALSE, NULL, NULL, OUTOPTS, NULL, NULL, "output filter HMM for CM in HMMER3 format", 0 }, /* { "--outfmt", eslARG_STRING, NULL, NULL, NULL, NULL, NULL,"-1,--mlhmm,--fhmm", "choose output legacy 1.x file formats by name, such as '1/a'", 0 },*/ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, }; static char usage[] = "[-options] "; static char banner[] = "convert CM file to a different Infernal format"; static int configure_model(CM_t *cm, char *errbuf); int main(int argc, char **argv) { ESL_GETOPTS *go = cm_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_ALPHABET *abc = NULL; char *cmfile = esl_opt_GetArg(go, 1); CM_FILE *cmfp = NULL; CM_t *cm = NULL; FILE *ofp = NULL; /*char *outfmt = esl_opt_GetString(go, "--outfmt");*/ int fmtcode = -1; /* -1 = write the current default format */ int status; char errbuf[eslERRBUFSIZE]; /* In the future, when we have another 1.1+ format besides '1/a' put this back in: * if (outfmt != NULL) { * if (strcmp(outfmt, "1/a") == 0) fmtcode = CM_FILE_1a; * else cm_Fail("No such 1.x output format code %s.\n", outfmt); * } */ status = cm_file_Open(cmfile, NULL, TRUE, &cmfp, errbuf); /* TRUE says: allow CM file to be in v1.0 --> v1.0.2 format */ if (status == eslENOTFOUND) cm_Fail("File existence/permissions problem in trying to open CM file %s.\n%s\n", cmfile, errbuf); else if (status == eslEFORMAT) cm_Fail("File format problem in trying to open CM file %s.\n%s\n", cmfile, errbuf); else if (status != eslOK) cm_Fail("Unexpected error %d in opening CM file %s.\n%s\n", status, cmfile, errbuf); /* open output file for writing, if nec */ if ( esl_opt_IsOn(go, "-o") ) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) ESL_FAIL(eslFAIL, errbuf, "Failed to open output file %s", esl_opt_GetString(go, "-o")); } else ofp = stdout; while ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) == eslOK) { if(cmfp->format == CM_FILE_1 || esl_opt_GetBoolean(go, "--mlhmm")) { /* if format == CM_FILE_1, we need to calculate QDBs * (cm->dmin, cm->dmax), cm->W, cm->consensus. These are * calculated during model configuration. If --mlhmm, we * need E-value params for the ML p7 HMM, we calc those * in configure_model(). */ if ((status = configure_model(cm, errbuf)) != eslOK) cm_Fail(errbuf); } /* append command line info to the appropriate comlog */ if (esl_opt_GetBoolean(go, "--mlhmm")) { if((status = p7_hmm_AppendComlog (cm->mlp7, go->argc, go->argv)) != eslOK) cm_Fail("Failed to record command log"); } else if (esl_opt_GetBoolean(go, "--fhmm")) { if((status = p7_hmm_AppendComlog (cm->fp7, go->argc, go->argv)) != eslOK) cm_Fail("Failed to record command log"); } else { if((status = cm_AppendComlog (cm, go->argc, go->argv, FALSE , 0)) != eslOK) cm_Fail("Failed to record command log"); } if (esl_opt_GetBoolean(go, "-a") == TRUE) cm_file_WriteASCII (ofp, fmtcode, cm); else if (esl_opt_GetBoolean(go, "-b") == TRUE) cm_file_WriteBinary(ofp, fmtcode, cm, NULL); else if (esl_opt_GetBoolean(go, "-1") == TRUE) cm_file_Write1p0ASCII(ofp, cm); else if (esl_opt_GetBoolean(go, "--mlhmm") == TRUE) p7_hmmfile_WriteASCII(ofp, -1, cm->mlp7); /* -1 = write the current default format */ else if (esl_opt_GetBoolean(go, "--fhmm") == TRUE) p7_hmmfile_WriteASCII(ofp, -1, cm->fp7); /* -1 = write the current default format */ FreeCM(cm); } if (status == eslEFORMAT) cm_Fail("bad file format in CM file %s\n%s", cmfile, cmfp->errbuf); else if (status == eslEINCOMPAT) cm_Fail("CM file %s contains different alphabets\n%s", cmfile, cmfp->errbuf); else if (status != eslEOF) cm_Fail("Unexpected error in reading CMs from %s\n%s", cmfile, cmfp->errbuf); cm_file_Close(cmfp); if(esl_opt_IsOn(go, "-o")) fclose(ofp); esl_alphabet_Destroy(abc); esl_getopts_Destroy(go); return 0; } /* configure_model() * Configure the model. This determines QDBs and W, which * the new file format includes, but v1.0-->v1.0.2 did not, * thus we have to calculate them for models read from * v1.0-->v1.0.2 cm files. */ static int configure_model(CM_t *cm, char *errbuf) { int status; int lmsvL, lvitL, lfwdL, gfwdL; int lmsvN, lvitN, lfwdN, gfwdN; float lftailp, gftailp; double fil_gfmu, fil_gflambda; /* Configure the model, we must calculate QDBs so we can write them to the CM file */ cm->config_opts |= CM_CONFIG_QDB; if ((status = cm_Configure(cm, errbuf, -1)) != eslOK) return status; if ((status = cm_SetConsensus(cm, cm->cmcons, NULL)) != eslOK) ESL_FAIL(status, errbuf, "Failed to calculate consensus sequence"); /* We'll define the filter HMM as the ML p7 HMM because that's the * only option available (by default, in cmbuild, a filter HMM gets * built separately that's different from the ml p7, but that * requires the cmbuild input alignment). The cm->mlp7 HMM was * created in cm_Configure(), and we calibrate it here. There are * more options than this in cmbuild, but here we enforce * defaults. See cmbuild.c::build_and_calibrate_p7_filter(). */ lmsvL = lvitL = 200; lfwdL = 100; gfwdL = ESL_MAX(100, 2.*cm->clen); lmsvN = lvitN = lfwdN = gfwdN = 200; lftailp = 0.055; gftailp = 0.065; /* Calibrate the ML p7 hmm */ if((status = cm_p7_Calibrate(cm->mlp7, errbuf, lmsvL, lvitL, lfwdL, gfwdL, /* length of sequences to search for local (lL) and glocal (gL) modes */ lmsvN, lvitN, lfwdN, gfwdN, /* number of seqs to search for each alg */ lftailp, /* fraction of tail mass to fit for local Fwd */ gftailp, /* fraction of tail mass to fit for glocal Fwd */ &fil_gfmu, &fil_gflambda)) != eslOK) return status; if((status = cm_SetFilterHMM(cm, cm->mlp7, fil_gfmu, fil_gflambda)) != eslOK) ESL_FAIL(status, errbuf, "Unable to set the HMM filter for the CM"); return eslOK; } /***************************************************************** * Infernal - inference of RNA secondary structure alignments * Version 1.1.1; July 2014 * Copyright (C) 2014 Howard Hughes Medical Institute. * Other copyrights also apply. See the COPYRIGHT file for a full list. * * Infernal is distributed under the terms of the GNU General Public License * (GPLv3). See the LICENSE file for details. *****************************************************************/