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, 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;
}
static void
utest_Compare(void)
{
ESL_RANDOMNESS *r = esl_randomness_CreateFast(42);
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_PROFILE *gm2 = NULL;
int M = 200;
int L = 400;
p7_modelsample(r, M, abc, &hmm); /* master and worker's sampled profiles are identical */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
gm2 = p7_profile_Create(hmm->M, abc);
p7_profile_Config(gm, hmm, bg);
p7_profile_Config(gm2, hmm, bg);
p7_profile_SetLength(gm, L);
p7_profile_SetLength(gm2, L);
if (p7_profile_Compare(gm, gm2, 0.001) != eslOK) p7_Die("identical profile comparison failed");
p7_profile_Destroy(gm);
p7_profile_Destroy(gm2);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
return;
}
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 = 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)
{
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;
}
static void
utest_SendRecv(ESL_RANDOMNESS *rng, int my_rank, int nproc)
{
char msg[] = "utest_SendRecv() failed";
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
P7_HMM *hmm = NULL;
P7_HMM *xhmm = NULL;
int M = 200;
char *wbuf = NULL;
int wn = 0;
int i;
uint32_t rngseed;
MPI_Status mpistatus;
char errmsg[eslERRBUFSIZE];
if (my_rank == 0)
{
/* First we send our RNG seed to all workers */
rngseed = esl_randomness_GetSeed(rng);
for (i = 1; i < nproc; i++)
if (MPI_Send( &rngseed, 1, MPI_UNSIGNED, i, 0, MPI_COMM_WORLD) != MPI_SUCCESS) esl_fatal(msg);
/* We sample an HMM that's going to be identical to the workers' */
if (p7_modelsample(rng, M, abc, &hmm) != eslOK) esl_fatal(msg);
for (i = 1; i < nproc; i++)
{
if (p7_hmm_mpi_Recv(MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &wbuf, &wn, &abc, &xhmm) != eslOK) esl_fatal(msg);
if (p7_hmm_Validate(xhmm, errmsg, 0.001) != eslOK) esl_fatal("%s:\n %s", msg, errmsg);
if (p7_hmm_Compare(hmm, xhmm, 0.001) != eslOK) esl_fatal(msg);
p7_hmm_Destroy(xhmm);
}
}
else
{
/* Worker(s) must first receive the exact same RNG seed that the master is using. */
if (MPI_Recv(&rngseed, 1, MPI_UNSIGNED, 0, 0, MPI_COMM_WORLD, &mpistatus) != MPI_SUCCESS) esl_fatal(msg);
/* and then the worker(s) can create the exact same RNG (and random number sequence) that the master has */
rng = esl_randomness_CreateFast(rngseed);
/* so when the worker samples this HMM, the master has independently sampled an exact duplicate of it... */
if (p7_modelsample(rng, M, abc, &hmm) != eslOK) esl_fatal(msg);
/* each worker sends the HMM to the master (it's the same HMM for each worker. The test is intended for one master, one worker.) */
if (p7_hmm_mpi_Send(hmm, 0, 0, MPI_COMM_WORLD, &wbuf, &wn) != eslOK) esl_fatal(msg);
/* worker's RNG is a private copy; destroy it. Master keeps its RNG, which the caller is responsible for. */
esl_randomness_Destroy(rng);
}
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
free(wbuf);
return;
}
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;
}
static void
utest_oprofileSendRecv(int my_rank, int nproc)
{
ESL_RANDOMNESS *r = esl_randomness_CreateFast(42);
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OPROFILE *om2 = NULL;
int M = 200;
int L = 400;
char *wbuf = NULL;
int wn = 0;
int i;
char errbuf[eslERRBUFSIZE];
p7_hmm_Sample(r, M, abc, &hmm); /* master and worker's sampled profiles are identical */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
om = p7_oprofile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
p7_oprofile_Convert(gm, om);
p7_bg_SetLength (bg, L);
if (my_rank == 0)
{
for (i = 1; i < nproc; i++)
{
ESL_DPRINTF1(("Master: receiving test profile\n"));
p7_oprofile_MPIRecv(MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &wbuf, &wn, &abc, &om2);
ESL_DPRINTF1(("Master: test profile received\n"));
if (p7_oprofile_Compare(om, om2, 0.001, errbuf) != eslOK)
p7_Die("Received profile not identical to what was sent\n%s", errbuf);
p7_oprofile_Destroy(om2);
}
}
else
{
ESL_DPRINTF1(("Worker %d: sending test profile\n", my_rank));
p7_oprofile_MPISend(om, 0, 0, MPI_COMM_WORLD, &wbuf, &wn);
ESL_DPRINTF1(("Worker %d: test profile sent\n", my_rank));
}
free(wbuf);
p7_profile_Destroy(gm);
p7_oprofile_Destroy(om);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
return;
}
int
main(int argc, char **argv)
{
char *hmmfile = argv[1]; /* name of HMM file to read one HMM from */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
ESL_RANDOMNESS *r = NULL; /* source of randomness */
P7_HMMFILE *hfp = NULL; /* open hmmfile */
P7_HMM *hmm = NULL; /* HMM to emit from */
P7_PROFILE *gm = NULL; /* profile HMM (scores) */
P7_BG *bg = NULL; /* null model */
P7_TRACE *tr = NULL; /* sampled trace */
ESL_SQ *sq = NULL; /* sampled digital sequence */
int n = 1000;
int counts[p7T_NSTATETYPES];
int i;
float sc;
float nullsc;
double bitscore;
r = esl_randomness_CreateFast(0);
tr = p7_trace_Create();
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("failed to open %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("failed to read HMM");
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
for (i = 0; i < n; i++)
{
p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
p7_trace_GetStateUseCounts(tr, counts);
p7_ReconfigLength(gm, sq->n);
p7_bg_SetLength(bg, sq->n);
p7_trace_Score(tr, sq->dsq, gm, &sc);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
bitscore = (sc - nullsc)/ eslCONST_LOG2;
printf("%d %8.4f\n",
counts[p7T_M] + (counts[p7T_I] + counts[p7T_D])/2,
bitscore);
}
p7_profile_Destroy(gm);
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
esl_randomness_Destroy(r);
esl_alphabet_Destroy(abc);
p7_hmmfile_Close(hfp);
p7_hmm_Destroy(hmm);
return eslOK;
}
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);
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;
}
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_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *fwd = NULL;
P7_GMX *bck = NULL;
ESL_DSQ *dsq = NULL;
int M = esl_opt_GetInteger(go, "-M");
int L = esl_opt_GetInteger(go, "-L");
/* Sample a random HMM */
p7_hmm_Sample(r, M, abc, &hmm);
/* Configure a profile from the sampled 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);
/* Other initial allocations */
dsq = malloc(sizeof(ESL_DSQ) * (L+2));
fwd = p7_gmx_Create(gm->M, L);
bck = p7_gmx_Create(gm->M, L);
p7_FLogsumInit();
utest_correct_normalization(r, gm, bg, dsq, L, fwd, bck);
free(dsq);
p7_gmx_Destroy(fwd);
p7_gmx_Destroy(bck);
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 = esl_alphabet_Create(eslAMINO);
P7_BG *bg = p7_bg_Create(abc);
int M = esl_opt_GetInteger(go, "-M");
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
float tol = esl_opt_GetReal (go, "-t");
p7_FLogsumInit();
utest_decoding(r, abc, bg, M, L, N, tol);
esl_getopts_Destroy(go);
esl_randomness_Destroy(r);
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
return eslOK;
}
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;
int M = esl_opt_GetInteger(go, "-M");
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
/* First round of tests for DNA alphabets. */
if ((abc = esl_alphabet_Create(eslDNA)) == NULL) esl_fatal("failed to create alphabet");
if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create null model");
if (esl_opt_GetBoolean(go, "-v")) printf("ViterbiFilter() tests, DNA\n");
utest_viterbi_filter(r, abc, bg, M, L, N);
utest_viterbi_filter(r, abc, bg, 1, L, 10);
utest_viterbi_filter(r, abc, bg, M, 1, 10);
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
/* Second round of tests for amino alphabets. */
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 (esl_opt_GetBoolean(go, "-v")) printf("ViterbiFilter() tests, protein\n");
utest_viterbi_filter(r, abc, bg, M, L, N);
utest_viterbi_filter(r, abc, bg, 1, L, 10);
utest_viterbi_filter(r, abc, bg, M, 1, 10);
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
esl_getopts_Destroy(go);
esl_randomness_Destroy(r);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_ALPHABET *abc = NULL;
ESL_RANDOMNESS *r = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
int M = 10000;
if ((abc = esl_alphabet_Create(eslAMINO)) == NULL) esl_fatal("failed to create amino alphabet");
if ((r = esl_randomness_CreateFast(0)) == NULL) esl_fatal("failed to create randomness");
if (p7_hmm_Sample(r, M, abc, &hmm) != eslOK) esl_fatal("failed to sample random HMM");
if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to created null model");
utest_Config(hmm, bg);
utest_occupancy(hmm);
p7_hmm_Destroy(hmm);
p7_bg_Destroy(bg);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
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_ReadWrite(rng);
utest_alphabet_config(eslAMINO);
utest_alphabet_config(eslDNA);
utest_alphabet_config(eslRNA);
utest_alphabet_config(eslCOINS);
utest_alphabet_config(eslDICE);
esl_randomness_Destroy(rng);
esl_getopts_Destroy(go);
fprintf(stderr, "# status = ok\n");
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_ALPHABET *abc = NULL;
P7_BG *bg = NULL;
int M = esl_opt_GetInteger(go, "-M");
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
/* first round of tests for DNA alphabets. */
if ((abc = esl_alphabet_Create(eslDNA)) == NULL) esl_fatal("failed to create alphabet");
if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create null model");
utest_optacc(go, r, abc, bg, M, L, N); /* normal sized models */
utest_optacc(go, r, abc, bg, 1, L, 10); /* size 1 models */
utest_optacc(go, r, abc, bg, M, 1, 10); /* size 1 sequences */
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
/* Second round of tests for amino alphabets. */
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");
utest_optacc(go, r, abc, bg, M, L, N);
utest_optacc(go, r, abc, bg, 1, L, 10);
utest_optacc(go, r, abc, bg, M, 1, 10);
esl_alphabet_Destroy(abc);
p7_bg_Destroy(bg);
esl_getopts_Destroy(go);
esl_randomness_Destroy(r);
return eslOK;
}
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_OPROFILE *om = NULL;
P7_OMX *ox1 = NULL;
P7_OMX *ox2 = 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,j,d,pos;
int nsamples = 200;
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);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
ox1 = p7_omx_Create(gm->M, L, L);
ox2 = p7_omx_Create(gm->M, L, L);
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_Forward (dsq, L, om, ox1, &fsc);
if (esl_opt_GetBoolean(go, "-t"))
{
P7_TRACE *tr = p7_trace_Create();
float *n2sc = malloc(sizeof(float) * (L+1));
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{ /* This is approximately what p7_domaindef.c::region_trace_ensemble() is doing: */
for (j = 0; j < nsamples; j++)
{
p7_StochasticTrace(r, dsq, L, om, ox1, tr);
p7_trace_Index(tr);
pos = 1;
for (d = 0; d < tr->ndom; d++)
{
p7_Null2_ByTrace(om, tr, tr->tfrom[d], tr->tto[d], ox2, null2);
for (; pos <= tr->sqfrom[d]; pos++) n2sc[pos] += 1.0;
for (; pos < tr->sqto[d]; pos++) n2sc[pos] += null2[dsq[pos]];
}
for (; pos <= L; pos++) n2sc[pos] += 1.0;
p7_trace_Reuse(tr);
}
for (pos = 1; pos <= L; pos++)
n2sc[pos] = logf(n2sc[pos] / nsamples);
}
esl_stopwatch_Stop(w);
free(n2sc);
p7_trace_Destroy(tr);
}
else
{
p7_Backward(dsq, L, om, ox1, ox2, &bsc);
p7_Decoding(om, ox1, ox2, ox2);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
p7_Null2_ByExpectation(om, ox2, null2);
esl_stopwatch_Stop(w);
}
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(ox1);
p7_omx_Destroy(ox2);
p7_oprofile_Destroy(om);
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 = esl_getopts_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 *gx = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc;
double base_time, bench_time, Mcs;
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");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
gx = p7_gmx_Create(gm->M, L);
/* Baseline time. */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
/* Benchmark time. */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_GViterbi (dsq, L, gm, gx, &sc);
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_gmx_Destroy(gx);
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 = 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;
P7_TRACE *tr = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float fsc, bsc, accscore;
double Mcs;
p7_FLogsumInit();
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_UNILOCAL);
gx1 = p7_gmx_Create(gm->M, L);
gx2 = p7_gmx_Create(gm->M, L);
tr = p7_trace_CreateWithPP();
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); /* <gx2> is now the posterior decoding matrix */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
p7_GOptimalAccuracy(gm, gx2, gx1, &accscore); /* <gx1> is now the OA matrix */
if (! esl_opt_GetBoolean(go, "--notrace"))
{
p7_GOATrace(gm, gx2, gx1, tr);
p7_trace_Reuse(tr);
}
}
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_trace_Destroy(tr);
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 = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
int N = esl_opt_GetInteger(go, "-N");
int M = esl_opt_GetInteger(go, "-M");
P7_TOPHITS **h = NULL;
P7_HIT *hit = NULL;
double *sortkeys = NULL;
char name[] = "not_unique_name";
char acc[] = "not_unique_acc";
char desc[] = "Test description for the purposes of making the benchmark allocate space";
int i,j;
int status;
/* prep work: generate our sort keys before starting to time anything */
ESL_ALLOC(h, sizeof(P7_TOPHITS *) * M); /* allocate pointers for M lists */
ESL_ALLOC(sortkeys, sizeof(double) * N * M);
for (i = 0; i < N*M; i++) sortkeys[i] = esl_random(r);
esl_stopwatch_Start(w);
/* generate M "random" lists and sort them */
for (j = 0; j < M; j++)
{
h[j] = p7_tophits_Create(p7_TOPHITS_DEFAULT_INIT_ALLOC);
for (i = 0; i < N; i++)
{
p7_tophits_CreateNextHit(h[j], &hit);
esl_strdup(name, -1, &(hit->name));
esl_strdup(acc, -1, &(hit->acc));
esl_strdup(desc, -1, &(hit->desc));
hit->sortkey = sortkeys[j*N + i];
hit->score = (float) sortkeys[j*N+i];
hit->pre_score = 0.0;
hit->sum_score = 0.0;
hit->lnP = sortkeys[j*N+i];
hit->pre_lnP = 0.0;
hit->sum_lnP = 0.0;
hit->ndom = N;
hit->noverlaps = 0;
hit->nexpected = 0;
hit->flags = 0;
hit->nreported = 0;
hit->nincluded = 0;
hit->best_domain = 0;
hit->dcl = NULL;
}
p7_tophits_SortBySortkey(h[j]);
}
/* then merge them into one big list in h[0] */
for (j = 1; j < M; j++)
{
p7_tophits_Merge(h[0], h[j]);
p7_tophits_Destroy(h[j]);
}
esl_stopwatch_Stop(w);
p7_tophits_Destroy(h[0]);
status = eslOK;
ERROR:
esl_getopts_Destroy(go);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
if (sortkeys != NULL) free(sortkeys);
if (h != NULL) free(h);
return status;
}
int
main(int argc, char **argv)
{
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_RANDOMNESS *r = NULL; /* source of randomness */
P7_HMM *hmm = NULL; /* sampled HMM to emit from */
P7_HMM *core = NULL; /* safe copy of the HMM, before config */
P7_BG *bg = NULL; /* null model */
ESL_SQ *sq = NULL; /* sampled sequence */
P7_TRACE *tr = NULL; /* sampled trace */
P7_PROFILE *gm = NULL; /* profile */
int i,j;
int i1,i2;
int k1,k2;
int iseq;
FILE *fp = NULL;
double expected;
int do_ilocal;
char *hmmfile = NULL;
int nseq;
int do_swlike;
int do_ungapped;
int L;
int M;
int do_h2;
char *ipsfile = NULL;
char *kpsfile = NULL;
ESL_DMATRIX *imx = NULL;
ESL_DMATRIX *kmx = NULL;
ESL_DMATRIX *iref = NULL; /* reference matrix: expected i distribution under ideality */
int Lbins;
int status;
char errbuf[eslERRBUFSIZE];
/*****************************************************************
* Parse the command line
*****************************************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal("Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") == TRUE) {
puts(usage);
puts("\n where options are:\n");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2 = indentation; 80=textwidth*/
return eslOK;
}
do_ilocal = esl_opt_GetBoolean(go, "-i");
hmmfile = esl_opt_GetString (go, "-m");
nseq = esl_opt_GetInteger(go, "-n");
do_swlike = esl_opt_GetBoolean(go, "-s");
do_ungapped = esl_opt_GetBoolean(go, "-u");
L = esl_opt_GetInteger(go, "-L");
M = esl_opt_GetInteger(go, "-M");
do_h2 = esl_opt_GetBoolean(go, "-2");
ipsfile = esl_opt_GetString (go, "--ips");
kpsfile = esl_opt_GetString (go, "--kps");
if (esl_opt_ArgNumber(go) != 0) {
puts("Incorrect number of command line arguments.");
printf("Usage: %s [options]\n", argv[0]);
return eslFAIL;
}
r = esl_randomness_CreateFast(0);
if (hmmfile != NULL)
{ /* Read the HMM (and get alphabet from it) */
P7_HMMFILE *hfp = NULL;
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);
if ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslOK) {
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 esl_fatal("Unexpected error in reading HMMs");
}
M = hmm->M;
p7_hmmfile_Close(hfp);
}
else
{ /* Or sample the HMM (create alphabet first) */
abc = esl_alphabet_Create(eslAMINO);
if (do_ungapped) p7_hmm_SampleUngapped(r, M, abc, &hmm);
else if (do_swlike) p7_hmm_SampleUniform (r, M, abc, 0.05, 0.5, 0.05, 0.2, &hmm); /* tmi, tii, tmd, tdd */
else p7_hmm_Sample (r, M, abc, &hmm);
}
Lbins = M;
imx = esl_dmatrix_Create(Lbins, Lbins);
iref = esl_dmatrix_Create(Lbins, Lbins);
kmx = esl_dmatrix_Create(M, M);
esl_dmatrix_SetZero(imx);
esl_dmatrix_SetZero(iref);
esl_dmatrix_SetZero(kmx);
tr = p7_trace_Create();
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
core = p7_hmm_Clone(hmm);
if (do_h2) {
gm = p7_profile_Create(hmm->M, abc);
p7_H2_ProfileConfig(hmm, bg, gm, p7_UNILOCAL);
} else {
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
if (p7_hmm_Validate (hmm, NULL, 0.0001) != eslOK) esl_fatal("whoops, HMM is bad!");
if (p7_profile_Validate(gm, NULL, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!");
}
/* Sample endpoints.
* Also sample an ideal reference distribution for i endpoints. i
* endpoints are prone to discretization artifacts, when emitted
* sequences have varying lengths. Taking log odds w.r.t. an ideal
* reference that is subject to the same discretization artifacts
* cancels out the effect.
*/
for (iseq = 0; iseq < nseq; iseq++)
{
if (do_ilocal) ideal_local_endpoints (r, core, sq, tr, Lbins, &i1, &i2, &k1, &k2);
else profile_local_endpoints(r, core, gm, sq, tr, Lbins, &i1, &i2, &k1, &k2);
imx->mx[i1-1][i2-1] += 1.;
kmx->mx[k1-1][k2-1] += 1.;
/* reference distribution for i */
ideal_local_endpoints (r, core, sq, tr, Lbins, &i1, &i2, &k1, &k2);
iref->mx[i1-1][i2-1] += 1.;
}
/* Adjust both mx's to log_2(obs/exp) ratio */
printf("Before normalization/log-odds:\n");
printf(" i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
printf(" k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));
printf("iref matrix values range from %f to %f\n", dmx_upper_min(iref), dmx_upper_max(iref));
expected = (double) nseq * 2. / (double) (M*(M+1));
for (i = 0; i < kmx->m; i++)
for (j = i; j < kmx->n; j++)
kmx->mx[i][j] = log(kmx->mx[i][j] / expected) / log(2.0);
for (i = 0; i < imx->m; i++)
for (j = i; j < imx->m; j++)
if (iref->mx[i][j] == 0. && imx->mx[i][j] == 0.)
imx->mx[i][j] = 0.;
else if (iref->mx[i][j] == 0.)
imx->mx[i][j] = eslINFINITY;
else if (imx->mx[i][j] == 0.)
imx->mx[i][j] = -eslINFINITY;
else
imx->mx[i][j] = log(imx->mx[i][j] / iref->mx[i][j]) / log(2.0);
/* Print ps files */
if (kpsfile != NULL) {
if ((fp = fopen(kpsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", kpsfile);
dmx_Visualize(fp, kmx, -4., 5.);
fclose(fp);
}
if (ipsfile != NULL) {
if ((fp = fopen(ipsfile, "w")) == NULL) esl_fatal("Failed to open output postscript file %s", ipsfile);
dmx_Visualize(fp, imx, -4., 5.);
/* dmx_Visualize(fp, imx, dmx_upper_min(imx), dmx_upper_max(imx)); */
fclose(fp);
}
printf("After normalization/log-odds:\n");
printf("i matrix values range from %f to %f\n", dmx_upper_min(imx), dmx_upper_max(imx));
printf("k matrix values range from %f to %f\n", dmx_upper_min(kmx), dmx_upper_max(kmx));
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(core);
p7_hmm_Destroy(hmm);
p7_trace_Destroy(tr);
esl_sq_Destroy(sq);
esl_dmatrix_Destroy(imx);
esl_dmatrix_Destroy(kmx);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return eslOK;
}
/* Function: p7_Calibrate()
* Synopsis: Calibrate the E-value parameters of a model.
* Incept: SRE, Thu Dec 25 09:29:31 2008 [Magallon]
*
* Purpose: Calibrate the E-value parameters of a model with
* one calculation ($\lambda$) and two brief simulations
* (Viterbi $\mu$, Forward $\tau$).
*
* Args: hmm - HMM to be calibrated
* cfg_b - OPTCFG: ptr to optional build configuration;
* if <NULL>, use default parameters.
* byp_rng - BYPASS optimization: pass ptr to <ESL_RANDOMNESS> generator
* if already known;
* <*byp_rng> == NULL> if <rng> return is desired;
* pass <NULL> to use and discard internal default.
* byp_bg - BYPASS optimization: pass ptr to <P7_BG> if already known;
* <*byp_bg == NULL> if <bg> return is desired;
* pass <NULL> to use and discard internal default.
* byp_gm - BYPASS optimization: pass ptr to <gm> profile if already known;
* pass <*byp_gm == NULL> if <gm> return desired;
* pass <NULL> to use and discard internal default.
* byp_om - BYPASS optimization: pass ptr to <om> profile if already known;
* pass <*byp_om == NULL> if <om> return desired;
* pass <NULL> to use and discard internal default.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
* <eslEINVAL> if <hmm>, <gm>, <om> aren't compatible somehow.
*
* Xref: J4/41
*/
int
p7_Calibrate(P7_HMM *hmm, P7_BUILDER *cfg_b, ESL_RANDOMNESS **byp_rng, P7_BG **byp_bg, P7_PROFILE **byp_gm, P7_OPROFILE **byp_om)
{
P7_BG *bg = (esl_byp_IsProvided(byp_bg) ? *byp_bg : NULL);
P7_PROFILE *gm = (esl_byp_IsProvided(byp_gm) ? *byp_gm : NULL);
P7_OPROFILE *om = (esl_byp_IsProvided(byp_om) ? *byp_om : NULL);
ESL_RANDOMNESS *r = (esl_byp_IsProvided(byp_rng) ? *byp_rng : NULL);
char *errbuf = ((cfg_b != NULL) ? cfg_b->errbuf : NULL);
int EmL = ((cfg_b != NULL) ? cfg_b->EmL : 200);
int EmN = ((cfg_b != NULL) ? cfg_b->EmN : 200);
int EvL = ((cfg_b != NULL) ? cfg_b->EvL : 200);
int EvN = ((cfg_b != NULL) ? cfg_b->EvN : 200);
int EfL = ((cfg_b != NULL) ? cfg_b->EfL : 100);
int EfN = ((cfg_b != NULL) ? cfg_b->EfN : 200);
double Eft = ((cfg_b != NULL) ? cfg_b->Eft : 0.04);
double lambda, mmu, vmu, tau;
int status;
/* Configure any objects we need
* that weren't already passed to us as a bypass optimization
*/
if (r == NULL) {
if ((r = esl_randomness_CreateFast(42)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create RNG");
} else if (cfg_b != NULL && cfg_b->do_reseeding) {
esl_randomness_Init(r, esl_randomness_GetSeed(r));
}
if (bg == NULL) {
if ((bg = p7_bg_Create(hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to allocate background");
}
/* there's an odd case where the <om> is provided and a <gm> isn't going to be returned
* where we don't need a <gm> at all, and <gm> stays <NULL> after the next block.
* Note that the <EvL> length in the ProfileConfig doesn't matter; the individual
* calibration routines MSVMu(), etc. contain their own length reconfig calls.
*/
if ((esl_byp_IsInternal(byp_gm) && ! esl_byp_IsProvided(byp_om)) || esl_byp_IsReturned(byp_gm)) {
if ( (gm = p7_profile_Create(hmm->M, hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to allocate profile");
if ( (status = p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL)) != eslOK) ESL_XFAIL(status, errbuf, "failed to configure profile");
}
if (om == NULL) {
if ((om = p7_oprofile_Create(hmm->M, hmm->abc)) == NULL) ESL_XFAIL(eslEMEM, errbuf, "failed to create optimized profile");
if ((status = p7_oprofile_Convert(gm, om)) != eslOK) ESL_XFAIL(status, errbuf, "failed to convert to optimized profile");
}
/* The calibration steps themselves */
if ((status = p7_Lambda(hmm, bg, &lambda)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine lambda");
if ((status = p7_MSVMu (r, om, bg, EmL, EmN, lambda, &mmu)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine msv mu");
if ((status = p7_ViterbiMu(r, om, bg, EvL, EvN, lambda, &vmu)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine vit mu");
if ((status = p7_Tau (r, om, bg, EfL, EfN, lambda, Eft, &tau)) != eslOK) ESL_XFAIL(status, errbuf, "failed to determine fwd tau");
/* Store results */
hmm->evparam[p7_MLAMBDA] = om->evparam[p7_MLAMBDA] = lambda;
hmm->evparam[p7_VLAMBDA] = om->evparam[p7_VLAMBDA] = lambda;
hmm->evparam[p7_FLAMBDA] = om->evparam[p7_FLAMBDA] = lambda;
hmm->evparam[p7_MMU] = om->evparam[p7_MMU] = mmu;
hmm->evparam[p7_VMU] = om->evparam[p7_VMU] = vmu;
hmm->evparam[p7_FTAU] = om->evparam[p7_FTAU] = tau;
hmm->flags |= p7H_STATS;
if (gm != NULL) {
gm->evparam[p7_MLAMBDA] = lambda;
gm->evparam[p7_VLAMBDA] = lambda;
gm->evparam[p7_FLAMBDA] = lambda;
gm->evparam[p7_MMU] = mmu;
gm->evparam[p7_VMU] = vmu;
gm->evparam[p7_FTAU] = tau;
}
if (byp_rng != NULL) *byp_rng = r; else esl_randomness_Destroy(r); /* bypass convention: no-op if rng was provided.*/
if (byp_bg != NULL) *byp_bg = bg; else p7_bg_Destroy(bg); /* bypass convention: no-op if bg was provided. */
if (byp_gm != NULL) *byp_gm = gm; else p7_profile_Destroy(gm); /* bypass convention: no-op if gm was provided. */
if (byp_om != NULL) *byp_om = om; else p7_oprofile_Destroy(om); /* bypass convention: no-op if om was provided. */
return eslOK;
ERROR:
if (! esl_byp_IsProvided(byp_rng)) esl_randomness_Destroy(r);
if (! esl_byp_IsProvided(byp_bg)) p7_bg_Destroy(bg);
if (! esl_byp_IsProvided(byp_gm)) p7_profile_Destroy(gm);
if (! esl_byp_IsProvided(byp_om)) p7_oprofile_Destroy(om);
return status;
}
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_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_OPROFILE *om = NULL;
double lambda = 0.0;
double mmu = 0.0;
double vmu = 0.0;
double ftau = 0.0;
int Z = esl_opt_GetInteger(go, "-Z");
int EmL = esl_opt_GetInteger(go, "--EmL");
int EmN = esl_opt_GetInteger(go, "--EmN");
int EvL = esl_opt_GetInteger(go, "--EvL");
int EvN = esl_opt_GetInteger(go, "--EvN");
int EfL = esl_opt_GetInteger(go, "--EfL");
int EfN = esl_opt_GetInteger(go, "--EfN");
int Eft = esl_opt_GetReal (go, "--Eft");
int iteration;
int do_msv, do_vit, do_fwd;
int status;
if (esl_opt_GetBoolean(go, "--msvonly") == TRUE) { do_msv = TRUE; do_vit = FALSE; do_fwd = FALSE; }
else if (esl_opt_GetBoolean(go, "--vitonly") == TRUE) { do_msv = FALSE; do_vit = TRUE; do_fwd = FALSE; }
else if (esl_opt_GetBoolean(go, "--fwdonly") == TRUE) { do_msv = FALSE; do_vit = FALSE; do_fwd = TRUE; }
else { do_msv = TRUE; do_vit = TRUE; do_fwd = TRUE; }
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
while ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
{
if (bg == NULL) bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, EvL, p7_LOCAL); /* the EvL doesn't matter */
om = p7_oprofile_Create(hmm->M, abc);
p7_oprofile_Convert(gm, om);
if (esl_opt_IsOn(go, "--lambda")) lambda = esl_opt_GetReal(go, "--lambda");
else p7_Lambda(hmm, bg, &lambda);
for (iteration = 0; iteration < Z; iteration++)
{
if (do_msv) p7_MSVMu (r, om, bg, EmL, EmN, lambda, &mmu);
if (do_vit) p7_ViterbiMu (r, om, bg, EvL, EvN, lambda, &vmu);
if (do_fwd) p7_Tau (r, om, bg, EfL, EfN, lambda, Eft, &ftau);
printf("%s %.4f %.4f %.4f %.4f\n", hmm->name, lambda, mmu, vmu, ftau);
}
p7_hmm_Destroy(hmm);
p7_profile_Destroy(gm);
p7_oprofile_Destroy(om);
}
p7_hmmfile_Close(hfp);
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);
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_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc1, sc2;
double base_time, bench_time, Mcs;
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");
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);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsVF(om, gm);
ox = p7_omx_Create(gm->M, 0, 0);
gx = p7_gmx_Create(gm->M, L);
/* Get a baseline time: how long it takes just to generate the sequences */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
/* Run the benchmark */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_ViterbiFilter(dsq, L, om, ox, &sc1);
if (esl_opt_GetBoolean(go, "-c"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
printf("%.4f %.4f\n", sc1, sc2);
}
if (esl_opt_GetBoolean(go, "-x"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
sc2 /= om->scale_w;
if (om->mode == p7_UNILOCAL) sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
printf("%.4f %.4f\n", sc1, sc2);
}
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
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;
}
