static int process_commandline(int argc, char **argv, ESL_GETOPTS **ret_go, char **ret_fmfile, char **ret_qfile) { 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) { esl_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_qfile = esl_opt_GetArg(go, 1)) == NULL) { if (puts("Failed to get <qfile> 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_fmfile, "-") == 0 && esl_strcmp(*ret_qfile, "-") == 0) { if (puts("Either <fmfile> or <qfile> 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); }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_STOPWATCH *w = esl_stopwatch_Create(); char *hmmfile = esl_opt_GetArg(go, 1); P7_HMMCACHE *hcache = NULL; char errbuf[eslERRBUFSIZE]; size_t tot_mem; int status; esl_stopwatch_Start(w); status = p7_hmmcache_Open(hmmfile, &hcache, errbuf); if (status == eslENOTFOUND) p7_Fail("Failed to read %s\n %s\n", hmmfile, errbuf); else if (status == eslEFORMAT) p7_Fail("Failed to parse %s\n %s\n", hmmfile, errbuf); else if (status == eslEINCOMPAT) p7_Fail("Mixed profile types in %s\n %s\n", hmmfile, errbuf); else if (status != eslOK) p7_Fail("Failed to cache %s: error code %d\n", hmmfile, status); p7_hmmcache_SetNumericNames(hcache); tot_mem = p7_hmmcache_Sizeof(hcache); esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("models = %d\n", hcache->n); printf("tot memory = %" PRIu64 "\n", (uint64_t) tot_mem); p7_hmmcache_Close(hcache); esl_getopts_Destroy(go); esl_stopwatch_Destroy(w); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); P7_ANCHORS *anch = p7_anchors_Create(); P7_ANCHORHASH *ah = p7_anchorhash_Create(); int L = 400; int M = 200; int maxD = 50; int nsamples = 1000; int32_t keyidx; int s; for (s = 0; s < nsamples; s++) { p7_anchors_Sample(rng, L, M, maxD, anch); p7_anchorhash_Store(ah, anch, 0, &keyidx); p7_anchors_Reuse(anch); } p7_anchorhash_Dump(stdout, ah); p7_anchorhash_Destroy(ah); p7_anchors_Destroy(anch); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = NULL; int stalling = esl_opt_GetBoolean(go, "--stall"); int my_rank; int nproc; /* The startup sequence below is designed in part to facilitate debugging. * To debug an MPI program, you start it with 'mpirun' as usual, but * with the --stall flag; this causes all processes to start, but then * wait for the developer to attach gdb's to each running process. * Example: * mpirun -n 2 ./p7_hmm_mpi_utest --stall * [pid's <pid0> and <pid1> are reported for processes 0 and 1] * in one terminal window: * gdb ./p7_hmm_mpi_utest <pid0> * [set desired breakpoint in the master] * set stalling=0 * c * and similarly in a second terminal window, for worker <pid1>. * * Additionally, we want to show the rng seed. This is so we can diagnose * failures that are rare; we can re-run the unit test until we see it fail, * get the rng seed, then reproduce exactly that failure. */ MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &my_rank); MPI_Comm_size(MPI_COMM_WORLD, &nproc); if (my_rank == 0) { rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); fprintf(stderr, "## %s\n", argv[0]); fprintf(stderr, "# rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(rng)); fprintf(stderr, "# MPI nproc = %d\n", nproc); } #ifdef HAVE_GETPID /* To debug an MPI program, you attach gdb's to each process, already running; * for this, you need the pid of each process. Provide the pid's to help the * developer. */ fprintf(stderr, "# %6d = %d\n", my_rank, getpid()); #endif /* This infinite loop waits on the developer to attach gdb's to each process. * In each gdb, developer may set a better breakpoint, then does "set stalling=0" * and "continue" to release the waiting process from this stall point. */ while (stalling); utest_SendRecv(rng, my_rank, nproc); if (my_rank == 0) { fprintf(stderr, "# status = ok\n"); esl_randomness_Destroy(rng); } MPI_Finalize(); esl_getopts_Destroy(go); exit(0); /* success */ }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_STOPWATCH *w = esl_stopwatch_Create(); int N = esl_opt_GetInteger(go, "-N"); float origx = 2.0; float x = origx; __m128 xv = _mm_set1_ps(x); int i; /* First, serial time. */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) { x = logf(x); x = expf(x); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# serial CPU time: "); /* Vector time */ esl_stopwatch_Start(w); for (i = 0; i < N; i++) { xv = esl_sse_logf(xv); xv = esl_sse_expf(xv); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# vector CPU time: "); /* If you don't do something with x and xv, the compiler may optimize them away */ printf("%g => many scalar logf,expf cycles => %g\n", origx, x); printf("%g => many vector logf,expf cycles => ", origx); esl_sse_dump_ps(stdout, xv); printf("\n"); esl_stopwatch_Destroy(w); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage); char *hmmfile = esl_opt_GetArg(go, 1); ESL_STOPWATCH *w = esl_stopwatch_Create(); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_GMX *gx1 = NULL; P7_GMX *gx2 = NULL; int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N"); ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2)); float null2[p7_MAXCODE]; int i; float fsc, bsc; double Mcs; if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL); gx1 = p7_gmx_Create(gm->M, L); gx2 = p7_gmx_Create(gm->M, L); esl_rsq_xfIID(r, bg->f, abc->K, L, dsq); p7_GForward (dsq, L, gm, gx1, &fsc); p7_GBackward(dsq, L, gm, gx2, &bsc); p7_GDecoding(gm, gx1, gx2, gx2); esl_stopwatch_Start(w); for (i = 0; i < N; i++) p7_GNull2_ByExpectation(gm, gx2, null2); esl_stopwatch_Stop(w); Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / w->user; esl_stopwatch_Display(stdout, w, "# CPU time: "); printf("# M = %d\n", gm->M); printf("# %.1f Mc/s\n", Mcs); free(dsq); p7_gmx_Destroy(gx1); p7_gmx_Destroy(gx2); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); p7_hmmfile_Close(hfp); esl_alphabet_Destroy(abc); esl_stopwatch_Destroy(w); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = NULL; ESL_RANDOMNESS *r = NULL; int be_verbose; go = esl_getopts_Create(options); if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK || esl_opt_VerifyConfig(go) != eslOK) esl_fatal("%s", go->errbuf); if (esl_opt_GetBoolean(go, "-h") == TRUE) { esl_usage(stdout, argv[0], usage); puts("\n where options are:"); esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2=indentation; 80=width */ exit(0); } if (esl_opt_ArgNumber(go) != 0) { printf("Incorrect number of command line arguments.\n"); esl_usage(stdout, argv[0], usage); exit(1); } be_verbose = esl_opt_GetBoolean(go, "-v"); if (esl_opt_GetBoolean(go, "-r")) { r = esl_randomness_CreateTimeseeded(); if (be_verbose) printf("seed = %ld\n", esl_randomness_GetSeed(r)); } else r = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); utest_LinearRegression(r, TRUE, be_verbose); utest_LinearRegression(r, FALSE, be_verbose); esl_getopts_Destroy(go); esl_randomness_Destroy(r); exit(0); }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_Create(esl_opt_GetInteger(go, "-s")); P7_COORDS2 *c2 = p7_coords2_Create(0, 0); P7_COORDS2_HASH *hash = p7_coords2_hash_Create(0, 0, 0); int L = 20; int maxseg = 1; int nsamples = 1000; int32_t *wrk = NULL; int32_t keyidx; int i; for (i = 0; i < nsamples; i++) { p7_coords2_Sample(rng, c2, maxseg, L, &wrk); p7_coords2_hash_Store(hash, c2, &keyidx); p7_coords2_Reuse(c2); } p7_coords2_hash_Dump(stdout, hash); if (wrk) free(wrk); p7_coords2_hash_Destroy(hash); p7_coords2_Destroy(c2); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; P7_BG *bg = NULL; int M = 100; int L = 200; int nseq = 20; char errbuf[eslERRBUFSIZE]; if ((abc = esl_alphabet_Create(eslAMINO)) == NULL) esl_fatal("failed to create alphabet"); if (p7_hmm_Sample(r, M, abc, &hmm) != eslOK) esl_fatal("failed to sample an HMM"); if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create null model"); if ((gm = p7_profile_Create(hmm->M, abc)) == NULL) esl_fatal("failed to create profile"); if (p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL) != eslOK) esl_fatal("failed to config profile"); if (p7_hmm_Validate (hmm, errbuf, 0.0001) != eslOK) esl_fatal("whoops, HMM is bad!: %s", errbuf); if (p7_profile_Validate(gm, errbuf, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!: %s", errbuf); utest_basic (go); utest_viterbi(go, r, abc, bg, gm, nseq, L); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_BG *bg = NULL; P7_HMM *hmm = NULL; P7_OPROFILE *om = NULL; int M = esl_opt_GetInteger(go, "-M"); int L = esl_opt_GetInteger(go, "-L"); /* Sample a random HMM and optimized profile, in amino acid alphabet. */ if ((abc = esl_alphabet_Create(eslAMINO)) == NULL) esl_fatal("failed to create alphabet"); if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create null model"); if (( p7_oprofile_Sample(r, abc, bg, M, L, &hmm, NULL, &om)) != eslOK) esl_fatal("failed to sample HMM and profile"); /* unit test(s) */ utest_ReadWrite(hmm, om); p7_oprofile_Destroy(om); p7_hmm_Destroy(hmm); p7_bg_Destroy(bg); esl_alphabet_Destroy(abc); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return eslOK; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_STOPWATCH *w = esl_stopwatch_Create(); char *hmmfile = esl_opt_GetArg(go, 1); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N"); int i; /* Read one HMM from <hmmfile> */ if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); p7_hmmfile_Close(hfp); bg = p7_bg_Create(abc); esl_stopwatch_Start(w); for (i = 0; i < N; i++) p7_bg_SetFilterByHMM(bg, hmm); esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_stopwatch_Destroy(w); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage); char *hmmfile = esl_opt_GetArg(go, 1); int N = esl_opt_GetInteger(go, "-N"); ESL_STOPWATCH *w = esl_stopwatch_Create(); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile); if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM"); p7_hmmfile_Close(hfp); esl_stopwatch_Start(w); while (N--) { /* cfg rng bg gm om */ p7_Calibrate(hmm, NULL, NULL, NULL, NULL, NULL); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_stopwatch_Destroy(w); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { char *msg = "p7_gmx unit test driver failed"; ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO); P7_BG *bg = p7_bg_Create(abc); P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; int M = esl_opt_GetInteger(go, "-M"); int L = esl_opt_GetInteger(go, "-L"); float tol = esl_opt_GetReal (go, "-t"); p7_FLogsumInit(); if (p7_hmm_Sample(r, M, abc, &hmm) != eslOK) esl_fatal(msg); if ((gm = p7_profile_Create(hmm->M, abc)) == NULL) esl_fatal(msg); if (p7_bg_SetLength(bg, L) != eslOK) esl_fatal(msg); if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL) != eslOK) esl_fatal(msg); utest_GrowTo(); utest_Compare(r, gm, bg, L, tol); esl_getopts_Destroy(go); esl_randomness_Destroy(r); esl_alphabet_Destroy(abc); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); p7_profile_Destroy(gm); return eslOK; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); char *hmmfile = esl_opt_GetArg(go, 1); int L = esl_opt_GetInteger(go, "-L"); int N = esl_opt_GetInteger(go, "-N"); ESL_ALPHABET *abc = NULL; P7_HMMFILE *hfp = NULL; P7_HMM *hmm = NULL; P7_BG *bg = NULL; P7_PROFILE *gm = NULL; P7_TRACE *tr = p7_trace_Create(); ESL_SQ *sq = NULL; char errbuf[eslERRBUFSIZE]; int i; int status; 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); if (status == eslEFORMAT) p7_Fail("Bad file format in HMM file %s:\n%s\n", hfp->fname, hfp->errbuf); else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type)); else if (status == eslEOF) p7_Fail("Empty HMM file %s? No HMM data found.\n", hfp->fname); else if (status != eslOK) p7_Fail("Unexpected error in reading HMMs from %s\n", hfp->fname); p7_hmmfile_Close(hfp); bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L); gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL); sq = esl_sq_CreateDigital(abc); for (i = 0; i < N; i++) { p7_ProfileEmit(rng, hmm, gm, bg, sq, tr); esl_sq_FormatName(sq, "%s-sample%d", hmm->name, i); esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE); if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) esl_fatal(errbuf); esl_sq_Reuse(sq); p7_trace_Reuse(tr); } esl_sq_Destroy(sq); p7_trace_Destroy(tr); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); int N = esl_opt_GetInteger(go, "-N"); P7_TOPHITS *h1 = NULL; P7_TOPHITS *h2 = NULL; P7_TOPHITS *h3 = NULL; char name[] = "not_unique_name"; char acc[] = "not_unique_acc"; char desc[] = "Test description for the purposes of making the test driver allocate space"; double key; int i; fprintf(stderr, "## %s\n", argv[0]); fprintf(stderr, "# rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(r)); h1 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC); h2 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC); h3 = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC); for (i = 0; i < N; i++) { key = esl_random(r); tophits_Add(h1, name, acc, desc, key); key = 10.0 * esl_random(r); tophits_Add(h2, name, acc, desc, key); key = 0.1 * esl_random(r); tophits_Add(h3, name, acc, desc, key); } tophits_Add(h1, "last", NULL, NULL, -1.0); tophits_Add(h1, "first", NULL, NULL, 20.0); p7_tophits_SortBySortkey(h1); if (strcmp(h1->hit[0]->name, "first") != 0) esl_fatal("sort failed (top is %s = %f)", h1->hit[0]->name, h1->hit[0]->sortkey); if (strcmp(h1->hit[N+1]->name, "last") != 0) esl_fatal("sort failed (last is %s = %f)", h1->hit[N+1]->name, h1->hit[N+1]->sortkey); p7_tophits_Merge(h1, h2); if (strcmp(h1->hit[0]->name, "first") != 0) esl_fatal("after merge 1, sort failed (top is %s = %f)", h1->hit[0]->name, h1->hit[0]->sortkey); if (strcmp(h1->hit[2*N+1]->name, "last") != 0) esl_fatal("after merge 1, sort failed (last is %s = %f)", h1->hit[2*N+1]->name, h1->hit[2*N+1]->sortkey); p7_tophits_Merge(h3, h1); if (strcmp(h3->hit[0]->name, "first") != 0) esl_fatal("after merge 2, sort failed (top is %s = %f)", h3->hit[0]->name, h3->hit[0]->sortkey); if (strcmp(h3->hit[3*N+1]->name, "last") != 0) esl_fatal("after merge 2, sort failed (last is %s = %f)", h3->hit[3*N+1]->name, h3->hit[3*N+1]->sortkey); if (p7_tophits_GetMaxNameLength(h3) != strlen(name)) esl_fatal("GetMaxNameLength() failed"); p7_tophits_Destroy(h1); p7_tophits_Destroy(h2); p7_tophits_Destroy(h3); esl_randomness_Destroy(r); esl_getopts_Destroy(go); fprintf(stderr, "# status = ok\n"); return eslOK; }
int main(int argc, char **argv) { ESL_GETOPTS *go = NULL; /* application configuration */ ESL_RANDOMNESS *r = NULL; /* random number generator */ FILE *ofp = NULL; /* data output stream */ int outfmt = eslSQFILE_FASTA; /* Parse command line */ go = esl_getopts_Create(options); if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf); if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf); if (esl_opt_GetBoolean(go, "-h") ) cmdline_help(argv[0], go); /* Open the output data file, if any */ if (esl_opt_GetString(go, "-o") != NULL) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "-o")); } else ofp = stdout; /* Initialize */ r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed")); /* Hand off execution to one of the three modes */ if (esl_opt_GetBoolean(go, "-A")) /* Alignment shuffling */ { if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n"); msa_shuffling(go, r, ofp, outfmt); } else if (esl_opt_GetBoolean(go, "-G")) /* Sequence generation */ { if (esl_opt_ArgNumber(go) != 0) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n"); seq_generation(go, r, ofp, outfmt); } else if (esl_opt_GetBoolean(go, "-S")) /* Sequence shuffling */ { if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n"); seq_shuffling(go, r, ofp, outfmt); } if (esl_opt_GetString(go, "-o") != NULL) fclose(ofp); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage); char *msafile = esl_opt_GetArg(go, 1); ESL_ALPHABET *abc = NULL; int infmt = eslMSAFILE_UNKNOWN; ESLX_MSAFILE *afp = NULL; ESL_MSA *msa = NULL; FILE *ofp = stdout; int nali = 0; int namewidth; double pid; int nid, n; int i,j; int status; /* allow user to assert the input MSA alphabet */ if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA); else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA); else if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO); /* allow user to assert the input MSA format */ if (esl_opt_IsOn(go, "--informat") && (infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN) esl_fatal("%s is not a valid MSA file format for --informat", esl_opt_GetString(go, "--informat")); /* digital open */ if ( ( status = eslx_msafile_Open(&abc, msafile, NULL, infmt, NULL, &afp)) != eslOK) eslx_msafile_OpenFailure(afp, status); while ((status = eslx_msafile_Read(afp, &msa)) == eslOK) { nali++; namewidth = esl_str_GetMaxWidth(msa->sqname, msa->nseq); for (i = 0; i < msa->nseq; i++) for (j = i+1; j < msa->nseq; j++) { esl_dst_XPairId(abc, msa->ax[i], msa->ax[j], &pid, &nid, &n); fprintf(ofp, "%-*s %-*s %6.2f %6d %6d\n", namewidth, msa->sqname[i], namewidth, msa->sqname[j], pid*100.0, nid, n); } esl_msa_Destroy(msa); } if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status); eslx_msafile_Close(afp); esl_alphabet_Destroy(abc); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_Create(0); char *msafile = esl_opt_GetArg(go, 1); int fmt = eslMSAFILE_UNKNOWN; ESL_ALPHABET *abc = NULL; ESLX_MSAFILE *afp = NULL; ESL_MSA *msa = NULL; int textmode = esl_opt_GetBoolean(go, "--text"); int nali = 0; int status; /* If you know the alphabet you want, create it - you'll pass it to eslx_msafile_Open() */ if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA); else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA); else if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO); /* Open in text or digital mode. * To let the Open() function autoguess the format, you pass <infmt=eslMSAFILE_UNKNOWN>. * To let it autoguess the alphabet, you set <abc=NULL> and pass <&abc>. * To open in text mode instead of digital, you pass <NULL> for the alphabet argument. * eslx_msafile_OpenFailure() is a convenience, printing various diagnostics of any * open failure to <stderr>. You can of course handle your own diagnostics instead. */ if (textmode) status = eslx_msafile_Open(NULL, msafile, NULL, fmt, NULL, &afp); else status = eslx_msafile_Open(&abc, msafile, NULL, fmt, NULL, &afp); if (status != eslOK) eslx_msafile_OpenFailure(afp, status); fmt = afp->format; while ((status = eslx_msafile_Read(afp, &msa)) == eslOK) { /* if digital MSA: msa->ax[idx=0..nseq-1][acol=1..alen] is the alignment data; * if text MSA: msa->aseq[idx=0..nseq-1][acol=0..alen-1] */ nali++; /* permute it */ esl_msashuffle_PermuteSequenceOrder(rng, msa); eslx_msafile_Write(stdout, msa, fmt); esl_msa_Destroy(msa); } if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status); /* a convenience, like eslx_msafile_OpenFailure() */ esl_alphabet_Destroy(abc); eslx_msafile_Close(afp); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); exit(0); }
void free_QueueData(QUEUE_DATA *data) { /* free the query data */ esl_getopts_Destroy(data->opts); if (data->abc != NULL) esl_alphabet_Destroy(data->abc); if (data->hmm != NULL) p7_hmm_Destroy(data->hmm); if (data->seq != NULL) esl_sq_Destroy(data->seq); if (data->cmd != NULL) free(data->cmd); memset(data, 0, sizeof(*data)); free(data); }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); fprintf(stderr, "## %s\n", argv[0]); utest_normalization(go); esl_getopts_Destroy(go); fprintf(stderr, "# status = ok\n"); exit(0); /* success */ }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); fprintf(stderr, "## %s\n", argv[0]); utest_Compare(); fprintf(stderr, "# status = ok\n"); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_Create(esl_opt_GetInteger(go, "-s"));; utest_logf(go); utest_expf(go); utest_odds(go, r); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
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; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage); ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO); ESL_SQ *sq = esl_sq_CreateDigital(abc); ESL_SQFILE *sqfp = NULL; ESL_HMM *hmm = create_test_hmm(abc); ESL_HMM *bg = create_null_hmm(abc); ESL_HMX *hmx = esl_hmx_Create(400, hmm->M); int format = eslSQFILE_UNKNOWN; char *seqfile = esl_opt_GetArg(go, 1); float fwdsc, nullsc; int status; status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp); if (status == eslENOTFOUND) esl_fatal("No such file."); else if (status == eslEFORMAT) esl_fatal("Format unrecognized."); else if (status != eslOK) esl_fatal("Open failed, code %d.", status); while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { esl_hmx_GrowTo(hmx, sq->n, hmm->M); esl_hmm_Forward(sq->dsq, sq->n, hmm, hmx, &fwdsc); esl_hmm_Forward(sq->dsq, sq->n, bg, hmx, &nullsc); printf("%-16s %5d %11.4f %8.4f %11.4f %8.4f %11.4f %8.4f\n", sq->name, (int) sq->n, fwdsc * eslCONST_LOG2R, (fwdsc * eslCONST_LOG2R) / sq->n, nullsc * eslCONST_LOG2R, (nullsc * eslCONST_LOG2R) / sq->n, (fwdsc - nullsc) * eslCONST_LOG2R, (fwdsc-nullsc) * eslCONST_LOG2R / sq->n); esl_sq_Reuse(sq); } if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp)); else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s", status, sqfp->filename); esl_sqfile_Close(sqfp); esl_sq_Destroy(sq); esl_hmm_Destroy(hmm); esl_hmm_Destroy(bg); esl_hmx_Destroy(hmx); esl_alphabet_Destroy(abc); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_STOPWATCH *w = esl_stopwatch_Create(); int N = esl_opt_GetInteger(go, "-N"); int i; float *A, *B, *C; p7_FLogsumInit(); /* Create the problem: sample N values A,B on interval -1000,1000: about the range of H3 scores */ A = malloc(sizeof(float) * N); B = malloc(sizeof(float) * N); C = malloc(sizeof(float) * N); for (i = 0; i < N; i++) { A[i] = esl_random(r) * 2000. - 1000.; B[i] = esl_random(r) * 2000. - 1000.; } /* Run */ esl_stopwatch_Start(w); if (esl_opt_GetBoolean(go, "-n")) { for (i = 0; i < N; i++) C[i] = naive2(A[i], B[i]); } else if (esl_opt_GetBoolean(go, "-r")) { for (i = 0; i < N; i++) C[i] = naive1(A[i], B[i]); } else { for (i = 0; i < N; i++) C[i] = p7_FLogsum(A[i], B[i]); } esl_stopwatch_Stop(w); esl_stopwatch_Display(stdout, w, "# CPU time: "); esl_stopwatch_Destroy(w); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); int be_verbose = esl_opt_GetBoolean(go, "-v"); if (be_verbose) printf("p7_bg unit test: rng seed %" PRIu32 "\n", esl_randomness_GetSeed(rng)); utest_ReadWrite(rng); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); p7_FLogsumInit(); utest_FLogsumError(go, r); utest_FLogsumSpecials(); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return eslOK; }
int main(int argc, char **argv) { ESL_GETOPTS *go = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *rng = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); fprintf(stderr, "## %s\n", argv[0]); fprintf(stderr, "# rng seed = %" PRIu32 "\n", esl_randomness_GetSeed(rng)); utest_sampling(rng); fprintf(stderr, "# status = ok\n"); esl_randomness_Destroy(rng); esl_getopts_Destroy(go); exit(0); /* success */ }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); double vertex[] = { 1.0, 2.0, 4.0, 5.0, 7.0, 8.0 }; int na1 = 3, a1[] = { 0, 0, 1, 1, 2, 2 }; /* correct answer when threshold = 1.5 */ int na2 = 6, a2[] = { 0, 1, 2, 3, 4, 5 }; /* correct answer when threshold < 1.0 */ int na3 = 1, a3[] = { 0, 0, 0, 0, 0, 0 }; /* correct answer when threshold > 2.0 */ int n = sizeof(vertex) / sizeof(double); utest_singlelinkage(vertex, n, 1.5, a1, na1); utest_singlelinkage(vertex, n, 0.5, a2, na2); utest_singlelinkage(vertex, n, 2.5, a3, na3); esl_getopts_Destroy(go); return 0; }
int main(int argc, char **argv) { ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage); ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s")); ESL_ALPHABET *abc = NULL; P7_HMM *hmm = NULL; P7_PROFILE *gm = NULL; P7_OPROFILE *om = NULL; P7_BG *bg = NULL; ESL_DSQ *dsq = NULL; ESL_SQ *sq = NULL; int M = 6; int L = 10; int ntrace = 1000; if ((abc = esl_alphabet_Create(eslAMINO)) == NULL) esl_fatal("failed to create alphabet"); if (p7_hmm_Sample(r, M, abc, &hmm) != eslOK) esl_fatal("failed to sample an HMM"); if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create null model"); if ((gm = p7_profile_Create(hmm->M, abc)) == NULL) esl_fatal("failed to create profile"); if (p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL) != eslOK) esl_fatal("failed to config profile"); if ((om = p7_oprofile_Create(gm->M, abc)) == NULL) esl_fatal("failed to create optimized profile"); if (p7_oprofile_Convert(gm, om) != eslOK) esl_fatal("failed to convert profile"); /* Test with randomly generated (iid) sequence */ if ((dsq = malloc(sizeof(ESL_DSQ) *(L+2))) == NULL) esl_fatal("malloc failed"); if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal("seq generation failed"); utest_stotrace(go, r, abc, gm, om, dsq, L, ntrace); /* Test with seq sampled from profile */ if ((sq = esl_sq_CreateDigital(abc)) == NULL) esl_fatal("sequence allocation failed"); if (p7_ProfileEmit(r, hmm, gm, bg, sq, NULL) != eslOK) esl_fatal("profile emission failed"); utest_stotrace(go, r, abc, gm, om, sq->dsq, sq->n, ntrace); esl_sq_Destroy(sq); free(dsq); p7_oprofile_Destroy(om); p7_profile_Destroy(gm); p7_bg_Destroy(bg); p7_hmm_Destroy(hmm); esl_alphabet_Destroy(abc); esl_randomness_Destroy(r); esl_getopts_Destroy(go); return 0; }