/* Function: p7_tophits_Merge()
* Synopsis: Merge two top hits lists.
*
* Purpose: Merge <h2> into <h1>. Upon return, <h1>
* contains the sorted, merged list. <h2>
* is effectively destroyed; caller should
* not access it further, and may as well free
* it immediately.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure, and
* both <h1> and <h2> remain valid.
*/
int
p7_tophits_Merge(P7_TOPHITS *h1, P7_TOPHITS *h2)
{
P7_HIT **new_hit = NULL;
P7_HIT *ori1 = h1->unsrt; /* original base of h1's data */
P7_HIT *new2;
int i,j,k;
int Nalloc = h1->Nalloc + h2->Nalloc;
int status;
/* Make sure the two lists are sorted */
if ((status = p7_tophits_SortBySortkey(h1)) != eslOK) goto ERROR;
if ((status = p7_tophits_SortBySortkey(h2)) != eslOK) goto ERROR;
/* Attempt our allocations, so we fail early if we fail.
* Reallocating h1->unsrt screws up h1->hit, so fix it.
*/
if (( status = p7_hit_Grow( &(h1->unsrt), h1->Nalloc, Nalloc)) != eslOK) goto ERROR;
ESL_ALLOC (new_hit, sizeof(P7_HIT *) * Nalloc);
for (i = 0; i < h1->N; i++)
h1->hit[i] = h1->unsrt + (h1->hit[i] - ori1);
/* Append h2's unsorted data array to h1. h2's data begin at <new2> */
new2 = h1->unsrt + h1->N;
memcpy(new2, h2->unsrt, sizeof(P7_HIT) * h2->N);
/* Merge the sorted hit lists */
for (i=0,j=0,k=0; i < h1->N && j < h2->N ; k++)
new_hit[k] = (hit_sorter_by_sortkey(&h1->hit[i], &h2->hit[j]) > 0) ? new2 + (h2->hit[j++] - h2->unsrt) : h1->hit[i++];
while (i < h1->N) new_hit[k++] = h1->hit[i++];
while (j < h2->N) new_hit[k++] = new2 + (h2->hit[j++] - h2->unsrt);
/* h2 now turns over management of name, acc, desc memory to h1;
* nullify its pointers, to prevent double free. */
for (i = 0; i < h2->N; i++)
{
h2->unsrt[i].name = NULL;
h2->unsrt[i].acc = NULL;
h2->unsrt[i].desc = NULL;
h2->unsrt[i].dcl = NULL;
}
/* Construct the new grown h1 */
free(h1->hit);
h1->hit = new_hit;
h1->Nalloc = Nalloc;
h1->N += h2->N;
/* and is_sorted is TRUE, as a side effect of p7_tophits_Sort() above. */
return eslOK;
ERROR:
if (new_hit != NULL) free(new_hit);
return status;
}
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 = 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;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmdb> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail().
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* output file for results (default stdout) */
FILE *tblfp = NULL; /* output stream for tabular per-seq (--tblout) */
FILE *dfamtblfp = NULL; /* output stream for tabular Dfam format (--dfamtblout) */
FILE *aliscoresfp = NULL; /* output stream for alignment scores (--aliscoresout) */
// P7_HMM *hmm = NULL; /* one HMM query */
// P7_SCOREDATA *scoredata = NULL;
int seqfmt = eslSQFILE_UNKNOWN; /* format of seqfile */
ESL_SQFILE *sqfp = NULL; /* open seqfile */
P7_HMMFILE *hfp = NULL; /* open HMM database file */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
P7_OPROFILE *om = NULL; /* target profile */
ESL_STOPWATCH *w = NULL; /* timing */
ESL_SQ *qsq = NULL; /* query sequence */
int nquery = 0;
int textw;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
P7_OM_BLOCK *block = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errbuf[eslERRBUFSIZE];
double window_beta = -1.0 ;
int window_length = -1;
if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) < 0 || window_beta > 1 ) esl_fatal("Invalid window-length beta value\n"); }
if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4 ) esl_fatal("Invalid window length value\n"); }
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
/* If caller declared an input format, decode it */
if (esl_opt_IsOn(go, "--qformat")) {
seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
}
/* validate options if running as a daemon */
// if (esl_opt_IsOn(go, "--daemon")) {
/* running as a daemon, the input format must be type daemon */
// if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
// esl_fatal("Input format %s not supported. Must be daemon\n", esl_opt_GetString(go, "--qformat"));
// seqfmt = eslSQFILE_DAEMON;
// if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
// }
/* Open the target profile database to get the sequence alphabet */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem, trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, cfg->hmmfile, errbuf);
if (! hfp->is_pressed) p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n", hfp->fname);
hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
if (hstatus == eslEFORMAT) p7_Fail("bad format, binary auxfiles, %s:\n%s", cfg->hmmfile, hfp->errbuf);
else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
else if (hstatus != eslOK) p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
p7_oprofile_Destroy(om);
p7_hmmfile_Close(hfp);
/* Open the query sequence database */
status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->seqfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->seqfile);
else if (status == eslEINVAL) p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
if (sqfp->format > 100) // breaking the law! That range is reserved for msa, for aligned formats
p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n", cfg->seqfile);
qsq = esl_sq_CreateDigital(abc);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
output_header(ofp, go, cfg->hmmfile, cfg->seqfile);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(abc);
#ifdef HMMER_THREADS
info[i].queue = queue;
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
block = p7_oprofile_CreateBlock(BLOCK_SIZE);
if (block == NULL) esl_fatal("Failed to allocate sequence block");
status = esl_workqueue_Init(queue, block);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
/* Outside loop: over each query sequence in <seqfile>. */
while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
{
if (sstatus == eslEMEM) p7_Fail("Memory allocation error reading sequence file\n", status);
if (sstatus == eslEINCONCEIVABLE) p7_Fail("Unexpected error %d reading sequence file\n", status);
// if (qsq->L > NHMMER_MAX_RESIDUE_COUNT) p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n", qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);
nquery++;
esl_stopwatch_Start(w);
/* Open the target profile database */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
if (status != eslOK) p7_Fail("Unexpected error %d in opening hmm file %s.\n", status, cfg->hmmfile);
#ifdef HMMER_THREADS
/* if we are threaded, create a lock to prevent multiple readers */
if (ncpus > 0)
{
status = p7_hmmfile_CreateLock(hfp);
if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
}
#endif
if (fprintf(ofp, "Query: %s [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->acc[0] != 0 && fprintf(ofp, "Accession: %s\n", qsq->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
info[i].pli->hfp = hfp; /* for two-stage input, pipeline needs <hfp> */
p7_pli_NewSeq(info[i].pli, qsq);
info[i].qsq = qsq;
if ( esl_opt_IsUsed(go, "--toponly") )
info[i].pli->strand = p7_STRAND_TOPONLY;
else if ( esl_opt_IsUsed(go, "--bottomonly") )
info[i].pli->strand = p7_STRAND_BOTTOMONLY;
else
info[i].pli->strand = p7_STRAND_BOTH;
#ifdef HMMER_THREADS
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
if (ncpus > 0) hstatus = thread_loop(threadObj, queue, hfp);
else hstatus = serial_loop(info, hfp);
#else
hstatus = serial_loop(info, hfp);
#endif
switch(hstatus)
{
case eslEFORMAT: p7_Fail("bad file format in HMM file %s", cfg->hmmfile); break;
case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile); break;
case eslEOF:
case eslOK: /* do nothing */
break;
default: p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
}
/* merge the results of the search results */
for (i = 1; i < infocnt; ++i)
{
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
}
/* modify e-value to account for number of models */
for (i = 0; i < info->th->N ; i++)
{
info->th->unsrt[i].lnP += log((float)info->pli->nmodels);
info->th->unsrt[i].dcl[0].lnP = info->th->unsrt[i].lnP;
info->th->unsrt[i].sortkey = -1.0 * info->th->unsrt[i].lnP;
}
/* it's possible to have duplicates based on how viterbi ranges can overlap */
p7_tophits_SortByModelnameAndAlipos(info->th);
p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);
/* Print results */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
//tally up total number of hits and target coverage
info->pli->n_output = info->pli->pos_output = 0;
for (i = 0; i < info->th->N; i++) {
if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
info->pli->n_output++;
info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
}
}
p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (tblfp) p7_tophits_TabularTargets(tblfp, qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp, qsq->name, NULL, info->th, info->pli);
if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );
esl_stopwatch_Stop(w);
info->pli->nseqs = 1;
p7_pli_Statistics(ofp, info->pli, w);
if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
fflush(ofp);
p7_hmmfile_Close(hfp);
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
esl_sq_Reuse(qsq);
}
if (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (sstatus != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
sstatus, sqfp->filename);
/* Terminate outputs - any last words?
*/
if (tblfp) p7_tophits_TabularTail(tblfp, "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
if (ofp) { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Cleanup - prepare for successful exit
*/
for (i = 0; i < infocnt; ++i)
p7_bg_Destroy(info[i].bg);
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
p7_oprofile_DestroyBlock(block);
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
esl_sq_Destroy(qsq);
esl_stopwatch_Destroy(w);
esl_alphabet_Destroy(abc);
esl_sqfile_Close(sqfp);
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return eslOK;
ERROR:
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return status;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmfile> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail(). We also use the
* ESL_EXCEPTION and ERROR: mechanisms, but only because we know we're
* using a fatal exception handler.
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* results output file (-o) */
P7_HMMFILE *hfp = NULL; /* open input HMM file */
ESL_SQFILE *dbfp = NULL; /* open input sequence file */
P7_HMM *hmm = NULL; /* one HMM query */
ESL_ALPHABET *abc = NULL; /* digital alphabet */
int dbfmt = eslSQFILE_UNKNOWN; /* format code for sequence database file */
ESL_STOPWATCH *w;
int textw = 0;
int nquery = 0;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
char errbuf[eslERRBUFSIZE];
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
if (esl_opt_IsOn(go, "--tformat")) {
dbfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--tformat"));
if (dbfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized sequence database file format\n", esl_opt_GetString(go, "--tformat"));
}
/* Open the target sequence database */
status = esl_sqfile_Open(cfg->dbfile, dbfmt, p7_SEQDBENV, &dbfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->dbfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->dbfile);
else if (status == eslEINVAL) p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->dbfile);
if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) {
if (esl_opt_IsUsed(go, "--ssifile"))
esl_sqfile_OpenSSI(dbfp, esl_opt_GetString(go, "--ssifile"));
else
esl_sqfile_OpenSSI(dbfp, NULL);
}
/* Open the query profile HMM file */
status = p7_hmmfile_OpenE(cfg->hmmfile, NULL, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, cfg->hmmfile, errbuf);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w+")) == NULL) p7_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
infocnt = 1;
ESL_ALLOC(info, sizeof(*info) * infocnt);
/* <abc> is not known 'til first HMM is read. */
hstatus = p7_hmmfile_Read(hfp, &abc, &hmm);
if (hstatus == eslOK)
{
/* One-time initializations after alphabet <abc> becomes known */
// output_header(ofp, go, cfg->hmmfile, cfg->dbfile);
// dbfp->abc = abc; //ReadBlock requires knowledge of the alphabet to decide how best to read blocks
// for (i = 0; i < infocnt; ++i)
// {
// info[i].bg = p7_bg_Create(abc);
// }
}
/* Outer loop: over each query HMM in <hmmfile>. */
// while (hstatus == eslOK)
// {
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL; /* optimized query profile */
nquery++;
esl_stopwatch_Start(w);
/* seqfile may need to be rewound (multiquery mode) */
if (nquery > 1)
{
if (! esl_sqfile_IsRewindable(dbfp))
esl_fatal("Target sequence file %s isn't rewindable; can't search it with multiple queries", cfg->dbfile);
if (! esl_opt_IsUsed(go, "--restrictdb_stkey") )
esl_sqfile_Position(dbfp, 0); //only re-set current position to 0 if we're not planning to set it in a moment
}
if ( cfg->firstseq_key != NULL ) { //it's tempting to want to do this once and capture the offset position for future passes, but ncbi files make this non-trivial, so this keeps it general
sstatus = esl_sqfile_PositionByKey(dbfp, cfg->firstseq_key);
if (sstatus != eslOK)
p7_Fail("Failure setting restrictdb_stkey to %d\n", cfg->firstseq_key);
}
// if (fprintf(ofp, "Query: %s [M=%d]\n", hmm->name, hmm->M) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
// if (hmm->acc) { if (fprintf(ofp, "Accession: %s\n", hmm->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
// if (hmm->desc) { if (fprintf(ofp, "Description: %s\n", hmm->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Convert to an optimized model */
gm = p7_profile_Create (hmm->M, abc);
om = p7_oprofile_Create(hmm->M, abc);
// p7_ProfileConfig(hmm, info->bg, gm, 100, p7_LOCAL); /* 100 is a dummy length for now; and MSVFilter requires local mode */
p7_oprofile_Convert(gm, om); /* <om> is now p7_LOCAL, multihit */
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].om = p7_oprofile_Clone(om);
info[i].pli = p7_pipeline_Create(go, om->M, 100, FALSE, p7_SEARCH_SEQS); /* L_hint = 100 is just a dummy for now */
P7_PIPELINE *pli = info[i].pli;
pli->nmodels++;
pli->nnodes += info[i].om->M;
// if (pli->Z_setby == p7_ZSETBY_NTARGETS && pli->mode == p7_SCAN_MODELS) pli->Z = pli->nmodels;
// if (pli->do_biasfilter) p7_bg_SetFilter(info[i].bg, info[i].om->M, info[i].om->compo);
// if (pli->mode == p7_SEARCH_SEQS)
// status = p7_pli_NewModelThresholds(pli, info[i].om);
pli->W = info[i].om->max_length;
}
sstatus = serial_loop(info, dbfp, cfg->n_targetseq, ofp);
switch(sstatus)
{
case eslEFORMAT:
esl_fatal("Parse failed (sequence file %s):\n%s\n",
dbfp->filename, esl_sqfile_GetErrorBuf(dbfp));
break;
case eslEOF:
/* do nothing */
break;
default:
esl_fatal("Unexpected error %d reading sequence file %s", sstatus, dbfp->filename);
}
/* merge the results of the search results */
for (i = 1; i < infocnt; ++i)
{
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
p7_oprofile_Destroy(info[i].om);
}
/* Print the results. */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
// p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
// p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
esl_stopwatch_Stop(w);
// p7_pli_Statistics(ofp, info->pli, w);
// if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
p7_oprofile_Destroy(info->om);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
// hstatus = p7_hmmfile_Read(hfp, &abc, &hmm);
// } /* end outer loop over query HMMs */
switch(hstatus) {
case eslEOD: p7_Fail("read failed, HMM file %s may be truncated?", cfg->hmmfile); break;
case eslEFORMAT: p7_Fail("bad file format in HMM file %s", cfg->hmmfile); break;
case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile); break;
case eslEOF:
case eslOK: /* do nothing. EOF is what we want. */ break;
default: p7_Fail("Unexpected error (%d) in reading HMMs from %s", hstatus, cfg->hmmfile);
}
/* Terminate outputs... any last words?
*/
/* Cleanup - prepare for exit
*/
// for (i = 0; i < infocnt; ++i)
// p7_bg_Destroy(info[i].bg);
free(info);
p7_hmmfile_Close(hfp);
esl_sqfile_Close(dbfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
if (ofp != stdout) fclose(ofp);
printf("44HHHH \n");
return eslOK;
ERROR:
return eslFAIL;
}
