/* onefetch():
* Given one <key> (a seq name or accession), retrieve the corresponding sequence.
* In SSI mode, we can do this quickly by positioning the file, then regurgitating
* every line until the end-of-record marker; we don't even have to parse.
* Without an SSI index, we have to parse the file sequentially 'til we find
* the one we're after.
*/
static void
onefetch(ESL_GETOPTS *go, FILE *ofp, char *key, ESL_SQFILE *sqfp)
{
ESL_SQ *sq = esl_sq_Create();
int do_revcomp = esl_opt_GetBoolean(go, "-r");
char *newname = esl_opt_GetString(go, "-n");
int status;
/* Try to position the file at the desired sequence with SSI. */
if (sqfp->data.ascii.ssi != NULL)
{
status = esl_sqfile_PositionByKey(sqfp, key);
if (status == eslENOTFOUND) esl_fatal("seq %s not found in SSI index for file %s\n", key, sqfp->filename);
else if (status == eslEFORMAT) esl_fatal("Failed to parse SSI index for %s\n", sqfp->filename);
else if (status != eslOK) esl_fatal("Failed to look up location of seq %s in SSI index of file %s\n", key, sqfp->filename);
status = esl_sqio_Read(sqfp, sq);
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status == eslEOF) esl_fatal("Unexpected EOF reading sequence file %s",
status, sqfp->filename);
else if (status != eslOK) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
if (strcmp(key, sq->name) != 0 && strcmp(key, sq->acc) != 0)
esl_fatal("whoa, internal error; found the wrong sequence %s, not %s", sq->name, key);
}
else
{ /* Else, we have to read the whole damn file sequentially until we find the seq */
while ((status = esl_sqio_Read(sqfp, sq)) != eslEOF) {
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
if (strcmp(key, sq->name) == 0 || strcmp(key, sq->acc) == 0) break;
esl_sq_Reuse(sq);
}
if (status == eslEOF) esl_fatal("Failed to find sequence %s in file %s\n", key, sqfp->filename);
}
if (do_revcomp == FALSE && newname == NULL && ! esl_sqio_IsAlignment(sqfp->format))
{ /* If we're not manipulating the sequence in any way, and it's not from an alignment file, we can Echo() it. */
if (esl_sqio_Echo(sqfp, sq, ofp) != eslOK) esl_fatal("Echo failed: %s\n", esl_sqfile_GetErrorBuf(sqfp));
}
else
{ /* Otherwise we Write() the parsed version. */
if (do_revcomp && esl_sq_ReverseComplement(sq) != eslOK) esl_fatal("Failed to reverse complement %s; is it a protein?\n", sq->name);
if (newname != NULL) esl_sq_SetName(sq, newname);
esl_sqio_Write(ofp, sq, eslSQFILE_FASTA, FALSE);
}
esl_sq_Destroy(sq);
}
/* 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;
}
