/* 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: 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;
}
/*
* cc -g -o testdriver -DTESTDRIVER -L. shuffle.c -lsquid -lm
*/
int
main(int argc, char **argv)
{
char s1[100];
char s2[100];
sre_srandom(42);
strcpy(s2, "GGGGGGGGGGCCCCCCCCCC");
/* strcpy(s2, "AGACATAAAGTTCCGTACTGCCGGGAT");
*/
StrDPShuffle(s1, s2);
printf("DPshuffle: %s\n", s1);
StrMarkov0(s1,s2);
printf("Markov 0 : %s\n", s1);
StrMarkov1(s1,s2);
printf("Markov 1 : %s\n", s1);
return 0;
}
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);
}
int main(int argc, char **argv)
{
const char *hmmfile; /* file to read HMMs from */
FILE *fp; /* output file handle */
HMMFILE *hmmfp; /* opened hmmfile for reading */
struct plan7_s *hmm; /* HMM to generate from */
int L; /* length of a sequence */
int i; /* counter over sequences */
char *ofile; /* output sequence file */
int nseq; /* number of seqs to sample */
int seed; /* random number generator seed */
int be_quiet; /* TRUE to silence header/footer */
int do_alignment; /* TRUE to output in aligned format */
int do_consensus; /* TRUE to do a single consensus seq */
AjBool ajselex;
AjBool ajcons;
AjPFile inf=NULL;
AjPFile outf=NULL;
AjPStr instr=NULL;
AjPStr outstr=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
***********************************************/
nseq = 10;
be_quiet = FALSE;
do_alignment = FALSE;
do_consensus = FALSE;
ofile = NULL;
embInitPV("ohmmemit",argc,argv,"HMMER",VERSION);
ajselex = ajAcdGetBoolean("selex");
ajcons = ajAcdGetBoolean("consensus");
nseq = ajAcdGetInt("number");
seed = ajAcdGetInt("seed");
inf = ajAcdGetInfile("infile");
outf = ajAcdGetOutfile("outfile");
if(!seed)
seed = time ((time_t *) NULL);
if(ajselex)
do_alignment=TRUE;
else
do_alignment=FALSE;
if(ajcons)
do_consensus=TRUE;
else
do_consensus=FALSE;
instr = ajStrNewC((char *)ajFileGetNameC(inf));
outstr = ajStrNewC((char *)ajFileGetNameC(outf));
hmmfile = ajStrGetPtr(instr);
sre_srandom(seed);
if (do_alignment && do_consensus)
ajFatal("Sorry, -selex and -consensus are incompatible.\n");
if (nseq != 10 && do_consensus)
ajWarn("-consensus overrides -number (# of sampled seqs)");
/***********************************************
* Open HMM file (might be in HMMERDB or current directory).
* Read a single HMM from it.
***********************************************/
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);
/* Configure the HMM to shut off N,J,C emission: so we
* do a simple single pass through the model.
*/
Plan7NakedConfig(hmm);
Plan7Renormalize(hmm);
/***********************************************
* Open the output file, or stdout
***********************************************/
fp = ajFileGetFileptr(outf);
/***********************************************
* Show the options banner
***********************************************/
be_quiet=TRUE;
if (! be_quiet)
{
printf("HMM file: %s\n", hmmfile);
if (! do_consensus)
{
printf("Number of seqs: %d\n", nseq);
printf("Random seed: %d\n", seed);
}
printf("- - - - - - - - - - - - - - - - - - - - - - - - - "
"- - - - - - -\n\n");
}
/***********************************************
* Do the work.
* If we're generating an alignment, we have to collect
* all our traces, then output. If we're generating unaligned
* sequences, we can emit one at a time.
***********************************************/
if (do_consensus)
{
char *seq;
SQINFO sqinfo; /* info about sequence (name/desc) */
EmitConsensusSequence(hmm, &seq, NULL, &L, NULL);
strcpy(sqinfo.name, "consensus");
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
WriteSeq(fp, kPearson, seq, &sqinfo);
free(seq);
}
else if (do_alignment)
{
struct p7trace_s **tr;
char **dsq;
SQINFO *sqinfo;
char **aseq;
AINFO ainfo;
float *wgt;
dsq = MallocOrDie(sizeof(char *) * nseq);
tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq);
sqinfo = MallocOrDie(sizeof(SQINFO) * nseq);
wgt = MallocOrDie(sizeof(float) * nseq);
FSet(wgt, nseq, 1.0);
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &(dsq[i]), &L, &(tr[i]));
sprintf(sqinfo[i].name, "seq%d", i+1);
sqinfo[i].len = L;
sqinfo[i].flags = SQINFO_NAME | SQINFO_LEN;
}
P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, FALSE,
&aseq, &ainfo);
/* Output the alignment */
WriteSELEX(fp, aseq, &ainfo, 50);
if (ofile != NULL && !be_quiet)
printf("Alignment saved in file %s\n", ofile);
/* Free memory
*/
for (i = 0; i < nseq; i++)
{
P7FreeTrace(tr[i]);
free(dsq[i]);
}
FreeAlignment(aseq, &ainfo);
free(sqinfo);
free(dsq);
free(wgt);
free(tr);
}
else /* unaligned sequence output */
{
struct p7trace_s *tr;
char *dsq;
char *seq;
SQINFO sqinfo;
for (i = 0; i < nseq; i++)
{
EmitSequence(hmm, &dsq, &L, &tr);
sprintf(sqinfo.name, "seq%d", i+1);
sqinfo.len = L;
sqinfo.flags = SQINFO_NAME | SQINFO_LEN;
seq = DedigitizeSequence(dsq, L);
WriteSeq(fp, kPearson, seq, &sqinfo);
P7FreeTrace(tr);
free(dsq);
free(seq);
}
}
ajFileClose(&outf);
FreePlan7(hmm);
SqdClean();
#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
ajStrDel(&instr);
ajStrDel(&outstr);
ajFileClose(&inf);
ajFileClose(&outf);
embExit();
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. */
}