/* Function: main_loop_threaded()
* Date: SRE, Wed Dec 1 12:43:09 1999 [St. Louis]
*
* Purpose: Given an HMM and parameters for synthesizing random
* sequences; return a histogram of scores.
* (Threaded version.)
*
* Args: hmm - an HMM to calibrate.
* seed - random number seed
* nsample - number of seqs to synthesize
* lenmean - mean length of random sequence
* lensd - std dev of random seq length
* fixedlen - if nonzero, override lenmean, always this len
* nthreads - number of threads to start
* ret_hist - RETURN: the score histogram
* ret_max - RETURN: highest score seen in simulation
* twatch - RETURN: accumulation of thread times
*
* Returns: (void)
* hist is alloc'ed here, and must be free'd by caller.
*/
static void
main_loop_threaded(struct plan7_s *hmm, int seed, int nsample,
float lenmean, float lensd, int fixedlen,
int nthreads,
struct histogram_s **ret_hist, float *ret_max,
Stopwatch_t *twatch)
{
struct histogram_s *hist;
float randomseq[MAXABET];
float p1;
struct workpool_s *wpool; /* pool of worker threads */
/* Initialize.
* We assume we've already set the alphabet (safe, because
* HMM input sets the alphabet).
*/
sre_srandom(seed);
P7Logoddsify(hmm, TRUE);
P7DefaultNullModel(randomseq, &p1);
hist = AllocHistogram(-200, 200, 100);
wpool = workpool_start(hmm, lenmean, lensd, fixedlen, randomseq, nsample,
hist, nthreads);
workpool_stop(wpool);
*ret_hist = hist;
*ret_max = wpool->max_score;
StopwatchInclude(twatch, &(wpool->watch));
workpool_free(wpool);
return;
}
/* Function: PrintPlan7Stats()
*
* Purpose: Given a newly constructed HMM and the tracebacks
* of the sequences it was trained on, print out all
* the interesting information at the end of hmmb
* and hmmt runs that convinces the user we actually
* did something.
*
* Args: fp - where to send the output (stdout, usually)
* hmm - the new HMM, probability form
* dsq - digitized training seqs
* nseq - number of dsq's
* tr - array of tracebacks for dsq
*
* Return: (void)
*/
void
PrintPlan7Stats(FILE *fp, struct plan7_s *hmm, char **dsq, int nseq,
struct p7trace_s **tr)
{
int idx; /* counter for sequences */
float score; /* an individual trace score */
float total, best, worst; /* for the avg. and range of the scores */
float sqsum, stddev; /* for the std. deviation of the scores */
P7Logoddsify(hmm, TRUE); /* make sure model scores are ready */
/* find individual trace scores */
score = P7TraceScore(hmm, dsq[0], tr[0]);
total = best = worst = score;
sqsum = score * score;
for (idx = 1; idx < nseq; idx++) {
/* P7PrintTrace(stdout, tr[idx], hmm, dsq[idx]); */
score = P7TraceScore(hmm, dsq[idx], tr[idx]);
total += score;
sqsum += score * score;
if (score > best) best = score;
if (score < worst) worst = score;
}
if (nseq > 1) {
stddev = (sqsum - (total * total / (float) nseq)) / ((float) nseq - 1.);
stddev = (stddev > 0) ? sqrt(stddev) : 0.0;
} else stddev = 0.0;
/* print out stuff. */
fprintf(fp, "Average score: %10.2f bits\n", total / (float) nseq);
fprintf(fp, "Minimum score: %10.2f bits\n", worst);
fprintf(fp, "Maximum score: %10.2f bits\n", best);
fprintf(fp, "Std. deviation: %10.2f bits\n", stddev);
}
/* Function: main_loop_serial()
* Date: SRE, Tue Aug 18 16:18:28 1998 [St. Louis]
*
* Purpose: Given an HMM and parameters for synthesizing random
* sequences; return a histogram of scores.
* (Serial version)
*
* Args: hmm - an HMM to calibrate.
* seed - random number seed
* nsample - number of seqs to synthesize
* lenmean - mean length of random sequence
* lensd - std dev of random seq length
* fixedlen - if nonzero, override lenmean, always this len
* ret_hist - RETURN: the score histogram
* ret_max - RETURN: highest score seen in simulation
*
* Returns: (void)
* hist is alloc'ed here, and must be free'd by caller.
*/
static void
main_loop_serial(struct plan7_s *hmm, int seed, int nsample,
float lenmean, float lensd, int fixedlen,
struct histogram_s **ret_hist, float *ret_max)
{
struct histogram_s *hist;
float randomseq[MAXABET];
float p1;
float max;
char *seq;
char *dsq;
float score;
int sqlen;
int idx;
/* Initialize.
* We assume we've already set the alphabet (safe, because
* HMM input sets the alphabet).
*/
sre_srandom(seed);
P7Logoddsify(hmm, TRUE);
P7DefaultNullModel(randomseq, &p1);
hist = AllocHistogram(-200, 200, 100);
max = -FLT_MAX;
for (idx = 0; idx < nsample; idx++)
{
/* choose length of random sequence */
if (fixedlen) sqlen = fixedlen;
else do sqlen = (int) Gaussrandom(lenmean, lensd); while (sqlen < 1);
/* generate it */
seq = RandomSequence(Alphabet, randomseq, Alphabet_size, sqlen);
dsq = DigitizeSequence(seq, sqlen);
if (P7ViterbiSize(sqlen, hmm->M) <= RAMLIMIT)
score = P7Viterbi(dsq, sqlen, hmm, NULL);
else
score = P7SmallViterbi(dsq, sqlen, hmm, NULL);
AddToHistogram(hist, score);
if (score > max) max = score;
free(dsq);
free(seq);
}
*ret_hist = hist;
*ret_max = max;
return;
}
void HMMCreateWPoolTask::runUnsafe() {
const UHMMCalibrateSettings& settings = pt->getSettings();
WorkPool_s* wpool = pt->getWorkPool();
SetAlphabet(wpool->hmm->atype);
sre_srandom(settings.seed);
wpool->fixedlen = settings.fixedlen;
wpool->hist = AllocHistogram(-200, 200, 100);
wpool->lenmean = settings.lenmean;
wpool->lensd = settings.lensd;
wpool->nsample = settings.nsample;
wpool->nseq = 0;
wpool->randomseq.resize(MAXABET);
wpool->max_score = -FLT_MAX;
float p1;
P7Logoddsify(wpool->hmm, TRUE);
P7DefaultNullModel(wpool->randomseq.data(), &p1);
}
QList<UHMMSearchResult> UHMMSearch::search(plan7_s* _hmm, const char* seq, int seqLen, const UHMMSearchSettings& s, TaskStateInfo& si)
{
plan7_s * hmm = HMMIO::cloneHMM( _hmm );
//Set up optional Pfam score thresholds.
threshold_s thresh; // contains all threshold (cutoff) info
thresh.globE = s.globE; // use a reasonable Eval threshold
thresh.globT = -FLT_MAX; // but no bit threshold
thresh.domT = s.domT; // no domain bit threshold
thresh.domE = s.domE; // and no domain Eval threshold
thresh.autocut = CUT_NONE; // and no Pfam cutoffs used
thresh.Z = s.eValueNSeqs; // Z not preset; use actual # of seqs
int do_null2 = TRUE; // TRUE to adjust scores with null model #2
int do_forward = FALSE; // TRUE to use Forward() not Viterbi()
int do_xnu = FALSE; // TRUE to filter sequences thru XNU
QList<UHMMSearchResult> res; // the results of the method
//get HMMERTaskLocalData
HMMERTaskLocalData *tld = getHMMERTaskLocalData();
alphabet_s *al = &tld->al;
SetAlphabet(hmm->atype);
P7Logoddsify(hmm, !do_forward); //TODO: clone model to avoid changes in it or make it thread safe??
if (do_xnu && al->Alphabet_type == hmmNUCLEIC) {
si.setError( "The HMM is a DNA model, and you can't use the --xnu filter on DNA data" );
return res;
}
/*****************************************************************
* Set up optional Pfam score thresholds.
* Can do this before starting any searches, since we'll only use 1 HMM.
*****************************************************************/
if (!SetAutocuts(&thresh, hmm)) {
si.setError( "HMM did not contain the GA, TC, or NC cutoffs you needed" );
return res;
}
// set up structures for storing output
histogram_s *histogram = AllocHistogram(-200, 200, 100); //keeps full histogram of all scores
tophit_s *ghit = AllocTophits(200); // per-seq hits: 200=lumpsize
tophit_s *dhit = AllocTophits(200); // domain hits: 200=lumpsize
int nseq = 0; // number of sequences searched
#ifdef UGENE_CELL
if( HMMSearchAlgo_CellOptimized == s.alg ) {
if( hmm->M < MAX_HMM_LENGTH ) {
main_loop_spe(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si);
} else {
main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si);
}
} else
#elif defined(HMMER_BUILD_WITH_SSE2)
if( HMMSearchAlgo_SSEOptimized == s.alg ) {
main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si, sseScoring);
} else
#endif
if( HMMSearchAlgo_Conservative == s.alg ) {
main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si);
}
else {
assert( false && "bad hmmsearch algorithm selected" );
}
// Process hit lists, produce text output
// Set the theoretical EVD curve in our histogram using calibration in the HMM, if available.
if (hmm->flags & PLAN7_STATS) {
ExtremeValueSetHistogram(histogram, hmm->mu, hmm->lambda, histogram->lowscore, histogram->highscore, 0);
}
if (!thresh.Z) {
thresh.Z = nseq; // set Z for good now that we're done
}
//report our output
FullSortTophits(dhit);
//int namewidth = MAX(8, TophitsMaxName(ghit)); // max width of sequence name
// Report domain hits (sorted on E-value)
for (int i = 0; i < dhit->num && !si.cancelFlag; i++) {
float sc; // score of an HMM search
double pvalue; // pvalue of an HMM score
double evalue; // evalue of an HMM score
char *name, *desc; // hit sequence name and description
double motherp; // pvalue of a whole seq HMM score
float mothersc; // score of a whole seq parent of domain
int sqfrom, sqto; // coordinates in sequence
int sqlen; // length of seq that was hit
int hmmfrom, hmmto; // coordinate in HMM
int ndom; // total # of domains in this seq
int domidx; // number of this domain
GetRankedHit(dhit, i, &pvalue, &sc, &motherp, &mothersc,
&name, NULL, &desc,
&sqfrom, &sqto, &sqlen, // seq position info
&hmmfrom, &hmmto, NULL, // HMM position info
&domidx, &ndom, // domain info
NULL); // alignment info
evalue = pvalue * (double) thresh.Z;
if (motherp * (double) thresh.Z > thresh.globE || mothersc < thresh.globT) {
continue;
} else if (evalue <= thresh.domE && sc >= thresh.domT) {
// hmm reports results in range [1...N] -> translate it to [0..N)
res.append(UHMMSearchResult(U2Region(sqfrom-1, sqto-sqfrom+1), sc, evalue));
}
}
//Clean-up and exit.
FreeHistogram(histogram);
FreeTophits(ghit);
FreeTophits(dhit);
FreePlan7( hmm );
return res;
}
int
main(void)
{
struct p7trace_s *tr; /* traceback of an alignment */
int master_tid; /* PVM TID of our master */
char *hmmfile; /* file to read HMM(s) from */
HMMFILE *hmmfp; /* opened hmmfile for reading */
struct plan7_s *hmm;
char *seq;
char *dsq;
int len;
int nhmm; /* number of HMM to work on */
float sc;
int my_idx = -1; /* my index, 0..nslaves-1 */
float globT; /* T parameter: keep only hits > globT bits */
double globE; /* E parameter: keep hits < globE E-value */
double pvalue; /* Z*pvalue = Evalue */
int Z; /* nseq to base E value calculation on */
int send_trace; /* TRUE if score is significant */
int do_xnu; /* TRUE to do XNU filter on seq */
int do_forward; /* TRUE to use Forward() scores not Viterbi */
int do_null2; /* TRUE to correct scores w/ ad hoc null2 */
int alphatype; /* alphabet type, hmmAMINO or hmmNUCLEIC */
int code; /* return code after initialization */
/* Register leave_pvm() cleanup function so any exit() call
* first calls pvm_exit().
*/
if (atexit(leave_pvm) != 0) { pvm_exit(); Die("slave couldn't register leave_pvm()"); }
/*****************************************************************
* initialization.
* Master broadcasts to us:
* 1) len of HMM file name (int)
* 2) name of HMM file (string)
* 3) length of sequence string (int)
* 4) sequence (string)
* 5) globT threshold
* 6) globE threshold
* 7) Z
* 8) do_xnu flag
* 9) do_forward flag
* 10) do_null2 flag
* 11) alphabet type
* We receive the broadcast and open the files.
******************************************************************/
master_tid = pvm_parent(); /* who's our master? */
pvm_recv(master_tid, HMMPVM_INIT);
pvm_upkint(&len, 1, 1);
hmmfile = MallocOrDie(sizeof(char *) * (len+1));
pvm_upkstr(hmmfile);
pvm_upkint(&len, 1, 1);
seq = MallocOrDie(sizeof(char *) * (len+1));
pvm_upkstr(seq);
pvm_upkfloat(&globT, 1, 1);
pvm_upkdouble(&globE, 1, 1);
pvm_upkint(&Z, 1, 1);
pvm_upkint(&do_xnu, 1, 1);
pvm_upkint(&do_forward, 1, 1);
pvm_upkint(&do_null2, 1, 1);
pvm_upkint(&alphatype, 1, 1);
SetAlphabet(alphatype);
/* Open HMM file (maybe in HMMERDB) */
code = HMMPVM_OK;
if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL)
code = HMMPVM_NO_HMMFILE;
else if (hmmfp->gsi == NULL)
code = HMMPVM_NO_INDEX;
/* report our status.
*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&code, 1, 1);
pvm_send(master_tid, HMMPVM_RESULTS);
dsq = DigitizeSequence(seq, len);
if (do_xnu) XNU(dsq, len);
/*****************************************************************
* Main loop.
* Receive an integer 0..nhmm-1 for which HMM to search against.
* If we receive a -1, we shut down.
*****************************************************************/
for (;;)
{
pvm_recv(master_tid, HMMPVM_WORK);
pvm_upkint(&nhmm, 1, 1);
if (my_idx < 0) my_idx = nhmm; /* first time thru, remember what index we are. */
if (nhmm == -1) break; /* shutdown signal */
/* move to our assigned HMM in the HMM file, and read it
*/
HMMFilePositionByIndex(hmmfp, nhmm);
if (! HMMFileRead(hmmfp, &hmm)) Die("unexpected end of HMM file");
if (hmm == NULL) Die("unexpected failure to parse HMM file");
P7Logoddsify(hmm, TRUE);
/* Score sequence, do alignment (Viterbi), recover trace
*/
if (P7ViterbiSize(len, hmm->M) <= RAMLIMIT)
{
SQD_DPRINTF1(("P7Viterbi(): Estimated size %d Mb\n", P7ViterbiSize(len, hmm->M)));
sc = P7Viterbi(dsq, len, hmm, &tr);
}
else
{
SQD_DPRINTF1(("P7SmallViterbi() called; %d Mb > %d\n", P7ViterbiSize(len, hmm->M), RAMLIMIT));
sc = P7SmallViterbi(dsq, len, hmm, &tr);
}
if (do_forward) sc = P7Forward(dsq, len, hmm, NULL);
if (do_null2) sc -= TraceScoreCorrection(hmm, tr, dsq);
pvalue = PValue(hmm, sc);
send_trace = (sc > globT && pvalue * (float) Z < globE) ? 1 : 0;
/* return output
*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&my_idx, 1, 1); /* tell master who we are */
pvm_pkstr(hmm->name); /* double check that we did the right thing */
pvm_pkfloat(&sc, 1, 1);
pvm_pkdouble(&pvalue, 1, 1);
pvm_pkint(&send_trace, 1, 1); /* flag for whether a trace structure is coming */
if (send_trace) PVMPackTrace(tr);
pvm_send(master_tid, HMMPVM_RESULTS);
/* cleanup
*/
FreePlan7(hmm);
P7FreeTrace(tr);
}
/***********************************************
* Cleanup, return.
***********************************************/
HMMFileClose(hmmfp);
free(seq);
free(dsq);
free(hmmfile);
return 0;
}
static void main_loop_serial(struct plan7_s *hmm, int seed, int nsample,
float lenmean, float lensd, int fixedlen,
struct histogram_s **ret_hist, float *ret_max, int& cancelFlag, int& progress)
{
struct histogram_s *hist;
struct dpmatrix_s *mx;
float randomseq[MAXABET];
float p1;
float max;
char *seq;
unsigned char *dsq;
float score;
int sqlen;
int idx;
// Initialize.
// We assume we've already set the alphabet (safe, because
// HMM input sets the alphabet).
sre_srandom(seed);
//get HMMERTaskLocalData
HMMERTaskLocalData *tls = getHMMERTaskLocalData();
alphabet_s &al = tls->al;
SetAlphabet(hmm->atype);
P7Logoddsify(hmm, TRUE);
P7DefaultNullModel(randomseq, &p1);
hist = AllocHistogram(-200, 200, 100);
mx = CreatePlan7Matrix(1, hmm->M, 25, 0);
max = -FLT_MAX;
progress = 0;
int pStub;
for (idx = 0; idx < nsample && !cancelFlag; idx++) {
// choose length of random sequence
if (fixedlen) {
sqlen = fixedlen;
} else {
do sqlen = (int) Gaussrandom(lenmean, lensd); while (sqlen < 1);
}
// generate it
seq = RandomSequence(al.Alphabet, randomseq, al.Alphabet_size, sqlen);
dsq = DigitizeSequence(seq, sqlen);
if (P7ViterbiSpaceOK(sqlen, hmm->M, mx)) {
score = P7Viterbi(dsq, sqlen, hmm, mx, NULL);
} else {
score = P7SmallViterbi(dsq, sqlen, hmm, mx, NULL, pStub);
}
AddToHistogram(hist, score);
max = qMax(score, max);
progress = int(100*idx/float(nsample));
free(dsq);
free(seq);
}
FreePlan7Matrix(mx);
*ret_hist = hist;
*ret_max = max;
}
int
main(void)
{
int master_tid; /* PVM TID of our master */
int slaveidx; /* my slave index (0..nslaves-1) */
struct plan7_s *hmm; /* HMM to calibrate, sent from master */
struct histogram_s *hist; /* score histogram */
int hmmidx; /* index of this HMM */
char *seq; /* synthetic random sequence */
char *dsq; /* digitized seq */
int len; /* length of seq */
float sc; /* score of seq aligned to HMM */
float max; /* maximum score seen in sample */
int seed; /* random number seed */
int nsample; /* number of seqs to sample */
int fixedlen; /* if nonzero, fixed length of seq */
float lenmean; /* Gaussian mean length of seq */
float lensd; /* Gaussian length std. dev. for seq */
int fitok; /* TRUE if EVD fit was OK */
float randomseq[MAXABET]; /* iid frequencies of residues */
float p1;
int alphatype; /* alphabet type, hmmAMINO or hmmNUCLEIC */
int idx;
int code;
/* Register leave_pvm() cleanup function so any exit() call
* first calls pvm_exit().
*/
if (atexit(leave_pvm) != 0) { pvm_exit(); Die("slave couldn't register leave_pvm()"); }
/*****************************************************************
* initialization.
* Master broadcasts the problem to us: parameters of the
* HMM calibration.
******************************************************************/
master_tid = pvm_parent(); /* who's our master? */
pvm_recv(master_tid, HMMPVM_INIT);
pvm_upkint(&nsample, 1, 1);
pvm_upkint(&fixedlen, 1, 1);
pvm_upkfloat(&lenmean, 1, 1);
pvm_upkfloat(&lensd, 1, 1);
/* tell the master we're OK and ready to go (or not)
*/
code = HMMPVM_OK;
pvm_initsend(PvmDataDefault);
pvm_pkint(&code, 1, 1);
pvm_send(master_tid, HMMPVM_RESULTS);
/*****************************************************************
* Main loop.
* Receive a random number seed, then an HMM to search against.
* If we receive a -1 seed, we shut down.
*****************************************************************/
slaveidx = -1;
for (;;)
{
pvm_recv(master_tid, HMMPVM_WORK);
pvm_upkint(&seed, 1, 1);
if (seed == -1) break; /* shutdown signal */
pvm_upkint(&hmmidx, 1, 1);
pvm_upkint(&alphatype,1, 1);
SetAlphabet(alphatype);
hmm = PVMUnpackHMM();
if (hmm == NULL) Die("oh no, the HMM never arrived");
if (slaveidx == -1) slaveidx = hmmidx;
P7DefaultNullModel(randomseq, &p1);
sre_srandom(seed);
P7Logoddsify(hmm, TRUE);
hist = AllocHistogram(-200, 200, 100);
max = -FLT_MAX;
for (idx = 0; idx < nsample; idx++)
{
/* choose length of random sequence */
if (fixedlen) len = fixedlen;
else do len = (int) Gaussrandom(lenmean, lensd); while (len < 1);
/* generate it */
seq = RandomSequence(Alphabet, randomseq, Alphabet_size, len);
dsq = DigitizeSequence(seq, len);
if (P7ViterbiSize(len, hmm->M) <= RAMLIMIT)
sc = P7Viterbi(dsq, len, hmm, NULL);
else
sc = P7SmallViterbi(dsq, len, hmm, NULL);
AddToHistogram(hist, sc);
if (sc > max) max = sc;
free(seq);
free(dsq);
}
/* Fit an EVD to the observed histogram.
* The TRUE left-censors and fits only the right slope of the histogram.
* The 9999. is an arbitrary high number that means we won't trim outliers
* on the right.
*/
fitok = ExtremeValueFitHistogram(hist, TRUE, 9999.);
/* Return output to master.
* Currently we don't send the histogram back, but we could.
*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&slaveidx, 1, 1);
pvm_pkint(&hmmidx, 1, 1);
PVMPackString(hmm->name);
pvm_pkint(&fitok, 1, 1);
pvm_pkfloat(&(hist->param[EVD_MU]), 1, 1);
pvm_pkfloat(&(hist->param[EVD_LAMBDA]), 1, 1);
pvm_pkfloat(&max, 1, 1);
pvm_send(master_tid, HMMPVM_RESULTS);
/* cleanup
*/
FreeHistogram(hist);
FreePlan7(hmm);
}
/***********************************************
* Cleanup, return.
***********************************************/
return 0; /* pvm_exit() is called by atexit() registration. */
}
int main(int argc, char **argv)
{
const char *hmmfile; /* file to read HMMs from */
HMMFILE *hmmfp; /* opened hmmfile for reading */
const char *seqfile; /* file to read target sequence from */
char **rseq; /* raw, unaligned sequences */
SQINFO *sqinfo; /* info associated with sequences */
char **dsq; /* digitized raw sequences */
int nseq; /* number of sequences */
char **aseq; /* aligned sequences */
AINFO ainfo; /* alignment information */
float *wgt; /* per-sequence weights */
int i;
struct plan7_s *hmm; /* HMM to align to */
struct p7trace_s **tr; /* traces for aligned sequences */
int be_quiet; /* TRUE to suppress verbose banner */
int matchonly; /* TRUE to show only match state syms */
const char *outfile; /* optional alignment output file */
FILE *ofp; /* handle on alignment output file */
AjPFile ajwithali; /* name of additional alignment file to align */
AjPFile ajmapali; /* name of additional alignment file to map */
AjBool ajmatch=ajFalse;
AjPFile outf=NULL;
AjPStr outfname=NULL;
AjPFile inf=NULL;
AjPStr infname=NULL;
AjPSeqset seqset=NULL;
AjPStr ajseqfile=NULL;
char* mapali=NULL;
char* withali=NULL;
#ifdef MEMDEBUG
unsigned long histid1, histid2, orig_size, current_size;
orig_size = malloc_inuse(&histid1);
fprintf(stderr, "[... memory debugging is ON ...]\n");
#endif
/***********************************************
* Parse command line
***********************************************/
matchonly = FALSE;
outfile = NULL;
be_quiet = FALSE;
withali = NULL;
mapali = NULL;
embInitPV("ohmmalign",argc,argv,"HMMER",VERSION);
ajmatch = ajAcdGetBoolean("matchonly");
if(ajmatch)
matchonly=TRUE;
else
matchonly=FALSE;
ajmapali = ajAcdGetInfile("mapalifile");
if (ajmapali)
mapali = ajCharNewS(ajFileGetNameS(ajmapali));
ajFileClose(&ajmapali);
ajwithali = ajAcdGetInfile("withalifile");
if (ajwithali)
withali = ajCharNewS(ajFileGetNameS(ajwithali));
ajFileClose(&ajwithali);
be_quiet=TRUE;
outf = ajAcdGetOutfile("outfile");
outfname = ajStrNewC((char *)ajFileGetNameC(outf));
if(*ajStrGetPtr(outfname)>31)
ajFileClose(&outf);
outfile = ajStrGetPtr(outfname);
inf = ajAcdGetInfile("hmmfile");
infname = ajStrNewC((char *)ajFileGetNameC(inf));
ajFileClose(&inf);
hmmfile = ajStrGetPtr(infname);
seqset = ajAcdGetSeqset("sequences");
ajseqfile = ajStrNewC(ajStrGetPtr(seqset->Filename));
seqfile = ajStrGetPtr(ajseqfile);
/***********************************************
* Open HMM file (might be in HMMERDB or current directory).
* Read a single HMM from it.
*
* Currently hmmalign disallows the J state and
* only allows one domain per sequence. To preserve
* the S/W entry information, the J state is explicitly
* disallowed, rather than calling a Plan7*Config() function.
* this is a workaround in 2.1 for the 2.0.x "yo!" bug.
***********************************************/
if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL)
ajFatal("Failed to open HMM file %s\n", hmmfile);
if (!HMMFileRead(hmmfp, &hmm))
ajFatal("Failed to read any HMMs from %s\n", hmmfile);
HMMFileClose(hmmfp);
if (hmm == NULL)
ajFatal("HMM file %s corrupt or in incorrect format? Parse failed", hmmfile);
hmm->xt[XTE][MOVE] = 1.; /* only 1 domain/sequence ("global" alignment) */
hmm->xt[XTE][LOOP] = 0.;
P7Logoddsify(hmm, TRUE);
/* do we have the map we might need? */
if (mapali != NULL && ! (hmm->flags & PLAN7_MAP))
ajFatal("HMMER: HMM file %s has no map; you can't use --mapali.", hmmfile);
/***********************************************
* Open sequence file in current directory.
* Read all seqs from it.
***********************************************/
/*
if (! SeqfileFormat(seqfile, &format, NULL))
switch (squid_errno) {
case SQERR_NOFILE:
ajFatal("Sequence file %s could not be opened for reading", seqfile);
case SQERR_FORMAT:
default:
ajFatal("Failed to determine format of sequence file %s", seqfile);
}
if (! ReadMultipleRseqs(seqfile, format, &rseq, &sqinfo, &nseq))
ajFatal("Failed to read any sequences from file %s", seqfile);
*/
emboss_rseqs(seqset,&rseq,&sqinfo,&nseq);
/***********************************************
* Show the banner
***********************************************/
be_quiet=TRUE;
if (! be_quiet)
{
/* Banner(stdout, banner); */
printf( "HMM file: %s\n", hmmfile);
printf( "Sequence file: %s\n", seqfile);
printf("- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n");
}
/***********************************************
* Do the work
***********************************************/
/* Allocations and initializations.
*/
dsq = MallocOrDie(sizeof(char *) * nseq);
tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq);
/* Align each sequence to the model, collect traces
*/
for (i = 0; i < nseq; i++)
{
dsq[i] = DigitizeSequence(rseq[i], sqinfo[i].len);
if (P7ViterbiSize(sqinfo[i].len, hmm->M) <= RAMLIMIT)
(void) P7Viterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i]));
else
(void) P7SmallViterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i]));
}
/* Include an aligned alignment, if desired.
*/
if (mapali != NULL)
include_alignment(mapali, hmm, TRUE, &rseq, &dsq, &sqinfo, &tr, &nseq);
if (withali != NULL)
include_alignment(withali, hmm, FALSE, &rseq, &dsq, &sqinfo, &tr, &nseq);
/* Turn traces into a multiple alignment
*/
wgt = MallocOrDie(sizeof(float) * nseq);
FSet(wgt, nseq, 1.0);
P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, matchonly,
&aseq, &ainfo);
/***********************************************
* Output the alignment
***********************************************/
if (outfile != NULL && (ofp = fopen(outfile, "w")) != NULL)
{
WriteSELEX(ofp, aseq, &ainfo, 50);
printf("Alignment saved in file %s\n", outfile);
fclose(ofp);
}
else
WriteSELEX(stdout, aseq, &ainfo, 50);
/***********************************************
* Cleanup and exit
***********************************************/
for (i = 0; i < nseq; i++)
{
P7FreeTrace(tr[i]);
FreeSequence(rseq[i], &(sqinfo[i]));
free(dsq[i]);
}
FreeAlignment(aseq, &ainfo);
FreePlan7(hmm);
free(sqinfo);
free(rseq);
free(dsq);
free(wgt);
free(tr);
SqdClean();
ajStrDel(&outfname);
ajStrDel(&infname);
ajStrDel(&ajseqfile);
#ifdef MEMDEBUG
current_size = malloc_inuse(&histid2);
if (current_size != orig_size) malloc_list(2, histid1, histid2);
else fprintf(stderr, "[No memory leaks.]\n");
#endif
ajSeqsetDel(&seqset);
ajFileClose(&ajwithali);
ajFileClose(&ajmapali);
embExit();
return 0;
}
