/* Function: p7_prior_CreateLaplace()
* Synopsis: Creates Laplace plus-one prior.
* Incept: SRE, Sat Jun 30 09:48:13 2007 [Janelia]
*
* Purpose: Create a Laplace plus-one prior for alphabet <abc>.
*/
P7_PRIOR *
p7_prior_CreateLaplace(const ESL_ALPHABET *abc)
{
P7_PRIOR *pri = NULL;
int status;
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); /* single component; 3 params */
pri->ti = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->td = esl_mixdchlet_Create(1, 2); /* single component; 2 params */
pri->em = esl_mixdchlet_Create(1, abc->K); /* single component; K params */
pri->ei = esl_mixdchlet_Create(1, abc->K); /* single component; K params */
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
pri->tm->pq[0] = 1.0; esl_vec_DSet(pri->tm->alpha[0], 3, 1.0); /* match transitions */
pri->ti->pq[0] = 1.0; esl_vec_DSet(pri->ti->alpha[0], 2, 1.0); /* insert transitions */
pri->td->pq[0] = 1.0; esl_vec_DSet(pri->td->alpha[0], 2, 1.0); /* delete transitions */
pri->em->pq[0] = 1.0; esl_vec_DSet(pri->em->alpha[0], abc->K, 1.0); /* match emissions */
pri->ei->pq[0] = 1.0; esl_vec_DSet(pri->ei->alpha[0], abc->K, 1.0); /* insert emissions */
return pri;
ERROR:
p7_prior_Destroy(pri);
return NULL;
}
/* seq_generation()
*
* Generating sequences.
*/
static int
seq_generation(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
ESL_ALPHABET *abc = NULL;
ESL_SQ *sq = NULL;
double *fq = NULL;
int alphatype = eslUNKNOWN; // static checkers can't see that 1 of --rna, --dna, --amino must be true
int N = esl_opt_GetInteger(go, "-N");
int L = esl_opt_GetInteger(go, "-L");
int i;
int status;
if (L <= 0) esl_fatal("To generate sequences, set -L option (length of generated seqs) > 0 ");
if (esl_opt_GetBoolean(go, "--rna")) alphatype = eslRNA;
if (esl_opt_GetBoolean(go, "--dna")) alphatype = eslDNA;
if (esl_opt_GetBoolean(go, "--amino")) alphatype = eslAMINO;
abc = esl_alphabet_Create(alphatype);
sq = esl_sq_CreateDigital(abc);
esl_sq_GrowTo(sq, L);
/* Pick the iid frequency distribution to use */
ESL_ALLOC(fq, sizeof(double) * abc->K);
switch (alphatype) {
case eslRNA:
case eslDNA: esl_vec_DSet(fq, 4, 0.25); break;
case eslAMINO: esl_composition_SW34(fq); break;
default: esl_vec_DSet(fq, abc->K, 1.0 / (double) abc->K); break;
}
/* generate */
for (i = 0; i < N; i++)
{
esl_rsq_xIID(r, fq, abc->K, L, sq->dsq);
if (N > 1) esl_sq_FormatName(sq, "random%d", i);
else esl_sq_SetName(sq, "random");
sq->n = L;
esl_sqio_Write(ofp, sq, outfmt, FALSE);
}
free(fq);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
return eslOK;
ERROR:
if (fq != NULL) free(fq);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
return status;
}
/* The gradient of the NLL w.r.t. each free parameter in p.
*/
static void
hyperexp_complete_gradient(double *p, int np, void *dptr, double *dp)
{
struct hyperexp_data *data = (struct hyperexp_data *) dptr;
ESL_HYPEREXP *h = data->h;
double pdf;
int i,k;
int pidx;
hyperexp_unpack_paramvector(p, np, h);
esl_vec_DSet(dp, np, 0.);
for (i = 0; i < data->n; i++)
{
/* FIXME: I think the calculation below may need to be done
* in log space, to avoid underflow errors; see complete_binned_gradient()
*/
/* Precalculate q_k PDF_k(x) terms, and their sum */
for (k = 0; k < h->K; k++)
h->wrk[k] = h->q[k] * esl_exp_pdf(data->x[i], h->mu, h->lambda[k]);
pdf = esl_vec_DSum(h->wrk, h->K);
pidx = 0;
if (! h->fixmix) {
for (k = 1; k < h->K; k++) /* generic d/dQ solution for mixture models */
dp[pidx++] -= h->wrk[k]/pdf - h->q[k];
}
for (k = 0; k < h->K; k++)
if (! h->fixlambda[k])
dp[pidx++] -= (1.-h->lambda[k]*(data->x[i]-h->mu))*h->wrk[k]/pdf; /* d/dw */
}
}
static void
hyperexp_complete_binned_gradient(double *p, int np, void *dptr, double *dp)
{
struct hyperexp_binned_data *data = (struct hyperexp_binned_data *) dptr;
ESL_HISTOGRAM *g = data->g;
ESL_HYPEREXP *h = data->h;
int i,k;
int pidx;
double z;
double tmp;
double ai, delta;
hyperexp_unpack_paramvector(p, np, h);
esl_vec_DSet(dp, np, 0.);
delta = g->w;
/* counting over occupied, uncensored histogram bins */
for (i = g->cmin; i <= g->imax; i++)
{
if (g->obs[i] == 0) continue;
ai = esl_histogram_Bin2LBound(g, i);
if (ai < h->mu) ai = h->mu; /* careful about the left boundary: no x < h->mu */
/* Calculate log (q_m alpha_m(a_i) terms
*/
for (k = 0; k < h->K; k++)
{
h->wrk[k] = log(h->q[k]) - h->lambda[k]*(ai-h->mu);
if (delta * h->lambda[k] < eslSMALLX1)
h->wrk[k] += log(delta * h->lambda[k]);
else
h->wrk[k] += log(1 - exp(-delta * h->lambda[k]));
}
z = esl_vec_DLogSum(h->wrk, h->K); /* z= log \sum_k q_k alpha_k(a_i) */
/* Bump the gradients for Q_1..Q_{K-1} */
pidx = 0;
if (! h->fixmix) {
for (k = 1; k < h->K; k++)
dp[pidx++] -= g->obs[i] * (exp(h->wrk[k] - z) - h->q[k]);
}
/* Bump the gradients for w_0..w_{K-1}
*/
for (k = 0; k < h->K; k++)
if (! h->fixlambda[k])
{
tmp = log(h->q[k]) + log(h->lambda[k])- h->lambda[k]*(ai-h->mu);
tmp = exp(tmp - z);
tmp *= (ai + delta - h->mu) * exp(-delta * h->lambda[k]) - (ai - h->mu);
dp[pidx++] -= g->obs[i] * tmp;
}
}
}
int main(void)
{
double *p;
char labels[] = "ACGT";
int n = 4;
p = malloc(sizeof(double) * n);
esl_vec_DSet(p, n, 1.0);
esl_vec_DNorm(p, n);
esl_vec_DDump(stdout, p, n, labels);
free(p);
return 0;
}
/* set_relative_weights():
* Set msa->wgt vector, using user's choice of relative weighting algorithm.
*/
static int
relative_weights(P7_BUILDER *bld, ESL_MSA *msa)
{
int status = eslOK;
if (bld->wgt_strategy == p7_WGT_NONE) { esl_vec_DSet(msa->wgt, msa->nseq, 1.); }
else if (bld->wgt_strategy == p7_WGT_GIVEN) ;
else if (bld->wgt_strategy == p7_WGT_PB) status = esl_msaweight_PB(msa);
else if (bld->wgt_strategy == p7_WGT_GSC) status = esl_msaweight_GSC(msa);
else if (bld->wgt_strategy == p7_WGT_BLOSUM) status = esl_msaweight_BLOSUM(msa, bld->wid);
else ESL_EXCEPTION(eslEINCONCEIVABLE, "no such weighting strategy");
if (status != eslOK) ESL_FAIL(status, bld->errbuf, "failed to set relative weights in alignment");
return eslOK;
}
/* Function: esl_paml_ReadE()
* Incept: SRE, Fri Jul 9 09:27:24 2004 [St. Louis]
*
* Purpose: Read an amino acid rate matrix in PAML format from stream
* <fp>. Return it in two pieces: the symmetric E
* exchangeability matrix in <E>, and the stationary
* probability vector $\pi$ in <pi>.
* Caller provides the memory for both <E> and <pi>. <E>
* is a $20 \times 20$ matrix allocated as
* <esl_dmatrix_Create(20, 20)>. <pi> is an array with
* space for at least 20 doubles.
*
* The <E> matrix is symmetric for off-diagonal elements:
* $E_{ij} = E_{ij}$ for $i \neq j$. The on-diagonal
* elements $E_{ii}$ are not valid and should not be
* accessed. (They are set to zero.)
* The rate matrix will later be obtained from <E>
* and <pi> as
* $Q_{ij} = E_{ij} \pi_j$ for $i \neq j$
* and
* $Q_{ii} = -\sum_{j \neq i} Q_{ij}$
* then scaled to units of one
* substitution/site; see <esl_ratemx_E2Q()> and
* <esl_ratemx_ScaleTo()>.
*
* Data file format: First 190 numbers are a
* lower-triangular matrix E of amino acid
* exchangeabilities $E_{ij}$. Next 20 numbers are the
* amino acid frequencies $\pi_i$. Remainder of the
* datafile is ignored.
*
* The alphabet order in the matrix and the frequency
* vector is assumed to be "ARNDCQEGHILKMFPSTWYV"
* (alphabetical by three-letter code), which appears to be
* PAML's default order. This is transformed to Easel's
* "ACDEFGHIKLMNPQRSTVWY" (alphabetical by one-letter code)
* in the $E_{ij}$ and $\pi_i$ that are returned.
*
* Args: fp - open datafile for reading.
* E - RETURN: E matrix of amino acid exchangeabilities e_ij,
* symmetric (E_ij = E_ji),
* in Easel amino acid alphabet order A..Y.
* Caller provides appropriately allocated space.
* pi - RETURN: \pi_i vector of amino acid frequencies,
* in Easel amino acid alphabet order A..Y.
* Caller provides appropriately allocated space.
*
* Returns: <eslOK> on success.
* Returns <eslEOF> on premature end of file (parse failed), in which
* case the contents of <E> and <pi> are undefined.
*
* Throws: <eslEMEM> on internal allocation failure,
* and the contents of <E> and <pi> are undefined.
*
* Xref: STL8/p.56.
*/
int
esl_paml_ReadE(FILE *fp, ESL_DMATRIX *E, double *pi)
{
int status;
ESL_FILEPARSER *efp = NULL;
char *tok;
int i,j;
char *pamlorder = "ARNDCQEGHILKMFPSTWYV";
char *eslorder = "ACDEFGHIKLMNPQRSTVWY";
int perm[20];
if ((status = esl_dmatrix_SetZero(E)) != eslOK) goto ERROR;
esl_vec_DSet(pi, 20, 0.);
if ((efp = esl_fileparser_Create(fp)) == NULL) goto ERROR;
if ((status = esl_fileparser_SetCommentChar(efp, '#')) != eslOK) goto ERROR;
/* Construct the alphabet permutation we need.
* perm[i] -> original row/column i goes to row/column perm[i]
*/
for (i = 0; i < 20; i++)
perm[i] = (int) (strchr(eslorder, pamlorder[i]) - eslorder);
/* Read the s_ij matrix data in, permuting as we go. */
for (i = 1; i < 20; i++)
for (j = 0; j < i; j++)
{
if ((status = esl_fileparser_GetToken(efp, &tok, NULL)) != eslOK) goto ERROR;
E->mx[perm[i]][perm[j]] = atof(tok);
E->mx[perm[j]][perm[i]] = E->mx[perm[i]][perm[j]];
}
/* Read the pi_i vector in, permuting as we read. */
for (i = 0; i < 20; i++)
{
if ((status = esl_fileparser_GetToken(efp, &tok, NULL)) != eslOK) goto ERROR;
pi[perm[i]] = atof(tok);
}
esl_fileparser_Destroy(efp);
return eslOK;
ERROR:
if (efp != NULL) esl_fileparser_Destroy(efp);
return status;
}
static void
utest_SetWAG(void)
{
char errbuf[eslERRBUFSIZE];
ESL_DMATRIX *Q = NULL;
ESL_DMATRIX *P = NULL;
double t = 50.0; /* sufficiently large to drive e^tQ to stationarity */
double pi[20];
int i;
if ((Q = esl_dmatrix_Create(20, 20)) == NULL) esl_fatal("malloc failed");
if ((P = esl_dmatrix_Create(20, 20)) == NULL) esl_fatal("malloc failed");
/* This tests that exponentiating WAG gives a stable conditional
* probability matrix solution. (It doesn't particularly test that
* WAG was set correctly, but how could we have screwed that up?)
*/
if (esl_rmx_SetWAG(Q, NULL) != eslOK) esl_fatal("_SetWAG() failed");
if (esl_dmx_Exp(Q, t, P) != eslOK) esl_fatal("matrix exponentiation failed");
if (esl_rmx_ValidateP(P, 1e-7, errbuf) != eslOK) esl_fatal("P validation failed: %s", errbuf);
if (esl_rmx_ValidateQ(Q, 1e-7, errbuf) != eslOK) esl_fatal("Q validation failed: %s", errbuf);
/* This tests setting WAG to different stationary pi's than default,
* then tests that exponentiating to large t reaches those stationaries.
*/
esl_vec_DSet(pi, 20, 0.05);
if (esl_rmx_SetWAG(Q, pi) != eslOK) esl_fatal("_SetWAG() failed");
if (esl_dmx_Exp(Q, t, P) != eslOK) esl_fatal("matrix exponentiation failed");
if (esl_rmx_ValidateP(P, 1e-7, errbuf) != eslOK) esl_fatal("P validation failed: %s", errbuf);
if (esl_rmx_ValidateQ(Q, 1e-7, errbuf) != eslOK) esl_fatal("Q validation failed: %s", errbuf);
for (i = 0; i < 20; i++)
if (esl_vec_DCompare(P->mx[i], pi, 20, 1e-7) != eslOK) esl_fatal("P didn't converge to right pi's");
esl_dmatrix_Destroy(Q);
esl_dmatrix_Destroy(P);
return;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line configuration */
struct cfg_s cfg; /* application configuration */
char *basename= NULL; /* base of the output file names */
char *alifile = NULL; /* alignment file name */
char *dbfile = NULL; /* name of seq db file */
char outfile[256]; /* name of an output file */
int alifmt; /* format code for alifile */
int dbfmt; /* format code for dbfile */
ESL_MSAFILE *afp = NULL; /* open alignment file */
ESL_MSA *origmsa = NULL; /* one multiple sequence alignment */
ESL_MSA *msa = NULL; /* MSA after frags are removed */
ESL_MSA *trainmsa= NULL; /* training set, aligned */
ESL_STACK *teststack=NULL; /* test set: stack of ESL_SQ ptrs */
int status; /* easel return code */
int nfrags; /* # of fragments removed */
int ntestdom; /* # of test domains */
int ntest; /* # of test sequences created */
int nali; /* number of alignments read */
double avgid;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h")) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 3) cmdline_failure(argv[0], "Incorrect number of command line arguments\n");
basename = esl_opt_GetArg(go, 1);
alifile = esl_opt_GetArg(go, 2);
dbfile = esl_opt_GetArg(go, 3);
alifmt = eslMSAFILE_STOCKHOLM;
dbfmt = eslSQFILE_FASTA;
/* Set up the configuration structure shared amongst functions here */
if (esl_opt_IsDefault(go, "--seed")) cfg.r = esl_randomness_CreateTimeseeded();
else cfg.r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
cfg.abc = NULL; /* until we open the MSA file, below */
cfg.fragfrac = esl_opt_GetReal(go, "-F");
cfg.idthresh1 = esl_opt_GetReal(go, "-1");
cfg.idthresh2 = esl_opt_GetReal(go, "-2");
cfg.test_lens = NULL;
cfg.ntest = 0;
/* Open the output files */
if (snprintf(outfile, 256, "%s.msa", basename) >= 256) esl_fatal("Failed to construct output MSA file name");
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.fa", basename) >= 256) esl_fatal("Failed to construct output FASTA file name");
if ((cfg.out_seqfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.pos", basename) >= 256) esl_fatal("Failed to construct pos test set summary file name");
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.neg", basename) >= 256) esl_fatal("Failed to construct neg test set summary file name");
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.tbl", basename) >= 256) esl_fatal("Failed to construct benchmark table file name");
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
/* Open the MSA file; determine alphabet */
status = esl_msafile_Open(alifile, alifmt, NULL, &afp);
if (status == eslENOTFOUND) esl_fatal("Alignment file %s doesn't exist or is not readable\n", alifile);
else if (status == eslEFORMAT) esl_fatal("Couldn't determine format of alignment %s\n", alifile);
else if (status != eslOK) esl_fatal("Alignment file open failed with error %d\n", status);
if (esl_opt_GetBoolean(go, "--amino")) cfg.abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) cfg.abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) cfg.abc = esl_alphabet_Create(eslRNA);
else {
int type;
status = esl_msafile_GuessAlphabet(afp, &type);
if (status == eslEAMBIGUOUS) esl_fatal("Failed to guess the bio alphabet used in %s.\nUse --dna, --rna, or --amino option to specify it.", alifile);
else if (status == eslEFORMAT) esl_fatal("Alignment file parse failed: %s\n", afp->errbuf);
else if (status == eslENODATA) esl_fatal("Alignment file %s is empty\n", alifile);
else if (status != eslOK) esl_fatal("Failed to read alignment file %s\n", alifile);
cfg.abc = esl_alphabet_Create(type);
}
esl_msafile_SetDigital(afp, cfg.abc);
if (cfg.abc->type == eslAMINO) esl_composition_SW34(cfg.fq);
else esl_vec_DSet(cfg.fq, cfg.abc->K, 1.0 / (double) cfg.abc->K);
/* Open and process the dbfile; make sure it's in the same alphabet */
process_dbfile(&cfg, dbfile, dbfmt);
/* Read and process MSAs one at a time */
nali = 0;
while ((status = esl_msa_Read(afp, &origmsa)) == eslOK)
{
remove_fragments(&cfg, origmsa, &msa, &nfrags);
separate_sets (&cfg, msa, &trainmsa, &teststack);
ntestdom = esl_stack_ObjectCount(teststack);
if (ntestdom >= 2)
{
esl_stack_Shuffle(cfg.r, teststack);
synthesize_positives(go, &cfg, msa->name, teststack, &ntest);
esl_msa_MinimGaps(trainmsa, NULL, NULL);
esl_msa_Write(cfg.out_msafp, trainmsa, eslMSAFILE_STOCKHOLM);
esl_dst_XAverageId(cfg.abc, trainmsa->ax, trainmsa->nseq, 10000, &avgid); /* 10000 is max_comparisons, before sampling kicks in */
fprintf(cfg.tblfp, "%-20s %3.0f%% %6d %6d %6d %6d %6d %6d\n", msa->name, 100.*avgid, (int) trainmsa->alen, msa->nseq, nfrags, trainmsa->nseq, ntestdom, ntest);
nali++;
}
esl_msa_Destroy(trainmsa);
esl_msa_Destroy(origmsa);
esl_msa_Destroy(msa);
}
if (status == eslEFORMAT) esl_fatal("Alignment file parse error, line %d of file %s:\n%s\nOffending line is:\n%s\n",
afp->linenumber, afp->fname, afp->errbuf, afp->buf);
else if (status != eslEOF) esl_fatal("Alignment file read failed with error code %d\n", status);
else if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
if (nali > 0)
synthesize_negatives(go, &cfg, esl_opt_GetInteger(go, "-N"));
fclose(cfg.out_msafp);
fclose(cfg.out_seqfp);
fclose(cfg.possummfp);
fclose(cfg.negsummfp);
fclose(cfg.tblfp);
esl_randomness_Destroy(cfg.r);
esl_alphabet_Destroy(cfg.abc);
esl_msafile_Close(afp);
esl_getopts_Destroy(go);
return 0;
}
/* Function: p7_prior_CreateNucleic()
*
* Purpose: Creates the default mixture Dirichlet prior for nucleotide
* sequences.
*
* The transition priors (match, insert, delete) are all
* single Dirichlets, trained on a portion of the rmark dataset
*
* The match emission prior is an eight-component mixture
* trained against a portion of the rmark dataset
*
* The insert emission prior is a single Dirichlet with
* high $|\alpha|$, such that insert emission probabilities
* are essentially fixed by the prior, regardless of
* observed count data.
*
* Returns: a pointer to the new <P7_PRIOR> structure.
*/
P7_PRIOR *
p7_prior_CreateNucleic(void)
{
int status;
P7_PRIOR *pri = NULL;
int q;
/* Plus-1 Laplace prior
int num_comp = 1;
static double defmq[2] = { 1.0 };
static double defm[1][4] = {
{ 1.0, 1.0, 1.0, 1.0} //
};
*/
/* Match emission priors are trained on Rmark3 database
* Xref: ~wheelert/notebook/2011/0325_nhmmer_new_parameters
*/
int num_comp = 4;
static double defmq[4] = { 0.24, 0.26, 0.08, 0.42 };
static double defm[4][4] = {
{ 0.16, 0.45, 0.12, 0.39},
{ 0.09, 0.03, 0.09, 0.04},
{ 1.29, 0.40, 6.58, 0.51},
{ 1.74, 1.49, 1.57, 1.95}
};
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); // match transitions; single component; 3 params
pri->ti = esl_mixdchlet_Create(1, 2); // insert transitions; single component; 2 params
pri->td = esl_mixdchlet_Create(1, 2); // delete transitions; single component; 2 params
pri->em = esl_mixdchlet_Create(num_comp, 4); // match emissions; X component; 4 params
pri->ei = esl_mixdchlet_Create(1, 4); // insert emissions; single component; 4 params
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
/* Transition priors: roughly, learned from rmark benchmark - hand-beautified (trimming overspecified significant digits)
*/
pri->tm->pq[0] = 1.0;
pri->tm->alpha[0][0] = 2.0; // TMM
pri->tm->alpha[0][1] = 0.1; // TMI
pri->tm->alpha[0][2] = 0.1; // TMD
pri->ti->pq[0] = 1.0;
pri->ti->alpha[0][0] = 0.06; // TIM
pri->ti->alpha[0][1] = 0.2; // TII
pri->td->pq[0] = 1.0;
pri->td->alpha[0][0] = 0.1; // TDM
pri->td->alpha[0][1] = 0.2; // TDD
/* Match emission priors */
for (q = 0; q < num_comp; q++)
{
pri->em->pq[q] = defmq[q];
esl_vec_DCopy(defm[q], 4, pri->em->alpha[q]);
}
/* Insert emission priors. Should that alphas be lower? higher?
*/
pri->ei->pq[0] = 1.0;
esl_vec_DSet(pri->ei->alpha[0], 4, 1.0);
return pri;
ERROR:
if (pri != NULL) p7_prior_Destroy(pri);
return NULL;
}
/* Function: esl_msaweight_PB()
* Synopsis: PB (position-based) weights.
* Incept: SRE, Sun Nov 5 08:59:28 2006 [Janelia]
*
* Purpose: Given a multiple alignment <msa>, calculate sequence
* weights according to the position-based weighting
* algorithm (Henikoff and Henikoff, JMB 243:574-578,
* 1994). These weights are stored internally in the <msa>
* object, replacing any weights that may have already been
* there. Weights are $\geq 0$ and they sum to <msa->nseq>.
*
* The <msa> may be in either digitized or text mode.
* Digital mode is preferred, so that the algorithm
* deals with degenerate residue symbols properly.
*
* The Henikoffs' algorithm does not give rules for dealing
* with gaps or degenerate residue symbols. The rule here
* is to ignore them. This means that longer sequences
* initially get more weight; hence a "double
* normalization" in which the weights are first divided by
* sequence length in canonical residues (to compensate for
* that effect), then normalized to sum to nseq.
*
* An advantage of the PB method is efficiency.
* It is $O(1)$ in memory and $O(NL)$ time, for an alignment of
* N sequences and L columns. This makes it a good method
* for ad hoc weighting of very deep alignments.
*
* When the alignment is in simple text mode, IUPAC
* degenerate symbols are not dealt with correctly; instead,
* the algorithm simply uses the 26 letters as "residues"
* (case-insensitively), and treats all other residues as
* gaps.
*
* Returns: <eslOK> on success, and the weights inside <msa> have been
* modified.
*
* Throws: <eslEMEM> on allocation error, in which case <msa> is
* returned unmodified.
*
* Xref: [Henikoff94b]; squid::weight.c::PositionBasedWeights().
*/
int
esl_msaweight_PB(ESL_MSA *msa)
{
int *nres = NULL; /* counts of each residue observed in a column */
int ntotal; /* number of different symbols observed in a column */
int rlen; /* number of residues in a sequence */
int idx, pos, i;
int K; /* alphabet size */
int status;
/* Contract checks
*/
ESL_DASSERT1( (msa->nseq >= 1) );
ESL_DASSERT1( (msa->alen >= 1) );
if (msa->nseq == 1) { msa->wgt[0] = 1.0; return eslOK; }
/* Initialize
*/
if (! (msa->flags & eslMSA_DIGITAL))
{ ESL_ALLOC(nres, sizeof(int) * 26); K = 26; }
#ifdef eslAUGMENT_ALPHABET
else
{ ESL_ALLOC(nres, sizeof(int) * msa->abc->K); K = msa->abc->K; }
#endif
esl_vec_DSet(msa->wgt, msa->nseq, 0.);
/* This section handles text alignments */
if (! (msa->flags & eslMSA_DIGITAL))
{
for (pos = 0; pos < msa->alen; pos++)
{
/* Collect # of letters A..Z in this column, and total */
esl_vec_ISet(nres, K, 0.);
for (idx = 0; idx < msa->nseq; idx++)
if (isalpha((int) msa->aseq[idx][pos]))
nres[toupper((int) msa->aseq[idx][pos]) - 'A'] ++;
for (ntotal = 0, i = 0; i < K; i++) if (nres[i] > 0) ntotal++;
/* Bump weight on each seq by PB rule */
if (ntotal > 0) {
for (idx = 0; idx < msa->nseq; idx++) {
if (isalpha((int) msa->aseq[idx][pos]))
msa->wgt[idx] += 1. /
(double) (ntotal * nres[toupper((int) msa->aseq[idx][pos]) - 'A'] );
}
}
}
/* first normalization by # of residues counted in each seq */
for (idx = 0; idx < msa->nseq; idx++) {
for (rlen = 0, pos = 0; pos < msa->alen; pos++)
if (isalpha((int) msa->aseq[idx][pos])) rlen++;
if (ntotal > 0) msa->wgt[idx] /= (double) rlen;
/* if rlen == 0 for this seq, its weight is still 0.0, as initialized. */
}
}
/* This section handles digital alignments. */
#ifdef eslAUGMENT_ALPHABET
else
{
for (pos = 1; pos <= msa->alen; pos++)
{
/* Collect # of residues 0..K-1 in this column, and total # */
esl_vec_ISet(nres, K, 0.);
for (idx = 0; idx < msa->nseq; idx++)
if (esl_abc_XIsCanonical(msa->abc, msa->ax[idx][pos]))
nres[(int) msa->ax[idx][pos]] ++;
for (ntotal = 0, i = 0; i < K; i++) if (nres[i] > 0) ntotal++;
/* Bump weight on each sequence by PB rule */
if (ntotal > 0) {
for (idx = 0; idx < msa->nseq; idx++) {
if (esl_abc_XIsCanonical(msa->abc, msa->ax[idx][pos]))
msa->wgt[idx] += 1. / (double) (ntotal * nres[msa->ax[idx][pos]]);
}
}
}
/* first normalization by # of residues counted in each seq */
for (idx = 0; idx < msa->nseq; idx++)
{
for (rlen = 0, pos = 1; pos <= msa->alen; pos++)
if (esl_abc_XIsCanonical(msa->abc, msa->ax[idx][pos])) rlen++;
if (rlen > 0) msa->wgt[idx] /= (double) rlen;
/* if rlen == 0 for this seq, its weight is still 0.0, as initialized. */
}
}
#endif
/* Make weights normalize up to nseq, and return. In pathological
* case where all wgts were 0 (no seqs contain any unambiguous
* residues), weights become 1.0.
*/
esl_vec_DNorm(msa->wgt, msa->nseq);
esl_vec_DScale(msa->wgt, msa->nseq, (double) msa->nseq);
msa->flags |= eslMSA_HASWGTS;
free(nres);
return eslOK;
ERROR:
if (nres != NULL) free(nres);
return status;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* command line configuration */
struct cfg_s cfg; /* application configuration */
char *basename= NULL; /* base of the output file names */
char *alifile = NULL; /* alignment file name */
char *dbfile = NULL; /* name of seq db file */
char outfile[256]; /* name of an output file */
int alifmt; /* format code for alifile */
int dbfmt; /* format code for dbfile */
ESLX_MSAFILE *afp = NULL; /* open alignment file */
ESL_MSA *origmsa = NULL; /* one multiple sequence alignment */
ESL_MSA *msa = NULL; /* MSA after frags are removed */
ESL_MSA *trainmsa= NULL; /* training set, aligned */
ESL_STACK *teststack=NULL; /* test set: stack of ESL_SQ ptrs */
int status; /* easel return code */
int nfrags; /* # of fragments removed */
int ntestdom; /* # of test domains */
int ntest; /* # of test sequences created */
int nali; /* number of alignments read */
double avgid;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h")) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 3) cmdline_failure(argv[0], "Incorrect number of command line arguments\n");
basename = esl_opt_GetArg(go, 1);
alifile = esl_opt_GetArg(go, 2);
dbfile = esl_opt_GetArg(go, 3);
alifmt = eslMSAFILE_STOCKHOLM;
dbfmt = eslSQFILE_FASTA;
/* Set up the configuration structure shared amongst functions here */
if (esl_opt_IsDefault(go, "--seed")) cfg.r = esl_randomness_CreateTimeseeded();
else cfg.r = esl_randomness_Create(esl_opt_GetInteger(go, "--seed"));
cfg.abc = NULL; /* until we open the MSA file, below */
cfg.fragfrac = esl_opt_GetReal(go, "-F");
cfg.idthresh1 = esl_opt_GetReal(go, "-1");
cfg.idthresh2 = esl_opt_GetReal(go, "-2");
cfg.test_lens = NULL;
cfg.ntest = 0;
cfg.max_ntest = (esl_opt_IsOn(go, "--maxtest") ? esl_opt_GetInteger(go, "--maxtest") : 0);
cfg.max_ntrain = (esl_opt_IsOn(go, "--maxtrain") ? esl_opt_GetInteger(go, "--maxtrain") : 0);
/* Open the output files */
if (snprintf(outfile, 256, "%s.msa", basename) >= 256) esl_fatal("Failed to construct output MSA file name");
if ((cfg.out_msafp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open MSA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.fa", basename) >= 256) esl_fatal("Failed to construct output FASTA file name");
if ((cfg.out_seqfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open FASTA output file %s\n", outfile);
if (snprintf(outfile, 256, "%s.pos", basename) >= 256) esl_fatal("Failed to construct pos test set summary file name");
if ((cfg.possummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open pos test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.neg", basename) >= 256) esl_fatal("Failed to construct neg test set summary file name");
if ((cfg.negsummfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open neg test set summary file %s\n", outfile);
if (snprintf(outfile, 256, "%s.tbl", basename) >= 256) esl_fatal("Failed to construct benchmark table file name");
if ((cfg.tblfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open benchmark table file %s\n", outfile);
if (esl_opt_GetBoolean(go, "--pid")) {
if (snprintf(outfile, 256, "%s.pid", basename) >= 256) esl_fatal("Failed to construct %%id table file name");
if ((cfg.pidfp = fopen(outfile, "w")) == NULL) esl_fatal("Failed to open %%id table file %s\n", outfile);
} else cfg.pidfp = NULL;
/* Open the MSA file, digital mode; determine alphabet */
if (esl_opt_GetBoolean(go, "--amino")) cfg.abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) cfg.abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) cfg.abc = esl_alphabet_Create(eslRNA);
status = eslx_msafile_Open(&(cfg.abc), alifile, NULL, alifmt, NULL, &afp);
if (status != eslOK) eslx_msafile_OpenFailure(afp, status);
if (cfg.abc->type == eslAMINO) esl_composition_SW34(cfg.fq);
else esl_vec_DSet(cfg.fq, cfg.abc->K, 1.0 / (double) cfg.abc->K);
/* Open and process the dbfile; make sure it's in the same alphabet */
process_dbfile(&cfg, dbfile, dbfmt);
/* Read and process MSAs one at a time */
nali = 0;
while ((status = eslx_msafile_Read(afp, &origmsa)) != eslEOF)
{
if (status != eslOK) eslx_msafile_ReadFailure(afp, status);
esl_msa_ConvertDegen2X(origmsa);
esl_msa_Hash(origmsa);
remove_fragments(&cfg, origmsa, &msa, &nfrags);
separate_sets (&cfg, msa, &trainmsa, &teststack);
if ( esl_stack_ObjectCount(teststack) >= 2)
{
/* randomize test domain order, and apply size limit if any */
esl_stack_Shuffle(cfg.r, teststack);
if (cfg.max_ntest) pstack_select_topn(&teststack, cfg.max_ntest);
ntestdom = esl_stack_ObjectCount(teststack);
/* randomize training set alignment order, and apply size limit if any */
esl_msashuffle_PermuteSequenceOrder(cfg.r, trainmsa);
if (cfg.max_ntrain) msa_select_topn(&trainmsa, cfg.max_ntrain);
esl_msa_MinimGaps(trainmsa, NULL, NULL, FALSE);
if (esl_opt_GetBoolean(go, "--pid")) write_pids(cfg.pidfp, origmsa, trainmsa, teststack);
synthesize_positives(go, &cfg, msa->name, teststack, &ntest);
eslx_msafile_Write(cfg.out_msafp, trainmsa, eslMSAFILE_STOCKHOLM);
esl_dst_XAverageId(cfg.abc, trainmsa->ax, trainmsa->nseq, 10000, &avgid); /* 10000 is max_comparisons, before sampling kicks in */
fprintf(cfg.tblfp, "%-20s %3.0f%% %6d %6d %6d %6d %6d %6d\n", msa->name, 100.*avgid, (int) trainmsa->alen, msa->nseq, nfrags, trainmsa->nseq, ntestdom, ntest);
nali++;
}
esl_msa_Destroy(trainmsa);
esl_msa_Destroy(origmsa);
esl_msa_Destroy(msa);
}
if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
synthesize_negatives(go, &cfg, esl_opt_GetInteger(go, "-N"));
fclose(cfg.out_msafp);
fclose(cfg.out_seqfp);
fclose(cfg.possummfp);
fclose(cfg.negsummfp);
fclose(cfg.tblfp);
if (cfg.pidfp) fclose(cfg.pidfp);
esl_randomness_Destroy(cfg.r);
esl_alphabet_Destroy(cfg.abc);
eslx_msafile_Close(afp);
esl_getopts_Destroy(go);
return 0;
}
/* dump_insert_info
*
* Given an MSA with RF annotation, print out information about how many 'insertions' come
* after each non-gap RF column (consensus column).
*/
static int dump_insert_info(FILE *fp, ESL_MSA *msa, int use_weights, int nali, int *i_am_rf, char *alifile, char *errbuf)
{
int status;
int apos, rfpos;
double **ict;
double *total_ict;
int i;
int rflen;
double seqwt; /* weight of current sequence */
double nseq;
/* contract check */
if(! (msa->flags & eslMSA_DIGITAL)) ESL_XFAIL(eslEINVAL, errbuf, "in dump_insert_info(), msa must be digitized.");
if(msa->rf == NULL) ESL_XFAIL(eslEINVAL, errbuf, "No #=GC RF markup in alignment, it is needed for --iinfo.");
if(i_am_rf == NULL) ESL_XFAIL(eslEINVAL, errbuf, "internal error, dump_insert_info() i_am_rf is NULL.");
if(use_weights && msa->wgt == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "dump_insert_info(): use_weights==TRUE but msa->wgt == NULL");
ESL_ALLOC(total_ict, sizeof(double) * (msa->alen+2));
esl_vec_DSet(total_ict, (msa->alen+2), 0.);
ESL_ALLOC(ict, sizeof(double *) * (msa->alen+2));
for(i = 0; i <= msa->alen; i++)
{
ESL_ALLOC(ict[i], sizeof(double) * (msa->nseq));
esl_vec_DSet(ict[i], (msa->nseq), 0.);
}
fprintf(fp, "# Insert information:\n");
fprintf(fp, "# Alignment file: %s\n", alifile);
fprintf(fp, "# Alignment idx: %d\n", nali);
if(msa->name != NULL) { fprintf(fp, "# Alignment name: %s\n", msa->name); }
fprintf(fp, "# rfpos is the nongap RF position after which insertions occur\n");
fprintf(fp, "# An rfpos of '0' indicates insertions before the first nongap RF position\n");
fprintf(fp, "# Number of sequences: %d\n", msa->nseq);
if(use_weights) { fprintf(fp, "# IMPORTANT: Counts are weighted based on sequence weights in alignment file.\n"); }
else { fprintf(fp, "# Sequence weights from alignment were ignored (if they existed).\n"); }
fprintf(fp, "#\n");
fprintf(fp, "# %8s %10s %8s %8s\n", "rfpos", "nseq w/ins", "freq ins", "avg len");
fprintf(fp, "# %8s %10s %8s %8s\n", "--------", "----------", "--------", "--------");
rflen = 0;
for(apos = 1; apos <= msa->alen; apos++)
if(i_am_rf[apos-1]) rflen++;
rfpos = 0;
for(apos = 1; apos <= msa->alen; apos++)
{
if(i_am_rf[apos-1]) rfpos++;
else {
for(i = 0; i < msa->nseq; i++) {
seqwt = use_weights ? msa->wgt[i] : 1.0;
if(esl_abc_XIsResidue(msa->abc, msa->ax[i][apos])) {
ict[rfpos][i]++;
total_ict[rfpos] += seqwt;
}
}
}
}
rflen = rfpos;
for(rfpos = 0; rfpos <= rflen; rfpos++)
{
nseq = 0.;
for(i = 0; i < msa->nseq; i++) {
if(ict[rfpos][i] >= 1) {
seqwt = use_weights ? msa->wgt[i] : 1.0;
nseq += seqwt;
}
}
if(nseq > 0.)
fprintf(fp, " %8d %10.1f %8.6f %8.3f\n", rfpos, nseq, nseq / (float) msa->nseq, ((float) total_ict[rfpos] / (float) nseq));
}
fprintf(fp, "//\n");
for(i = 0; i <= msa->alen; i++) free(ict[i]);
free(ict);
free(total_ict);
return eslOK;
ERROR:
return status;
}
/* dump_infocontent_info
*
* Given an MSA with RF annotation, dump information content per column data to
* an open output file.
*/
static int dump_infocontent_info(FILE *fp, ESL_ALPHABET *abc, double **abc_ct, int use_weights, int nali, int64_t alen, int nseq, int *i_am_rf, char *msa_name, char *alifile, char *errbuf)
{
int status;
int apos, rfpos;
double bg_ent;
double *bg = NULL;
double *abc_freq = NULL;
double nnongap;
ESL_ALLOC(bg, sizeof(double) * abc->K);
esl_vec_DSet(bg, abc->K, 1./(abc->K));
bg_ent = esl_vec_DEntropy(bg, abc->K);
free(bg);
ESL_ALLOC(abc_freq, sizeof(double) * abc->K);
fprintf(fp, "# Information content per column (bits):\n");
fprintf(fp, "# Alignment file: %s\n", alifile);
fprintf(fp, "# Alignment idx: %d\n", nali);
if(msa_name != NULL) { fprintf(fp, "# Alignment name: %s\n", msa_name); }
fprintf(fp, "# Number of sequences: %d\n", nseq);
if(use_weights) { fprintf(fp, "# IMPORTANT: Counts are weighted based on sequence weights in alignment file.\n"); }
else { fprintf(fp, "# Sequence weights from alignment were ignored (if they existed).\n"); }
fprintf(fp, "#\n");
if(i_am_rf != NULL) {
fprintf(fp, "# %7s %7s %10s %10s\n", "rfpos", "alnpos", "freqnongap", "info(bits)");
fprintf(fp, "# %7s %7s %10s %10s\n", "-------", "-------", "----------", "----------");
}
else {
fprintf(fp, "# %7s %10s %10s\n", "alnpos", "freqnongap", "info(bits)");
fprintf(fp, "# %7s %10s %10s\n", "-------", "----------", "----------");
}
rfpos = 0;
for(apos = 0; apos < alen; apos++) {
if(i_am_rf != NULL) {
if(i_am_rf[apos]) {
fprintf(fp, " %7d", rfpos+1);
rfpos++;
}
else {
fprintf(fp, " %7s", "-");
}
}
nnongap = esl_vec_DSum(abc_ct[apos], abc->K);
esl_vec_DCopy(abc_ct[apos], abc->K, abc_freq);
esl_vec_DNorm(abc_freq, abc->K);
fprintf(fp, " %7d %10.8f %10.8f\n", apos+1,
nnongap / (nnongap + abc_ct[apos][abc->K]),
(bg_ent - esl_vec_DEntropy(abc_freq, abc->K)));
}
fprintf(fp, "//\n");
if(abc_freq != NULL) free(abc_freq);
return eslOK;
ERROR:
ESL_FAIL(eslEINVAL, errbuf, "out of memory");
return status; /* NEVERREACHED */
}
/* count_msa()
*
* Given an msa, count residues, and optionally base pairs and
* posterior probabilities per column and store them in <ret_abc_ct>
* and <ret_pp_ct>.
*
* <ret_abc_ct> [0..apos..alen-1][0..abc->K]:
* - per position count of each symbol in alphabet over all seqs.
*
* <ret_bp_ct> [0..apos..alen-1][0..abc->Kp-1][0..abc->Kp-1]
* - per (non-pknotted) consensus basepair count of each possible basepair
* over all seqs basepairs are indexed by 'i' the minimum of 'i:j' for a
* pair between i and j, where i < j. Note that non-canonicals and
* gaps and the like are all stored independently.
*
* <ret_pp_ct> [0..apos..alen-1][0..11]
* - per position count of each posterior probability code over all seqs.
*
* A 'gap' has a looser definition than in esl_abc here, esl_abc's gap,
* missing residues and nonresidues are all considered 'gaps' here.
*
* If we encounter an error, we return non-eslOK status and fill
* errbuf with error message.
*
* Returns eslOK upon success.
*/
static int count_msa(ESL_MSA *msa, char *errbuf, int nali, int no_ambig, int use_weights, double ***ret_abc_ct, double ****ret_bp_ct, double ***ret_pp_ct)
{
int status;
double **abc_ct = NULL;
double ***bp_ct = NULL;
int apos, rpos, i, x;
int nppvals = 12; /* '0'-'9' = 0-9, '*' = 10, gap = '11' */
double **pp_ct = NULL; /* [0..alen-1][0..nppvals-1] per position count of each possible PP char over all seqs */
int ppidx;
/* variables related to getting bp counts */
int *ct = NULL; /* 0..alen-1 base pair partners array for current sequence */
char *ss_nopseudo = NULL; /* no-pseudoknot version of structure */
double seqwt; /* weight of current sequence, always 1.0 if !use_weights */
if(! (msa->flags & eslMSA_DIGITAL)) ESL_FAIL(eslEINVAL, errbuf, "count_msa() contract violation, MSA is not digitized");
if(use_weights && msa->wgt == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "count_msa(): use_weights==TRUE but msa->wgt == NULL");
/* allocate pp_ct array, if nec */
if(ret_pp_ct != NULL) {
if(msa->pp == NULL) ESL_FAIL(eslEINVAL, errbuf, "count_msa() ret_pp_ct != NULL, but msa->pp is NULL");
ESL_ALLOC(pp_ct, sizeof(double *) * msa->alen);
for(apos = 0; apos < msa->alen; apos++) {
ESL_ALLOC(pp_ct[apos], sizeof(double) * nppvals);
esl_vec_DSet(pp_ct[apos], nppvals, 0.);
}
}
/* allocate and initialize bp_ct, if nec */
if(ret_bp_ct != NULL) {
ESL_ALLOC(bp_ct, sizeof(double **) * msa->alen);
/* get ct array which defines the consensus base pairs */
ESL_ALLOC(ct, sizeof(int) * (msa->alen+1));
ESL_ALLOC(ss_nopseudo, sizeof(char) * (msa->alen+1));
esl_wuss_nopseudo(msa->ss_cons, ss_nopseudo);
if ((status = esl_wuss2ct(ss_nopseudo, msa->alen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus structure string is inconsistent.");
for(apos = 0; apos < msa->alen; apos++) {
/* careful ct is indexed 1..alen, not 0..alen-1 */
if(ct[(apos+1)] > (apos+1)) { /* apos+1 is an 'i' in an i:j pair, where i < j */
ESL_ALLOC(bp_ct[apos], sizeof(double *) * (msa->abc->Kp));
for(x = 0; x < msa->abc->Kp; x++) {
ESL_ALLOC(bp_ct[apos][x], sizeof(double) * (msa->abc->Kp));
esl_vec_DSet(bp_ct[apos][x], msa->abc->Kp, 0.);
}
}
else { /* apos+1 is not an 'i' in an i:j pair, where i < j, set to NULL */
bp_ct[apos] = NULL;
}
}
}
ESL_ALLOC(abc_ct, sizeof(double *) * msa->alen);
for(apos = 0; apos < msa->alen; apos++) {
ESL_ALLOC(abc_ct[apos], sizeof(double) * (msa->abc->K+1));
esl_vec_DSet(abc_ct[apos], (msa->abc->K+1), 0.);
}
for(i = 0; i < msa->nseq; i++) {
seqwt = use_weights ? msa->wgt[i] : 1.0;
for(apos = 0; apos < msa->alen; apos++) { /* update appropriate abc count, careful, ax ranges from 1..msa->alen (but abc_ct is 0..msa->alen-1) */
if((! no_ambig) || (! esl_abc_XIsDegenerate(msa->abc, msa->ax[i][apos+1]))) { /* skip ambiguities (degenerate residues) if no_ambig is TRUE */
if((status = esl_abc_DCount(msa->abc, abc_ct[apos], msa->ax[i][apos+1], seqwt)) != eslOK) ESL_FAIL(status, errbuf, "problem counting residue %d of seq %d", apos, i);
}
}
/* get bp counts, if nec */
if(bp_ct != NULL) {
for(apos = 0; apos < msa->alen; apos++) { /* update appropriate abc count, careful, ax ranges from 1..msa->alen (but abc_ct is 0..msa->alen-1) */
if(bp_ct[apos] != NULL) { /* our flag for whether position (apos+1) is an 'i' in an i:j pair where i < j */
rpos = ct[apos+1] - 1; /* ct is indexed 1..alen */
bp_ct[apos][msa->ax[i][apos+1]][msa->ax[i][rpos+1]] += seqwt;
}
}
}
/* get PP counts, if nec */
if(pp_ct != NULL) {
if(msa->pp[i] != NULL) {
for(apos = 0; apos < msa->alen; apos++) {
if((! no_ambig) || (! esl_abc_XIsDegenerate(msa->abc, msa->ax[i][apos+1]))) { /* skip ambiguities (degenerate residues) if no_ambig is TRUE */
if((ppidx = get_pp_idx(msa->abc, msa->pp[i][apos])) == -1) ESL_FAIL(eslEFORMAT, errbuf, "bad #=GR PP char: %c", msa->pp[i][apos]);
pp_ct[apos][ppidx] += seqwt;
}
}
}
}
}
*ret_abc_ct = abc_ct;
if(ret_bp_ct != NULL) *ret_bp_ct = bp_ct; /* we only allocated bp_ct if ret_bp_ct != NULL */
if(ret_pp_ct != NULL) *ret_pp_ct = pp_ct; /* we only allocated pp_ct if ret_pp_ct != NULL */
if(ss_nopseudo != NULL) free(ss_nopseudo);
if(ct != NULL) free(ct);
return eslOK;
ERROR:
if(abc_ct != NULL) esl_Free2D((void **) abc_ct, msa->alen);
if(bp_ct != NULL) esl_Free3D((void ***) bp_ct, msa->alen, msa->abc->Kp);
if(pp_ct != NULL) esl_Free2D((void **) pp_ct, msa->alen);
ESL_FAIL(status, errbuf, "Error, out of memory while counting important values in the msa.");
return status; /* NEVERREACHED */
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
char *seqfile = NULL;
ESL_SQFILE *sqfp = NULL;
int infmt = eslSQFILE_UNKNOWN;
int alphatype = eslUNKNOWN;
ESL_ALPHABET *abc = NULL;
ESL_SQ *sq = NULL;
int64_t nseq = 0;
int64_t nres = 0;
int64_t small = 0;
int64_t large = 0;
double *monoc = NULL; /* monoresidue composition per sequence */
double *monoc_all = NULL; /* monoresidue composition over all seqs */
int do_comp = FALSE;
int status = eslOK;
int wstatus;
int i;
int x;
/* Parse command line */
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in app configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help(argv[0], go);
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
seqfile = esl_opt_GetArg(go, 1);
do_comp = esl_opt_GetBoolean(go, "-c");
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_FormatCode(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", seqfile);
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
if (esl_opt_GetBoolean(go, "--rna")) alphatype = eslRNA;
else if (esl_opt_GetBoolean(go, "--dna")) alphatype = eslDNA;
else if (esl_opt_GetBoolean(go, "--amino")) alphatype = eslAMINO;
else {
status = esl_sqfile_GuessAlphabet(sqfp, &alphatype);
if (status == eslEAMBIGUOUS) esl_fatal("Couldn't guess alphabet from first sequence in %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Sequence file parse error, line %d of file %s:\n%s\n",
sqfp->linenumber, seqfile, sqfp->errbuf);
else if (status == eslENODATA) esl_fatal("Sequence file %s contains no data?", seqfile);
else if (status != eslOK) esl_fatal("Failed to guess alphabet (error code %d)\n", status);
}
abc = esl_alphabet_Create(alphatype);
sq = esl_sq_CreateDigital(abc);
esl_sqfile_SetDigital(sqfp, abc);
if (do_comp) {
ESL_ALLOC(monoc, (abc->Kp) * sizeof(double));
ESL_ALLOC(monoc_all, (abc->Kp) * sizeof(double));
esl_vec_DSet(monoc_all, abc->Kp, 0.0);
esl_vec_DSet(monoc, abc->Kp, 0.0);
}
while ((wstatus = esl_sqio_ReadWindow(sqfp, 0, 4096, sq)) != eslEOF)
{
if (wstatus == eslOK)
{
if (do_comp)
for (i = 1; i <= sq->n; i++)
monoc[sq->dsq[i]]++;
}
else if (wstatus == eslEOD)
{
if (nseq == 0) { small = large = sq->L; }
else {
small = ESL_MIN(small, sq->L);
large = ESL_MAX(large, sq->L);
}
if (esl_opt_GetBoolean(go, "-a")) {
printf("= %-20s %8" PRId64 " %s\n", sq->name, sq->L, (sq->desc != NULL) ? sq->desc : "");
}
nres += sq->L;
nseq++;
esl_sq_Reuse(sq);
if (do_comp) {
esl_vec_DAdd(monoc_all, monoc, abc->Kp);
esl_vec_DSet(monoc, abc->Kp, 0.0);
}
}
else if (wstatus == eslEFORMAT)
{
esl_fatal("Failed to parse sequence at line %ld, file %s:\n%s",
(long) sqfp->linenumber, sqfp->filename, sqfp->errbuf);
}
else
esl_fatal("Failed in reading sequence:\n%s\n", sqfp->errbuf);
}
printf("Format: %s\n", esl_sqio_DescribeFormat(sqfp->format));
printf("Alphabet type: %s\n", esl_abc_DescribeType(abc->type));
printf("Number of sequences: %" PRId64 "\n", nseq);
printf("Total # residues: %" PRId64 "\n", nres);
printf("Smallest: %" PRId64 "\n", small);
printf("Largest: %" PRId64 "\n", large);
printf("Average length: %.1f\n", (float) nres / (float) nseq);
if (do_comp) {
printf("\nResidue composition:\n");
for (x = 0; x < abc->Kp; x++)
if (x < abc->K || monoc_all[x] > 0)
printf("residue: %c %10.0f %.4f\n", abc->sym[x], monoc_all[x], monoc_all[x] / (double) nres);
free(monoc);
free(monoc_all);
}
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
return 0;
ERROR:
return status;
}
/* Function: p7_prior_CreateNucleicNew()
* Incept: TJW, Thu Nov 12 21:15:11 EST 2009 [Couch at home]
*
* Purpose: Creates the default mixture Dirichlet prior for nucleotiden
* sequences.
*
* The transition priors (match, insert, delete) are all
* single Dirichlets, originally trained by Graeme
* Mitchison in the mid-1990's. Notes have been lost, but
* we believe they were trained on an early version of
* Pfam.
*
* The match emission prior is an eight-component mixture
* trained against a portion of the rmark dataset
*
* The insert emission prior is a single Dirichlet with
* high $|\alpha|$, such that insert emission probabilities
* are essentially fixed by the prior, regardless of
* observed count data.
*
* Returns: a pointer to the new <P7_PRIOR> structure.
*/
P7_PRIOR *
p7_prior_CreateNucleic(void)
{
int status;
P7_PRIOR *pri = NULL;
int q;
/* Match emission priors are trained on rmark database [Nawrocki 08]
*/
/* Plus-1 Laplace prior
int num_comp = 1;
static double defmq[2] = { 1.0 };
static double defm[1][4] = {
{ 1.0, 1.0, 1.0, 1.0} //
};
*/
/*
int num_comp = 2;
static double defmq[2] = { 0.42, 0.58 };
static double defm[2][4] = {
{ 0.94, 0.90, 0.89, 1.13}, //
{ 0.096, 0.078, 0.093, 0.089} //
};
*/
/*
//weird - but this performs marginally better than the best 2- 5- or 8-component mixtures tested
// (on rmark - MER: 2 better than 5/8-comp , 3 better than 2-comp )
int num_comp = 4;
static double defmq[4] = { 0.16, 0.29, 0.12, 0.43 };
static double defm[4][4] = {
{ 0.36, 0.10, 5.3, 0.13}, // G
{ 0.05, 0.18, 0.03, 0.19}, // CT
{ 7.1, 0.13, 0.35, 0.17}, // A
{ 0.96, 0.92, 0.91, 1.19} // uniform
};
*/
/*On rmark, this model does only slightly better than the 2-component model
It's chosen as the default on grounds of reasonableness, given that it shows
a non-uniform transition:transversion ratio. It's based on the results
of training against a portion of rmark, but the overspecified numbers
resulting from that training have been rounded/simplified.
*/
int num_comp = 5;
static double defmq[5] = { 0.16, 0.13, 0.17, 0.15, 0.39 };
static double defm[5][4] = {
{ 6.0, 0.2, 0.5, 0.2}, // A
{ 0.2, 8.0, 0.2, 0.5}, // C
{ 0.5, 0.2, 8.0, 0.2}, // G
{ 0.2, 0.5, 0.2, 4.0}, // T
{ 1.3, 1.2, 1.2, 1.4} // uniform
};
/* gives no improved performance in my hands over the 5-component model
int num_comp = 8;
static double defmq[8] = { 0.13, 0.08, 0.08, 0.13, 0.08, 0.08, 0.17, 0.25 } ;
static double defm[8][4] = {
{ 4.0, 0.3, 0.5, 0.4}, // A
{ 0.3, 22.0, 0.3, 0.8}, // C
{ 1.0, 0.4, 28.0, 0.4}, // G
{ 0.5, 0.8, 0.3, 6.0}, // T
{ 1.8, 0.8, 6.0, 1.0}, // AG
{ 0.6, 6.0, 0.6, 2.4}, // CT
{ 0.03, 0.01, 0.02, 0.02}, // anything, but highly conserved
{ 2.0, 2.0, 2.0, 2.0} // anything, not much conservation
};
*/
ESL_ALLOC(pri, sizeof(P7_PRIOR));
pri->tm = pri->ti = pri->td = pri->em = pri->ei = NULL;
pri->tm = esl_mixdchlet_Create(1, 3); // match transitions; single component; 3 params
pri->ti = esl_mixdchlet_Create(1, 2); // insert transitions; single component; 2 params
pri->td = esl_mixdchlet_Create(1, 2); // delete transitions; single component; 2 params
pri->em = esl_mixdchlet_Create(num_comp, 4); // match emissions; X component; 4 params
pri->ei = esl_mixdchlet_Create(1, 4); // insert emissions; single component; 4 params
if (pri->tm == NULL || pri->ti == NULL || pri->td == NULL || pri->em == NULL || pri->ei == NULL) goto ERROR;
/* Transition priors: roughly, learned from rmark benchmark - hand-beautified (trimming overspecified significant digits)
*/
pri->tm->pq[0] = 1.0;
pri->tm->alpha[0][0] = 2.0; // TMM
pri->tm->alpha[0][1] = 0.1; // TMI
pri->tm->alpha[0][2] = 0.1; // TMD
pri->ti->pq[0] = 1.0;
pri->ti->alpha[0][0] = 0.06; // TIM
pri->ti->alpha[0][1] = 0.2; // TII
pri->td->pq[0] = 1.0;
pri->td->alpha[0][0] = 0.1; // TDM
pri->td->alpha[0][1] = 0.2; // TDD
/* Match emission priors */
for (q = 0; q < num_comp; q++)
{
pri->em->pq[q] = defmq[q];
esl_vec_DCopy(defm[q], 4, pri->em->alpha[q]);
}
/* Insert emission priors. Should that alphas be lower? higher?
*/
pri->ei->pq[0] = 1.0;
esl_vec_DSet(pri->ei->alpha[0], 4, 1.0);
return pri;
ERROR:
if (pri != NULL) p7_prior_Destroy(pri);
return NULL;
}
int
main(int argc, char **argv)
{
int i,j;
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_STOPWATCH *w = esl_stopwatch_Create();
int status;
ESL_MSA *msa = NULL;
FILE *ofp = NULL; /* output file (default is stdout) */
ESL_ALPHABET *abc = NULL; /* digital alphabet */
char *alifile; /* name of the alignment file we're building HMMs from */
ESLX_MSAFILE *afp = NULL; /* open alifile */
int infmt = eslMSAFILE_UNKNOWN; /* autodetect alignment format by default. */
int outfmt = eslMSAFILE_STOCKHOLM;
char *postmsafile; /* optional file to resave annotated, modified MSAs to */
FILE *postmsafp = NULL; /* open <postmsafile>, or NULL */
int mask_range_cnt = 0;
uint32_t mask_starts[100]; // over-the-top allocation.
uint32_t mask_ends[100];
char *rangestr;
char *range;
int *map = NULL; /* map[i]=j, means model position i comes from column j of the alignment; 1..alen */
int keep_mm;
/* Set processor specific flags */
impl_Init();
alifile = NULL;
postmsafile = NULL;
/* Parse the command line
*/
process_commandline(argc, argv, &go, &alifile, &postmsafile);
keep_mm = esl_opt_IsUsed(go, "--apendmask");
/* Initialize what we can in the config structure (without knowing the alphabet yet).
* Fields controlled by masters are set up in usual_master() or mpi_master()
* Fields used by workers are set up in mpi_worker()
*/
ofp = NULL;
infmt = eslMSAFILE_UNKNOWN;
afp = NULL;
abc = NULL;
if (esl_opt_IsOn(go, "--informat")) {
infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslMSAFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--informat"));
}
/* Determine output alignment file format */
outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
if (outfmt == eslMSAFILE_UNKNOWN) p7_Fail(argv[0], "%s is not a recognized output MSA file format\n", esl_opt_GetString(go, "--outformat"));
/* Parse the ranges */
if (esl_opt_IsUsed(go, "--alirange")) {
esl_strdup(esl_opt_GetString(go, "--alirange"), -1, &rangestr) ;
} else if (esl_opt_IsUsed(go, "--modelrange")) {
esl_strdup(esl_opt_GetString(go, "--modelrange"), -1, &rangestr) ;
} else if (esl_opt_IsUsed(go, "--model2ali")) {
esl_strdup(esl_opt_GetString(go, "--model2ali"), -1, &rangestr) ;
} else if (esl_opt_IsUsed(go, "--ali2model")) {
esl_strdup(esl_opt_GetString(go, "--ali2model"), -1, &rangestr) ;
} else {
if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR;
}
while ( (status = esl_strtok(&rangestr, ",", &range) ) == eslOK) {
status = esl_regexp_ParseCoordString(range, mask_starts + mask_range_cnt, mask_ends + mask_range_cnt );
if (status == eslESYNTAX) esl_fatal("range flags take coords <from>..<to>; %s not recognized", range);
if (status == eslFAIL) esl_fatal("Failed to find <from> or <to> coord in %s", range);
mask_range_cnt++;
}
/* Start timing. */
esl_stopwatch_Start(w);
/* Open files, set alphabet.
* afp - open alignment file for input
* abc - alphabet expected or guessed in ali file
* postmsafp - open MSA output file
* ofp - optional open output file, or stdout
*/
if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
else abc = NULL;
status = eslx_msafile_Open(&abc, alifile, NULL, infmt, NULL, &afp);
if (status != eslOK) eslx_msafile_OpenFailure(afp, status);
if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
postmsafp = fopen(postmsafile, "w");
if (postmsafp == NULL) p7_Fail("Failed to MSA output file %s for writing", postmsafile);
}
if (esl_opt_IsUsed(go, "-o"))
{
ofp = fopen(esl_opt_GetString(go, "-o"), "w");
if (ofp == NULL) p7_Fail("Failed to open -o output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Looks like the i/o is set up successfully...
* Initial output to the user
*/
output_header(go, ofp, alifile, postmsafile); /* cheery output header */
/* read the alignment */
if ((status = eslx_msafile_Read(afp, &msa)) != eslOK) eslx_msafile_ReadFailure(afp, status);
if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
/* add/modify mmline for the mask */
if (msa->mm == NULL) {
ESL_ALLOC(msa->mm, msa->alen);
keep_mm = FALSE;
}
if (!keep_mm)
for (i=0; i<msa->alen; i++) msa->mm[i] = '.';
}
// convert model coordinates to alignment coordinates, if necessary
if (esl_opt_IsUsed(go, "--modelrange") || esl_opt_IsUsed(go, "--model2ali") || esl_opt_IsUsed(go, "--ali2model") ) {
float symfrac = esl_opt_GetReal(go, "--symfrac");
int do_hand = esl_opt_IsOn(go, "--hand");
int L;
//same as p7_builder relative_weights
if (esl_opt_IsOn(go, "--wnone") ) { esl_vec_DSet(msa->wgt, msa->nseq, 1.); }
else if (esl_opt_IsOn(go, "--wgiven") ) ;
else if (esl_opt_IsOn(go, "--wpb") ) status = esl_msaweight_PB(msa);
else if (esl_opt_IsOn(go, "--wgsc") ) status = esl_msaweight_GSC(msa);
else if (esl_opt_IsOn(go, "--wblosum")) status = esl_msaweight_BLOSUM(msa, esl_opt_GetReal(go, "--wid"));
if ((status = esl_msa_MarkFragments(msa, esl_opt_GetReal(go, "--fragthresh"))) != eslOK) goto ERROR;
//build a map of model mask coordinates to alignment coords
ESL_ALLOC(map, sizeof(int) * (msa->alen+1));
L = p7_Alimask_MakeModel2AliMap(msa, do_hand, symfrac, map );
if ( esl_opt_IsUsed(go, "--model2ali") ) {
//print mapping
printf ("model coordinates alignment coordinates\n");
for (i=0; i<mask_range_cnt; i++)
printf ("%8d..%-8d -> %8d..%-8d\n", mask_starts[i], mask_ends[i], map[mask_starts[i]-1], map[mask_ends[i]-1]);
/* If I wanted to, I could print all the map values independently:
printf("\n\n-----------\n");
printf("Map\n");
printf("---\n");
for (i=0; i<L; i++)
printf("%d -> %d\n", i+1, map[i]);
*/
} else if ( esl_opt_IsUsed(go, "--ali2model") ) {
//print mapping (requires scanning the inverted map
int alistart = 0;
int aliend = 0;
printf ("alignment coordinates model coordinates\n");
for (i=0; i<mask_range_cnt; i++) {
//find j for ali positions
while (map[alistart] < mask_starts[i] )
alistart++;
aliend = alistart;
while (map[aliend] < mask_ends[i] )
aliend++;
printf (" %8d..%-8d -> %8d..%-8d\n", map[alistart], map[aliend], alistart+1, aliend+1);
}
} else {
//convert the mask coords based on map
for (i=0; i<mask_range_cnt; i++) {
mask_starts[i] = map[mask_starts[i]-1]; //-1 because mmline is offset by one relative to the 1-base alignment
mask_ends[i] = map[mask_ends[i]-1];
}
}
}
if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
//overwrite '.' with 'm' everywhere the range says to do it
for (i=0; i<mask_range_cnt; i++)
for (j=mask_starts[i]; j<=mask_ends[i]; j++)
msa->mm[j-1] = 'm';
if ((status = eslx_msafile_Write(postmsafp, msa, outfmt)) != eslOK) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
}
esl_stopwatch_Stop(w);
if (esl_opt_IsOn(go, "-o")) fclose(ofp);
if (postmsafp) fclose(postmsafp);
if (afp) eslx_msafile_Close(afp);
if (abc) esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
esl_stopwatch_Destroy(w);
return 0;
ERROR:
return eslFAIL;
}
/* annotate_posterior_probability()
* Synopsis: Add posterior probability annotation lines to new MSA.
*/
static int
annotate_posterior_probability(ESL_MSA *msa, P7_TRACE **tr, const int *matmap, int M, int optflags)
{
double *totp = NULL; /* total posterior probability in column <apos>: [0..alen-1] */
int *matuse = NULL; /* #seqs with pp annotation in column <apos>: [0..alen-1] */
int idx; /* counter over sequences [0..nseq-1] */
int apos; /* counter for alignment columns: pp's are [0..alen-1] (unlike ax) */
int z; /* counter over trace positions [0..tr->N-1] */
int status;
/* Determine if any of the traces have posterior probability annotation. */
for (idx = 0; idx < msa->nseq; idx++)
if (tr[idx]->pp != NULL) break;
if (idx == msa->nseq) return eslOK;
ESL_ALLOC(matuse, sizeof(double) * (msa->alen)); esl_vec_ISet(matuse, msa->alen, 0);
ESL_ALLOC(totp, sizeof(double) * (msa->alen)); esl_vec_DSet(totp, msa->alen, 0.0);
ESL_ALLOC(msa->pp, sizeof(char *) * msa->sqalloc);
for (idx = 0; idx < msa->nseq; idx++)
{
if (tr[idx]->pp == NULL) { msa->pp[idx] = NULL; continue; }
ESL_ALLOC(msa->pp[idx], sizeof(char) * (msa->alen+1));
for (apos = 0; apos < msa->alen; apos++) msa->pp[idx][apos] = '.';
msa->pp[idx][msa->alen] = '\0';
apos = 0;
for (z = 0; z < tr[idx]->N; z++)
{
switch (tr[idx]->st[z]) {
case p7T_M:
msa->pp[idx][matmap[tr[idx]->k[z]]-1] = p7_alidisplay_EncodePostProb(tr[idx]->pp[z]);
totp [matmap[tr[idx]->k[z]]-1]+= tr[idx]->pp[z];
matuse[matmap[tr[idx]->k[z]]-1]++;
case p7T_D:
apos = matmap[tr[idx]->k[z]];
break;
case p7T_I:
if ( !(optflags & p7_TRIM) || (tr[idx]->k[z] != 0 && tr[idx]->k[z] != M)) {
msa->pp[idx][apos] = p7_alidisplay_EncodePostProb(tr[idx]->pp[z]);
apos++;
}
break;
case p7T_N:
case p7T_C:
if (! (optflags & p7_TRIM) && tr[idx]->i[z] > 0) {
msa->pp[idx][apos] = p7_alidisplay_EncodePostProb(tr[idx]->pp[z]);
apos++;
}
break;
case p7T_E:
apos = matmap[M]; /* set position for C-terminal tail */
break;
default:
break;
}
}
}
for (; idx < msa->sqalloc; idx++) msa->pp[idx] = NULL; /* for completeness, following easel MSA conventions, but should be a no-op: nseq==sqalloc */
/* Consensus posterior probability annotation: only on match columns */
ESL_ALLOC(msa->pp_cons, sizeof(char) * (msa->alen+1));
for (apos = 0; apos < msa->alen; apos++) msa->pp_cons[apos] = '.';
msa->pp_cons[msa->alen] = '\0';
for (apos = 0; apos < msa->alen; apos++)
if (matuse[apos]) msa->pp_cons[apos] = p7_alidisplay_EncodePostProb( totp[apos] / (double) matuse[apos]);
free(matuse);
free(totp);
return eslOK;
ERROR:
if (matuse != NULL) free(matuse);
if (totp != NULL) free(totp);
if (msa->pp != NULL) esl_Free2D((void **) msa->pp, msa->sqalloc);
return status;
}
