static void
main_loop_serial(struct plan7_s *hmm, const char* seq, int seqLen, struct threshold_s *thresh, int do_forward,
int do_null2, int do_xnu, struct histogram_s *histogram, struct tophit_s *ghit, struct tophit_s *dhit,
int *ret_nseq, TaskStateInfo& ti)
{
//get HMMERTaskLocalData
HMMERTaskLocalData *tld = getHMMERTaskLocalData();
alphabet_s *al = &tld->al;
struct dpmatrix_s *mx; // DP matrix, growable
struct p7trace_s *tr; // traceback
unsigned char *dsq; // digitized target sequence
float sc; // score of an HMM search
double pvalue; // pvalue of an HMM score
double evalue; // evalue of an HMM score
// Create a DP matrix; initially only two rows big, but growable;
// we overalloc by 25 rows (L dimension) when we grow; not growable
// in model dimension, since we know the hmm size
mx = CreatePlan7Matrix(1, hmm->M, 25, 0);
assert(seqLen > 0);
dsq = DigitizeSequence(seq, seqLen);
if (do_xnu && al->Alphabet_type == hmmAMINO) {
XNU(dsq, seqLen);
}
// 1. Recover a trace by Viterbi.
// In extreme cases, the alignment may be literally impossible;
// in which case, the score comes out ridiculously small (but not
// necessarily <= -INFTY, because we're not terribly careful
// about underflow issues), and tr will be returned as NULL.
if (P7ViterbiSpaceOK(seqLen, hmm->M, mx)) {
sc = P7Viterbi(dsq, seqLen, hmm, mx, &tr);
} else {
sc = P7SmallViterbi(dsq, seqLen, hmm, mx, &tr, ti.progress);
}
// 2. If we're using Forward scores, calculate the
// whole sequence score; this overrides anything
// PostprocessSignificantHit() is going to do to the per-seq score.
if (do_forward) {
sc = P7Forward(dsq, seqLen, hmm, NULL);
if (do_null2) sc -= TraceScoreCorrection(hmm, tr, dsq);
}
// 2. Store score/pvalue for global alignment; will sort on score,
// which in hmmsearch is monotonic with E-value.
// Keep all domains in a significant sequence hit.
// We can only make a lower bound estimate of E-value since
// we don't know the final value of nseq yet, so the list
// of hits we keep in memory is >= the list we actually
// output.
//
pvalue = PValue(hmm, sc);
evalue = thresh->Z ? (double) thresh->Z * pvalue : (double) pvalue;
if (sc >= thresh->globT && evalue <= thresh->globE) {
sc = PostprocessSignificantHit(ghit, dhit,
tr, hmm, dsq, seqLen,
(char *)"sequence", //todo: sqinfo.name,
NULL,
NULL,
do_forward, sc,
do_null2,
thresh,
FALSE); // FALSE-> not hmmpfam mode, hmmsearch mode
}
AddToHistogram(histogram, sc);
P7FreeTrace(tr);
free(dsq);
FreePlan7Matrix(mx);
return;
}
/* Function: EmitSequence()
* Date: SRE, Sun Mar 8 12:28:03 1998 [St. Louis]
*
* Purpose: Given a model, sample a sequence and/or traceback.
*
* Args: hmm - the model
* ret_dsq - RETURN: generated digitized sequence (pass NULL if unwanted)
* ret_L - RETURN: length of generated sequence
* ret_tr - RETURN: generated trace (pass NULL if unwanted)
*
* Returns: void
*/
void
EmitSequence(struct plan7_s *hmm, char **ret_dsq, int *ret_L, struct p7trace_s **ret_tr)
{
struct p7trace_s *tr;
enum p7stype type; /* current state type */
int k; /* current node index */
char *dsq; /* generated sequence, digitized */
int L; /* length of sequence */
int alloc_tlen; /* allocated space for traceback */
int alloc_L; /* allocated space for sequence */
int tpos; /* position in traceback */
int sym; /* a generated symbol index */
float t[4]; /* little array for choosing M transition from */
/* Initialize; allocations
*/
P7AllocTrace(64, &tr);
alloc_tlen = 64;
dsq = MallocOrDie(sizeof(char) * 64);
alloc_L = 64;
TraceSet(tr, 0, STS, 0, 0);
TraceSet(tr, 1, STN, 0, 0);
dsq[0] = (char) Alphabet_iupac;
L = 1;
k = 0;
type = STN;
tpos = 2;
while (type != STT)
{
/* Deal with state transition
*/
switch (type) {
case STB: type = STM; k = FChoose(hmm->begin+1, hmm->M) + 1; break;
case STI: type = (FChoose(hmm->t[k]+TIM, 2) == 0) ? STM : STI; if (type == STM) k++; break;
case STN: type = (FChoose(hmm->xt[XTN], 2) == LOOP) ? STN : STB; k = 0; break;
case STE: type = (FChoose(hmm->xt[XTE], 2) == LOOP) ? STJ : STC; k = 0; break;
case STC: type = (FChoose(hmm->xt[XTC], 2) == LOOP) ? STC : STT; k = 0; break;
case STJ: type = (FChoose(hmm->xt[XTJ], 2) == LOOP) ? STJ : STB; k = 0; break;
case STD:
if (k < hmm->M) {
type = (FChoose(hmm->t[k]+TDM, 2) == 0) ? STM : STD;
k++;
} else {
type = STE;
k = 0;
}
break;
case STM:
if (k < hmm->M) {
FCopy(t, hmm->t[k], 3);
t[3] = hmm->end[k];
switch (FChoose(t,4)) {
case 0: k++; type = STM; break;
case 1: type = STI; break;
case 2: k++; type = STD; break;
case 3: k=0; type = STE; break;
default: Die("never happens");
}
} else {
k = 0;
type = STE;
}
break;
case STT:
case STBOGUS:
default:
Die("can't happen.");
}
/* Choose a symbol emission, if necessary
*/
sym = -1;
if (type == STM) sym = FChoose(hmm->mat[k], Alphabet_size);
else if (type == STI) sym = FChoose(hmm->ins[k], Alphabet_size);
else if ((type == STN && tr->statetype[tpos-1] == STN) ||
(type == STC && tr->statetype[tpos-1] == STC) ||
(type == STJ && tr->statetype[tpos-1] == STJ))
sym = FChoose(hmm->null, Alphabet_size);
/* Add to the traceback; deal with realloc if necessary
*/
TraceSet(tr, tpos, type, k, (sym != -1) ? L : 0);
tpos++;
if (tpos == alloc_tlen) {
alloc_tlen += 64;
P7ReallocTrace(tr, alloc_tlen);
}
/* Add to the digitized seq; deal with realloc, if necessary
*/
if (sym != -1) {
dsq[L] = (char) sym;
L++;
if (L+1 == alloc_L) { /* L+1 leaves room for sentinel byte + \0 */
alloc_L += 64;
dsq = ReallocOrDie(dsq, sizeof(char) * alloc_L);
}
}
}
/* Finish off the trace
*/
tr->tlen = tpos;
/* Finish off the dsq with sentinel byte and null terminator.
* Emitted Sequence length is L-1.
*/
dsq[L] = (char) Alphabet_iupac;
dsq[L+1] = '\0';
L--;
/* Return
*/
if (ret_dsq != NULL) *ret_dsq = dsq; else free(dsq);
if (ret_L != NULL) *ret_L = L;
if (ret_tr != NULL) *ret_tr = tr; else P7FreeTrace(tr);
return;
}
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;
}
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;
}
/* Function: EmitConsensusSequence()
* Date: SRE, Wed Nov 11 11:08:59 1998 [St. Louis]
*
* Purpose: Generate a "consensus sequence". For the purposes
* of a profile HMM, this is defined as:
* - for each node:
* - if StateOccupancy() says that M is used
* with probability >= 0.5, this M is "consensus".
* Then, choose maximally likely residue.
* if P>0.5 (protein) or P>0.9 (DNA), make
* it upper case; else make it lower case.
* - if StateOccupancy() says that I
* is used with P >= 0.5, this I is "consensus";
* use it 1/(1-TII) times (its expectation value).
* Generate an "x" from each I.
*
* The function expects that the model is config'ed
* by Plan7NakedConfig(): that is, for a single global pass
* with no N,C,J involvement.
*
*
* Args: hmm - the model
* ret_seq - RETURN: consensus sequence (pass NULL if unwanted)
* ret_dsq - RETURN: digitized consensus sequence (pass NULL if unwanted)
* ret_L - RETURN: length of generated sequence
* ret_tr - RETURN: generated trace (pass NULL if unwanted)
*
* Returns: void
*/
void
EmitConsensusSequence(struct plan7_s *hmm, char **ret_seq, char **ret_dsq, int *ret_L, struct p7trace_s **ret_tr)
{
struct p7trace_s *tr; /* RETURN: traceback */
char *dsq, *seq; /* sequence in digitized and undigitized form */
float *mp, *ip, *dp; /* state occupancies from StateOccupancy() */
int nmat, ndel, nins; /* number of matches, deletes, inserts used */
int k; /* counter for nodes */
int tpos; /* position in trace */
int i; /* position in seq (equiv pos in dsq is i+1 */
int x; /* symbol choice (M) or # symbols (I) */
float mthresh; /* >= this, show symbol as upper case */
if (Alphabet_type == hmmAMINO) mthresh = 0.5;
else mthresh = 0.9;
StateOccupancy(hmm, &mp, &ip, &dp);
/* First pass: how many states do we need in the trace?
* how long will the sequence be?
*/
nmat = ndel = nins = 0;
for (k = 1; k <= hmm->M; k++)
{
if (mp[k] >= 0.5) nmat++; else ndel++;
if (k < hmm->M && ip[k] >= 0.5)
nins += (int) (1.f / (1.f - hmm->t[k][TII]));
}
/* Allocations
*/
P7AllocTrace(6 + nmat + ndel + nins, &tr);
dsq = MallocOrDie(sizeof(char) * (nmat+nins+3));
seq = MallocOrDie(sizeof(char) * (nmat+nins+1));
/* Main pass.
* Construct consensus trace, seq, and dsq.
*/
TraceSet(tr, 0, STS, 0, 0);
TraceSet(tr, 1, STN, 0, 0);
TraceSet(tr, 2, STB, 0, 0);
dsq[0] = Alphabet_iupac; /* guard byte */
tpos = 3;
i = 0;
for (k = 1; k <= hmm->M; k++)
{
if (mp[k] >= 0.5)
{
x = FMax(hmm->mat[k], Alphabet_size);
TraceSet(tr, tpos, STM, k, i+1);
seq[i] = Alphabet[x];
dsq[i+1] = x;
if (hmm->mat[k][x] < mthresh)
seq[i] = tolower((int) seq[i]);
i++;
tpos++;
}
else
{
TraceSet(tr, tpos, STD, k, 0);
tpos++;
}
if (k < hmm->M && ip[k] >= 0.5)
{
x = (int) (1.f / (1.f - hmm->t[k][TII]));
while (x--)
{
TraceSet(tr, tpos, STI, k, i+1);
seq[i] = 'x';
dsq[i+1] = Alphabet_iupac - 1;
i++;
tpos++;
}
}
}
TraceSet(tr, tpos, STE, 0, 0); tpos++;
TraceSet(tr, tpos, STC, 0, 0); tpos++;
TraceSet(tr, tpos, STT, 0, 0); tpos++;
dsq[i+1] = Alphabet_iupac;
free(mp);
free(ip);
free(dp);
if (ret_seq != NULL) *ret_seq = seq; else free(seq);
if (ret_dsq != NULL) *ret_dsq = dsq; else free(dsq);
if (ret_L != NULL) *ret_L = i;
if (ret_tr != NULL) *ret_tr = tr; else P7FreeTrace(tr);
}
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;
}
/* Function: include_alignment()
* Date: SRE, Sun Jul 5 15:25:13 1998 [St. Louis]
*
* Purpose: Given the name of a multiple alignment file,
* align that alignment to the HMM, and add traces
* to an existing array of traces. If do_mapped
* is TRUE, we use the HMM's map file. If not,
* we use P7ViterbiAlignAlignment().
*
* Args: seqfile - name of alignment file
* hmm - model to align to
* do_mapped- TRUE if we're to use the HMM's alignment map
* rsq - RETURN: array of rseqs to add to
* dsq - RETURN: array of dsq to add to
* sqinfo - RETURN: array of SQINFO to add to
* tr - RETURN: array of traces to add to
* nseq - RETURN: number of seqs
*
* Returns: new, realloc'ed arrays for rsq, dsq, sqinfo, tr; nseq is
* increased to nseq+ainfo.nseq.
*/
void
include_alignment(char *seqfile, struct plan7_s *hmm, int do_mapped,
char ***rsq, char ***dsq, SQINFO **sqinfo,
struct p7trace_s ***tr, int *nseq)
{
int format; /* format of alignment file */
char **aseq; /* aligned seqs */
char **newdsq;
char **newrseq;
AINFO ainfo; /* info that goes with aseq */
int idx; /* counter over aseqs */
struct p7trace_s *master; /* master trace */
struct p7trace_s **addtr; /* individual traces for aseq */
if (! SeqfileFormat(seqfile, &format, NULL))
switch (squid_errno) {
case SQERR_NOFILE:
ajFatal("Alignment file %s could not be opened for reading", seqfile);
/*FALLTHRU*/ /* a white lie to shut lint up */
case SQERR_FORMAT:
default:
ajFatal("Failed to determine format of alignment file %s", seqfile);
}
/* read the alignment from file */
if (! ReadAlignment(seqfile, format, &aseq, &ainfo))
ajFatal("Failed to read aligned sequence file %s", seqfile);
for (idx = 0; idx < ainfo.nseq; idx++)
s2upper(aseq[idx]);
/* Verify checksums before mapping */
if (do_mapped && GCGMultchecksum(aseq, ainfo.nseq) != hmm->checksum)
ajFatal("The checksums for alignment file %s and the HMM alignment map don't match.",
seqfile);
/* Get a master trace */
if (do_mapped) master = MasterTraceFromMap(hmm->map, hmm->M, ainfo.alen);
else master = P7ViterbiAlignAlignment(aseq, &ainfo, hmm);
/* convert to individual traces */
ImposeMasterTrace(aseq, ainfo.nseq, master, &addtr);
/* add those traces to existing ones */
*tr = MergeTraceArrays(*tr, *nseq, addtr, ainfo.nseq);
/* additional bookkeeping: add to dsq, sqinfo */
*rsq = ReallocOrDie((*rsq), sizeof(char *) * (*nseq + ainfo.nseq));
DealignAseqs(aseq, ainfo.nseq, &newrseq);
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
(*rsq)[idx] = newrseq[idx - (*nseq)];
free(newrseq);
*dsq = ReallocOrDie((*dsq), sizeof(char *) * (*nseq + ainfo.nseq));
DigitizeAlignment(aseq, &ainfo, &newdsq);
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
(*dsq)[idx] = newdsq[idx - (*nseq)];
free(newdsq);
/* unnecessarily complex, but I can't be bothered... */
*sqinfo = ReallocOrDie((*sqinfo), sizeof(SQINFO) * (*nseq + ainfo.nseq));
for (idx = *nseq; idx < *nseq + ainfo.nseq; idx++)
SeqinfoCopy(&((*sqinfo)[idx]), &(ainfo.sqinfo[idx - (*nseq)]));
*nseq = *nseq + ainfo.nseq;
/* Cleanup */
P7FreeTrace(master);
FreeAlignment(aseq, &ainfo);
/* Return */
return;
}
