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);
int N = esl_opt_GetInteger(go, "-N");
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_TRACE *tr = NULL;
ESL_SQ *sq = NULL;
P7_ALIDISPLAY *ad = NULL;
int i,z;
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);
p7_bg_SetLength(bg, 0);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, 0, p7_UNIGLOCAL); /* that sets N,C,J to generate nothing */
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
if (esl_opt_GetBoolean(go, "-p")) tr = p7_trace_CreateWithPP();
else tr = p7_trace_Create();
sq = esl_sq_CreateDigital(abc);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
esl_sq_SetName(sq, "random");
if (! esl_opt_GetBoolean(go, "-b"))
{
if (esl_opt_GetBoolean(go, "-p"))
for (z = 0; z < tr->N; z++)
if (tr->i[z] > 0) tr->pp[z] = esl_random(r);
ad = p7_alidisplay_Create(tr, 0, om, sq);
p7_alidisplay_Print(stdout, ad, 40, 80, FALSE);
p7_alidisplay_Destroy(ad);
}
p7_trace_Reuse(tr);
esl_sq_Reuse(sq);
}
esl_stopwatch_Stop(w);
esl_stopwatch_Display(stdout, w, "# CPU time: ");
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
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_stopwatch_Destroy(w);
esl_getopts_Destroy(go);
return 0;
}
/* Function: p7_tophits_Domains()
* Synopsis: Standard output format for top domain hits and alignments.
*
* Purpose: For each reportable target sequence, output a tabular summary
* of reportable domains found in it, followed by alignments of
* each domain.
*
* Similar to <p7_tophits_Targets()>; see additional notes there.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> if a write to <ofp> fails; for example, if
* the disk fills up.
*/
int
p7_tophits_Domains(FILE *ofp, P7_TOPHITS *th, P7_PIPELINE *pli, int textw)
{
int h, d;
int nd;
int namew, descw;
char *showname;
int status;
if (pli->long_targets)
{
if (fprintf(ofp, "Annotation for each hit %s:\n",
pli->show_alignments ? " (and alignments)" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "Domain annotation for each %s%s:\n",
pli->mode == p7_SEARCH_SEQS ? "sequence" : "model",
pli->show_alignments ? " (and alignments)" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
for (h = 0; h < th->N; h++)
if (th->hit[h]->flags & p7_IS_REPORTED)
{
if (pli->show_accessions && th->hit[h]->acc != NULL && th->hit[h]->acc[0] != '\0')
{
showname = th->hit[h]->acc;
namew = strlen(th->hit[h]->acc);
}
else
{
showname = th->hit[h]->name;
namew = strlen(th->hit[h]->name);
}
if (textw > 0)
{
descw = ESL_MAX(32, textw - namew - 5);
if (fprintf(ofp, ">> %s %-.*s\n", showname, descw, (th->hit[h]->desc == NULL ? "" : th->hit[h]->desc)) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, ">> %s %s\n", showname, (th->hit[h]->desc == NULL ? "" : th->hit[h]->desc)) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if (th->hit[h]->nreported == 0)
{
if (fprintf(ofp," [No individual domains that satisfy reporting thresholds (although complete target did)]\n\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
continue;
}
if (pli->long_targets) {
/* The dna hit table is 119 char wide:
score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to hqfrom hq to sq len acc
------ ----- --------- ------- ------- --------- --------- --------- --------- --------- --------- --------- ----
! 82.7 104.4 4.9e-22 782 998 .. 241981174 241980968 .. 241981174 241980966 .. 241981174 241980968 234234233 0.78
*/
if (fprintf(ofp, " %6s %5s %9s %9s %9s %2s %9s %9s %2s %9s %9s %9s %2s %4s\n", "score", "bias", " Evalue", "hmmfrom", "hmm to", " ", " alifrom ", " ali to ", " ", " envfrom ", " env to ", " sq len ", " ", "acc") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (fprintf(ofp, " %6s %5s %9s %9s %9s %2s %9s %9s %2s %9s %9s %9s %2s %4s\n", "------", "-----", "---------", "-------", "-------", " ", "---------", "---------", " ", "---------", "---------", "---------", " ", "----") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
} else {
/* The domain table is 101 char wide:
# score bias Evalue hmmfrom hmmto alifrom ali to envfrom env to acc
--- ------ ----- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 123.4 23.1 6.8e-9 3 1230 .. 1 492 [] 2 490 .] 0.90
123 ! 1234.5 123.4 123456789 1234567 1234567 .. 1234567 1234567 [] 1234567 1234568 .] 0.12
*/
if (fprintf(ofp, " %3s %6s %5s %9s %9s %7s %7s %2s %7s %7s %2s %7s %7s %2s %4s\n", "#", "score", "bias", "c-Evalue", "i-Evalue", "hmmfrom", "hmm to", " ", "alifrom", "ali to", " ", "envfrom", "env to", " ", "acc") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (fprintf(ofp, " %3s %6s %5s %9s %9s %7s %7s %2s %7s %7s %2s %7s %7s %2s %4s\n", "---", "------", "-----", "---------", "---------", "-------", "-------", " ", "-------", "-------", " ", "-------", "-------", " ", "----") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
nd = 0;
for (d = 0; d < th->hit[h]->ndom; d++)
if (th->hit[h]->dcl[d].is_reported)
{
nd++;
if (pli->long_targets)
{
if (fprintf(ofp, " %c %6.1f %5.1f %9.2g %9d %9d %c%c %9" PRId64 " %9" PRId64 " %c%c %9d %9d %c%c %9" PRId64 " %4.2f\n",
//nd,
th->hit[h]->dcl[d].is_included ? '!' : '?',
th->hit[h]->dcl[d].bitscore,
th->hit[h]->dcl[d].dombias * eslCONST_LOG2R, /* convert NATS to BITS at last moment */
exp(th->hit[h]->dcl[d].lnP),
th->hit[h]->dcl[d].ad->hmmfrom,
th->hit[h]->dcl[d].ad->hmmto,
(th->hit[h]->dcl[d].ad->hmmfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->hmmto == th->hit[h]->dcl[d].ad->M) ? ']' : '.',
th->hit[h]->dcl[d].ad->sqfrom,
th->hit[h]->dcl[d].ad->sqto,
(th->hit[h]->dcl[d].ad->sqfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->sqto == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].iae,
th->hit[h]->dcl[d].ibe,
(th->hit[h]->dcl[d].iae == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ibe == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].ad->L,
(th->hit[h]->dcl[d].oasc / (1.0 + fabs((float) (th->hit[h]->dcl[d].ibe - th->hit[h]->dcl[d].iae))))) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, " %3d %c %6.1f %5.1f %9.2g %9.2g %7d %7d %c%c %7" PRId64 " %7" PRId64 " %c%c %7d %7d %c%c %4.2f\n",
nd,
th->hit[h]->dcl[d].is_included ? '!' : '?',
th->hit[h]->dcl[d].bitscore,
th->hit[h]->dcl[d].dombias * eslCONST_LOG2R, /* convert NATS to BITS at last moment */
exp(th->hit[h]->dcl[d].lnP) * pli->domZ,
exp(th->hit[h]->dcl[d].lnP) * pli->Z,
th->hit[h]->dcl[d].ad->hmmfrom,
th->hit[h]->dcl[d].ad->hmmto,
(th->hit[h]->dcl[d].ad->hmmfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->hmmto == th->hit[h]->dcl[d].ad->M) ? ']' : '.',
th->hit[h]->dcl[d].ad->sqfrom,
th->hit[h]->dcl[d].ad->sqto,
(th->hit[h]->dcl[d].ad->sqfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->sqto == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].iae,
th->hit[h]->dcl[d].ibe,
(th->hit[h]->dcl[d].iae == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ibe == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
(th->hit[h]->dcl[d].oasc / (1.0 + fabs((float) (th->hit[h]->dcl[d].ibe - th->hit[h]->dcl[d].iae))))) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
if (pli->show_alignments)
{
if (pli->long_targets)
{
if (fprintf(ofp, "\n Alignment:\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "\n Alignments for each domain:\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
nd = 0;
}
for (d = 0; d < th->hit[h]->ndom; d++)
if (th->hit[h]->dcl[d].is_reported)
{
nd++;
if (!pli->long_targets)
{
if (fprintf(ofp, " == domain %d", nd ) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if (fprintf(ofp, " score: %.1f bits", th->hit[h]->dcl[d].bitscore) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (!pli->long_targets)
{
if (fprintf(ofp, "; conditional E-value: %.2g\n", exp(th->hit[h]->dcl[d].lnP) * pli->domZ) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if ((status = p7_alidisplay_Print(ofp, th->hit[h]->dcl[d].ad, 40, textw, pli->show_accessions)) != eslOK) return status;
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
else
{
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
if (th->nreported == 0)
{
if (fprintf(ofp, "\n [No targets detected that satisfy reporting thresholds]\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
return eslOK;
}
