/*!
* Build a single lambda function by "folding" the chain. Folding means
* that the chain is processed from back to front and each emitter is
* composed using previous lambda functions.
*
* \return Single "folded" lambda function representing the chain.
*/
auto fold() const {
const size_t Size = sizeof ... (Lambdas);
return EmitSequence(common::make_index_sequence<Size>{ });
}
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;
}
