/* General routines used throughout HMMER. * * Contents: * 1. Miscellaneous functions for H3 * 2. Unit tests * 3. Test driver * * SRE, Fri Jan 12 13:19:38 2007 [Janelia] [Franz Ferdinand, eponymous] */ #include "p7_config.h" #include #include #include "easel.h" #include "esl_getopts.h" #include "hmmer.h" /***************************************************************** * 1. Miscellaneous functions for H3 *****************************************************************/ /* Function: p7_banner() * Synopsis: print standard HMMER application output header * Incept: SRE, Wed May 23 10:45:53 2007 [Janelia] * * Purpose: Print the standard HMMER command line application banner * to , constructing it from (the name of the * program) and a short one-line description . * For example, * * might result in: * * \begin{cchunk} * # hmmsim :: collect profile HMM score distributions * # HMMER 3.0 (May 2007) * # Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus * # Freely licensed under the Janelia Software License. * # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - * \end{cchunk} * * would typically be an application's * , rather than a fixed string. This allows the * program to be renamed, or called under different names * via symlinks. Any path in the is discarded; * for instance, if is "/usr/local/bin/hmmsim", * "hmmsim" is used as the program name. * * Note: * Needs to pick up preprocessor #define's from p7_config.h, * as set by ./configure: * * symbol example * ------ ---------------- * HMMER_VERSION "3.0" * HMMER_DATE "May 2007" * HMMER_COPYRIGHT "Copyright (C) 2004-2007 HHMI Janelia Farm Research Campus" * HMMER_LICENSE "Freely licensed under the Janelia Software License." * * Returns: (void) */ void p7_banner(FILE *fp, char *progname, char *banner) { char *appname = NULL; if (esl_FileTail(progname, FALSE, &appname) != eslOK) appname = progname; fprintf(fp, "# %s :: %s\n", appname, banner); fprintf(fp, "# 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; } /* Function: p7_CreateDefaultApp() * Synopsis: Initialize a small/simple/standard HMMER application * Incept: SRE, Thu Oct 28 15:03:21 2010 [Janelia] * * Purpose: Identical to , but * specialized for HMMER. See documentation in * . * * Args: options - array of structures for getopts * nargs - number of cmd line arguments expected (excl. of cmdname) * argc - from main() * argv - from main() * banner - optional one-line description of program (or NULL) * usage - optional one-line usage hint (or NULL) * * Returns: ptr to new object. * * On command line errors, this routine prints an error * message to then calls 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 structure), * then calls 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; } /* Function: p7_AminoFrequencies() * Incept: SRE, Fri Jan 12 13:46:41 2007 [Janelia] * * Purpose: Fills a vector with amino acid background frequencies, * in [A..Y] alphabetic order, same order that Easel digital * alphabet uses. Caller must provide allocated for at * least 20 floats. * * These were updated 4 Sept 2007, from Swiss-Prot 50.8, * (Oct 2006), counting over 85956127 (86.0M) residues. * * Returns: on success. */ int p7_AminoFrequencies(float *f) { f[0] = 0.0787945; /* A */ f[1] = 0.0151600; /* C */ f[2] = 0.0535222; /* D */ f[3] = 0.0668298; /* E */ f[4] = 0.0397062; /* F */ f[5] = 0.0695071; /* G */ f[6] = 0.0229198; /* H */ f[7] = 0.0590092; /* I */ f[8] = 0.0594422; /* K */ f[9] = 0.0963728; /* L */ f[10]= 0.0237718; /* M */ f[11]= 0.0414386; /* N */ f[12]= 0.0482904; /* P */ f[13]= 0.0395639; /* Q */ f[14]= 0.0540978; /* R */ f[15]= 0.0683364; /* S */ f[16]= 0.0540687; /* T */ f[17]= 0.0673417; /* V */ f[18]= 0.0114135; /* W */ f[19]= 0.0304133; /* Y */ return eslOK; } /***************************************************************** * 2. Unit tests *****************************************************************/ #ifdef p7HMMER_TESTDRIVE static void utest_alphabet_config(int alphatype) { char *msg = "HMMER alphabet config unit test failed"; ESL_ALPHABET *abc = NULL; if ((abc = esl_alphabet_Create(alphatype)) == NULL) esl_fatal(msg); if (abc->K > p7_MAXABET) esl_fatal(msg); if (abc->Kp > p7_MAXCODE) esl_fatal(msg); esl_alphabet_Destroy(abc); } #endif /*p7HMMER_TESTDRIVE*/ /***************************************************************** * 3. Test driver *****************************************************************/ #ifdef p7HMMER_TESTDRIVE /* gcc -o hmmer_utest -g -Wall -I../easel -L../easel -I. -L. -Dp7HMMER_TESTDRIVE hmmer.c -lhmmer -leasel -lm * ./hmmer_utest */ #include "esl_getopts.h" static ESL_OPTIONS options[] = { /* name type default env range toggles reqs incomp help docgroup*/ { "-h", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "show brief help on version and usage", 0 }, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, }; static char usage[] = "[-options]"; static char banner[] = "test driver for hmmer.c"; int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); utest_alphabet_config(eslAMINO); utest_alphabet_config(eslDNA); utest_alphabet_config(eslRNA); utest_alphabet_config(eslCOINS); utest_alphabet_config(eslDICE); esl_getopts_Destroy(go); return 0; } #endif /*p7HMMER_TESTDRIVE*/