int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *fwd = NULL;
P7_GMX *bck = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float fsc, bsc;
float nullsc;
int status;
/* Initialize log-sum calculator */
p7_FLogsumInit();
/* Read in one HMM */
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);
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
/* Now reconfig the models however we were asked to */
if (esl_opt_GetBoolean(go, "--fs")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
else if (esl_opt_GetBoolean(go, "--sw")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
else if (esl_opt_GetBoolean(go, "--ls")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_GLOCAL);
else if (esl_opt_GetBoolean(go, "--s")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNIGLOCAL);
/* Allocate matrices */
fwd = p7_gmx_Create(gm->M, sq->n);
bck = p7_gmx_Create(gm->M, sq->n);
printf("%-30s %-10s %-10s %-10s %-10s\n", "# seq name", "fwd (raw)", "bck (raw) ", "fwd (bits)", "bck (bits)");
printf("%-30s %10s %10s %10s %10s\n", "#--------------", "----------", "----------", "----------", "----------");
while ( (status = esl_sqio_Read(sqfp, sq)) != eslEOF)
{
if (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslOK) p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);
/* Resize the DP matrices if necessary */
p7_gmx_GrowTo(fwd, gm->M, sq->n);
p7_gmx_GrowTo(bck, gm->M, sq->n);
/* Set the profile and null model's target length models */
p7_bg_SetLength(bg, sq->n);
p7_ReconfigLength(gm, sq->n);
/* Run Forward, Backward */
p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);
p7_gmx_Dump(stdout, fwd, p7_DEFAULT);
/* Those scores are partial log-odds likelihoods in nats.
* Subtract off the rest of the null model, convert to bits.
*/
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
printf("%-30s %10.4f %10.4f %10.4f %10.4f\n",
sq->name,
fsc, bsc,
(fsc - nullsc) / eslCONST_LOG2, (bsc - nullsc) / eslCONST_LOG2);
p7_gmx_Reuse(fwd);
p7_gmx_Reuse(bck);
esl_sq_Reuse(sq);
}
/* Cleanup */
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
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_getopts_Destroy(go);
return 0;
}
void run_hmmer_pipeline(const char* seq) {
int index, i, status;
ESL_SQ* sq = esl_sq_CreateFrom(NULL, seq, NULL, NULL, NULL);
P7_OPROFILE *om = NULL;
P7_PROFILE *gm = NULL;
float usc, vfsc, fwdsc; /* filter scores */
float filtersc; /* HMM null filter score */
float nullsc; /* null model score */
float seqbias;
float seq_score; /* the corrected per-seq bit score */
double P;
WRAPPER_RESULT* result;
num_results = 0;
if(sq->n == 0) {
esl_sq_Destroy(sq);
return;
}
esl_sq_Digitize(abc, sq);
int n = 0;
float oasc;
for(index = 0;index < num_models;index++) {
om = models[index];
p7_omx_Reuse(oxf);
p7_omx_Reuse(oxb);
p7_omx_GrowTo(oxf, om->M, sq->n, sq->n);
p7_omx_GrowTo(oxb, om->M, sq->n, sq->n);
p7_oprofile_ReconfigLength(om, sq->n);
p7_bg_SetFilter(bg, om->M, om->compo);
p7_bg_SetLength(bg, sq->n);
//Calibrate null model
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
//MSV Filter
p7_MSVFilter(sq->dsq, sq->n, om, oxf, &usc);
seq_score = (usc - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Bias filter (model compo)
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
seq_score = (usc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Viterbi filter (Only do if P value from Bias is high)
if(P > f2) {
p7_ViterbiFilter(sq->dsq, sq->n, om, oxf, &vfsc);
seq_score = (vfsc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
if (P > f2) continue;
}
//Get the real probability (forward)
p7_Forward(sq->dsq, sq->n, om, oxf, &fwdsc);
seq_score = (fwdsc - filtersc) / eslCONST_LOG2;
P = esl_exp_surv(seq_score, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]);
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
if (P > f3) continue;
//Real hit, go in to posterior decoding and alignment
p7_omx_Reuse(oxb);
p7_trace_Reuse(tr);
p7_Backward(sq->dsq, sq->n, om, oxf, oxb, NULL);
status = p7_Decoding(om, oxf, oxb, oxb);
if(status == eslOK) {
//And then trace the result
p7_OptimalAccuracy(om, oxb, oxf, &oasc);
p7_OATrace(om, oxb, oxf, tr);
} else if(status == eslERANGE) {
fprintf(stderr, "Decoding overflow on model %s\n", om->name);
gm = gmodels[index];
if(gxf == NULL) {
gxf = p7_gmx_Create(gm->M, sq->n);
gxb = p7_gmx_Create(gm->M, sq->n);
} else {
p7_gmx_GrowTo(gxf, gm->M, sq->n);
p7_gmx_GrowTo(gxb, gm->M, sq->n);
}
p7_ReconfigLength(gm, sq->n);
p7_GForward (sq->dsq, sq->n, gm, gxf, &fwdsc);
p7_GBackward(sq->dsq, sq->n, gm, gxb, NULL);
p7_GDecoding(gm, gxf, gxb, gxb);
p7_GOptimalAccuracy(gm, gxb, gxf, &oasc);
p7_GOATrace (gm, gxb, gxf, tr);
p7_gmx_Reuse(gxf);
p7_gmx_Reuse(gxb);
}
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
result = wrapper_results[num_results];
reuse_result(result, tr->N + om->M, om->name); //We're way overallocating here, but it's hard to know at this point how much space we'll need for the alignment (plus leading and trailing gaps)
trace_into(tr, result, sq, abc, om->M);
result->bits = seq_score;
num_results++;
}
esl_sq_Destroy(sq);
}
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 *fwd = NULL;
P7_GMX *bck = 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_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);
fwd = p7_gmx_Create(gm->M, L);
bck = 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);
if (! esl_opt_GetBoolean(go, "-B")) p7_GForward (dsq, L, gm, fwd, &sc);
if (! esl_opt_GetBoolean(go, "-F")) p7_GBackward(dsq, L, gm, bck, NULL);
p7_gmx_Reuse(fwd);
p7_gmx_Reuse(bck);
}
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(bck);
p7_gmx_Destroy(fwd);
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;
}