/* Function: p7_Fastmodelmaker()
*
* Purpose: Heuristic model construction.
* Construct an HMM from an alignment by a simple rule,
* based on the fractional occupancy of each columns w/
* residues vs gaps. Any column w/ a fractional
* occupancy of $\geq$ <symfrac> is assigned as a MATCH column;
* for instance, if thresh = 0.5, columns w/ $\geq$ 50\%
* residues are assigned to match... roughly speaking.
*
* "Roughly speaking" because sequences may be weighted
* in the input <msa>, and because missing data symbols are
* ignored, in order to deal with sequence fragments.
*
* The <msa> must be in digital mode.
*
* If the caller wants to designate any sequences as
* fragments, it does so by converting all N-terminal and
* C-terminal flanking gap symbols to missing data symbols.
*
* NOTE: p7_Fastmodelmaker() will slightly revise the
* alignment if the assignment of columns implies
* DI and ID transitions.
*
* Returns the HMM in counts form (ready for applying Dirichlet
* priors as the next step). Also returns fake traceback
* for each training sequence.
*
* Models must have at least one node, so if the <msa> defined
* no consensus columns, a <eslENORESULT> error is returned.
*
* Args: msa - multiple sequence alignment
* symfrac - threshold for residue occupancy; >= assigns MATCH
* bld - holds information on regions requiring masking, optionally NULL -> no masking
* ret_hmm - RETURN: counts-form HMM
* opt_tr - optRETURN: array of tracebacks for aseq's
*
* Return: <eslOK> on success. ret_hmm and opt_tr allocated here,
* and must be free'd by the caller (FreeTrace(tr[i]), free(tr),
* FreeHMM(hmm)).
*
* Returns <eslENORESULT> if no consensus columns were annotated;
* in this case, <ret_hmm> and <opt_tr> are returned NULL.
*
* Throws: <eslEMEM> on allocation failure; <eslEINVAL> if the
* <msa> isn't in digital mode.
*/
int
p7_Fastmodelmaker(ESL_MSA *msa, float symfrac, P7_BUILDER *bld, P7_HMM **ret_hmm, P7_TRACE ***opt_tr)
{
int status; /* return status flag */
int *matassign = NULL; /* MAT state assignments if 1; 1..alen */
int idx; /* counter over sequences */
int apos; /* counter for aligned columns */
float r; /* weighted residue count */
float totwgt; /* weighted residue+gap count */
if (! (msa->flags & eslMSA_DIGITAL)) ESL_XEXCEPTION(eslEINVAL, "need digital MSA");
/* Allocations: matassign is 1..alen array of bit flags.
*/
ESL_ALLOC(matassign, sizeof(int) * (msa->alen+1));
/* Determine weighted sym freq in each column, set matassign[] accordingly.
*/
for (apos = 1; apos <= msa->alen; apos++)
{
r = totwgt = 0.;
for (idx = 0; idx < msa->nseq; idx++)
{
if (esl_abc_XIsResidue(msa->abc, msa->ax[idx][apos])) { r += msa->wgt[idx]; totwgt += msa->wgt[idx]; }
else if (esl_abc_XIsGap(msa->abc, msa->ax[idx][apos])) { totwgt += msa->wgt[idx]; }
else if (esl_abc_XIsMissing(msa->abc, msa->ax[idx][apos])) continue;
}
if (r > 0. && r / totwgt >= symfrac) matassign[apos] = TRUE;
else matassign[apos] = FALSE;
}
/* Once we have matassign calculated, modelmakers behave
* the same; matassign2hmm() does this stuff (traceback construction,
* trace counting) and sets up ret_hmm and opt_tr.
*/
if ((status = matassign2hmm(msa, matassign, ret_hmm, opt_tr)) != eslOK) {
fprintf (stderr, "hmm construction error during trace counting\n");
goto ERROR;
}
free(matassign);
return eslOK;
ERROR:
if (matassign != NULL) free(matassign);
return status;
}
/* Function: p7_Alimask_MakeModel2AliMap()
* Synopsis: Compute map of coordinate in the alignment corresponding to each model position.
*
* Args: msa - The alignment for which the mapped model is to be computed. We assume
* the MSA has already been manipulated to account for model building
* flags (e.g. weighting).
* do_hand - TRUE when the model is to follow a hand-build RF line (which must be
* part of the file.
* symfraq - if weighted occupancy exceeds this value, include the column in the model.
* map - int array into which the map values will be stored. Calling function
* must allocate (msa->alen+1) ints.
*
* Returns: The number of mapped model positions.
*/
int
p7_Alimask_MakeModel2AliMap(ESL_MSA *msa, int do_hand, float symfrac, int *map )
{
int i = 0;
int apos, idx;
float r; /* weighted residue count */
float totwgt; /* weighted residue+gap count */
i = 0;
if ( do_hand ) {
if (msa->rf == NULL) p7_Fail("Model file does not contain an RF line, required for --hand.\n");
/* Watch for off-by-one. rf is [0..alen-1]*/
for (apos = 1; apos <= msa->alen; apos++) {
if (!esl_abc_CIsGap(msa->abc, msa->rf[apos-1]) ) {
map[i] = apos;
i++;
}
}
} else {
for (apos = 1; apos <= msa->alen; apos++)
{
r = totwgt = 0.;
for (idx = 0; idx < msa->nseq; idx++)
{
if (esl_abc_XIsResidue(msa->abc, msa->ax[idx][apos])) { r += msa->wgt[idx]; totwgt += msa->wgt[idx]; }
else if (esl_abc_XIsGap(msa->abc, msa->ax[idx][apos])) { totwgt += msa->wgt[idx]; }
else if (esl_abc_XIsMissing(msa->abc, msa->ax[idx][apos])) continue;
}
if (r > 0. && r / totwgt >= symfrac) {
map[i] = apos;
i++;
}
}
}
return i;
}
/* Function: rejustify_insertions_digital()
* Synopsis:
* Incept: SRE, Thu Oct 23 13:06:12 2008 [Janelia]
*
* Purpose:
*
* Args: msa - alignment to rejustify
* digital mode: ax[0..nseq-1][1..alen] and abc is valid
* text mode: aseq[0..nseq-1][0..alen-1]
* inserts - # of inserted columns following node k, for k=0.1..M
* inserts[0] is for N state; inserts[M] is for C state
* matmap - index of column associated with node k [k=0.1..M; matmap[0] = 0]
* this is an alignment column index 1..alen, same offset as <ax>
* if applied to text mode aseq or annotation, remember to -1
* if no residues use match state k, matmap[k] is the
* index of the last column used before node k's columns
* start: thus matmap[k]+1 is always the start of
* node k's insertion (if any).
* matuse - TRUE if an alignment column is associated with node k: [k=0.1..M; matuse[0] = 0].
* if matuse[k] == 0, every sequence deleted at node k,
* and we're collapsing the column rather than showing all
* gaps.
*
* Note: The insertion for node k is of length <inserts[k]> columns,
* and in 1..alen coords it runs from
* matmap[k]+1 .. matmap[k+1]-matuse[k+1].
*
*
* Returns:
*
* Throws: (no abnormal error conditions)
*
* Xref:
*/
static int
rejustify_insertions_digital(ESL_MSA *msa, const int *inserts, const int *matmap, const int *matuse, int M)
{
int idx;
int k;
int apos;
int nins;
int npos, opos;
for (idx = 0; idx < msa->nseq; idx++)
{
for (k = 0; k < M; k++)
if (inserts[k] > 1)
{
for (nins = 0, apos = matmap[k]+1; apos <= matmap[k+1]-matuse[k+1]; apos++)
if (esl_abc_XIsResidue(msa->abc, msa->ax[idx][apos])) nins++;
if (k == 0) nins = 0; /* N-terminus is right justified */
else nins /= 2; /* split in half; nins now = # of residues left left-justified */
opos = npos = matmap[k+1]-matuse[k+1];
while (opos >= matmap[k]+1+nins) {
if (esl_abc_XIsGap(msa->abc, msa->ax[idx][opos])) opos--;
else {
msa->ax[idx][npos] = msa->ax[idx][opos];
if (msa->pp != NULL && msa->pp[idx] != NULL) msa->pp[idx][npos-1] = msa->pp[idx][opos-1];
npos--;
opos--;
}
}
while (npos >= matmap[k]+1+nins) {
msa->ax[idx][npos] = esl_abc_XGetGap(msa->abc);
if (msa->pp != NULL && msa->pp[idx] != NULL) msa->pp[idx][npos-1] = '.';
npos--;
}
}
}
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go; /* application configuration */
int kstatus, tstatus;/* return code from Easel routine */
int fmt; /* expected format of kfile, tfile */
char *kfile, *tfile; /* known, test structure file */
ESL_MSAFILE *kfp, *tfp; /* open kfile, tfile */
ESL_MSA *ka, *ta; /* known, trusted alignment */
int64_t klen, tlen; /* lengths of dealigned seqs */
int i; /* counter over sequences */
int apos; /* counter over alignment columns */
int rfpos; /* counter over consensus (non-gap RF) columns */
int is_rfpos; /* TRUE if current apos is a consensus pos, FALSE if not */
int uapos; /* counter over unaligned residue positions */
int nali; /* number of alignment we're on in each file */
int **kp; /* [0..i..nseq-1][1..r..sq->n] = x known non-gap RF position of residue r in sequence i */
int **tp; /* [0..i..nseq-1][1..r..sq->n] = x predicted non-gap RF position of residue r in sequence i */
/* for both kp and pp, if x <= 0, residue r for seq i is not aligned to a non-gap RF position, but rather as an 'insert'
* after non-gap RF position (x * -1)
*/
int *km_pos; /* [0..rflen] = x, in known aln, number of residues aligned to non-gap RF column x; special case: mct[0] = 0 */
int *ki_pos; /* [0..rflen] = x, in known aln, number of residues inserted after non-gap RF column x */
int *tm_pos; /* [0..rflen] = x, in predicted aln, number of residues aligned to non-gap RF column x; special case: mct[0] = 0 */
int *ti_pos; /* [0..rflen] = x, in predicted aln, number of residues inserted after non-gap RF column x */
int *cor_tm_pos; /* [0..rflen] = x, in predicted aln, number of correctly predicted residues aligned to non-gap RF column x; special case: mct[0] = 0 */
int *cor_ti_pos; /* [0..rflen] = x, in predicted aln, number of correctly predicted residues inserted after non-gap RF column x */
int *km_seq; /* [0..i..nseq-1] = x, in known aln, number of residues aligned to non-gap RF columns in seq i; */
int *ki_seq; /* [0..i..nseq-1] = x, in known aln, number of residues inserted in seq i */
int *tm_seq; /* [0..i..nseq-1] = x, in predicted aln, number of residues aligned to non-gap RF columns in seq i; */
int *ti_seq; /* [0..i..nseq-1] = x, in predicted aln, number of residues inserted in seq i */
int *cor_tm_seq; /* [0..i..nseq-1] = x, in predicted aln, number of correctly predicted residues aligned to non-gap RF columns in seq i */
int *cor_ti_seq; /* [0..i..nseq-1] = x, in predicted aln, number of correctly predicted residues inserted in seq i */
int *seqlen; /* [0..i..nseq-1] = x, unaligned seq i has length x */
ESL_ALPHABET *abc = NULL; /* alphabet for all alignments */
int rflen, t_rflen; /* non-gap RF length (consensus lengths) */
int status;
char *namedashes;
int ni;
int namewidth = 8; /* length of 'seq name' */
int cor_tm, cor_ti, km, ki; /* correct predicted match, correct predicted insert, total match, total insert */
char *mask = NULL;
int masklen;
ESL_DSQ *ks;
ESL_DSQ *ts;
FILE *dfp = NULL; /* for --c2dfile */
/* variables needed for -p and related options */
int do_post = FALSE; /* TRUE if -p enabled */
int do_post_for_this_rfpos = FALSE; /* set for each consensus position, always TRUE unless --mask-p2xm */
int p; /* counter over integerized posteriors */
int *ptm = NULL; /* [0..p..10] number of total matches with posterior value p (10="*")*/
int *pti = NULL; /* [0..p..10] number of total inserts with posterior value p */
int *cor_ptm = NULL; /* [0..p..10] number of correct matches with posterior value p */
int *cor_pti = NULL; /* [0..p..10] number of correct inserts with posterior value p */
int npostvals = 11; /* number of posterior values 0-9, * */
int ppidx; /* index of PP */
char ppchars[11] = "0123456789*";
int cm_cor_ptm, cm_cor_pti, cm_ptm, cm_pti, cm_incor_ptm, cm_incor_pti; /* cumulative counts of posteriors */
// int tot_cor_ptm, tot_cor_pti, tot_ptm, tot_pti; /* total counts of posteriors */
// int tot_incor_ptm,tot_incor_pti; // SRE: commented out; don't seem to be used; need to silence compiler warning
char errbuf[eslERRBUFSIZE];
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK ||
esl_opt_VerifyConfig(go) != eslOK)
{
printf("Failed to parse command line: %s\n", go->errbuf);
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_GetBoolean(go, "-h") )
{
esl_banner(stdout, argv[0], banner);
esl_usage (stdout, argv[0], usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
exit(EXIT_SUCCESS);
}
if (esl_opt_ArgNumber(go) != 2)
{
printf("Incorrect number of command line arguments.\n");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
kfile = esl_opt_GetArg(go, 1);
tfile = esl_opt_GetArg(go, 2);
fmt = eslMSAFILE_STOCKHOLM;
/***********************************************
* Open the two Stockholm files.
***********************************************/
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);
if ( (kstatus = esl_msafile_Open(&abc, kfile, NULL, fmt, NULL, &kfp)) != eslOK) esl_msafile_OpenFailure(kfp, kstatus);
if ( (tstatus = esl_msafile_Open(&abc, tfile, NULL, fmt, NULL, &tfp)) != eslOK) esl_msafile_OpenFailure(tfp, tstatus);
do_post = esl_opt_GetBoolean(go, "-p");
/* read the mask file if --p-mask is enabled */
if(! esl_opt_IsDefault(go, "--p-mask")) {
if((status = read_mask_file(esl_opt_GetString(go, "--p-mask"), errbuf, &mask, &masklen)) != eslOK) esl_fatal(errbuf);
}
/* open the c2dfile for output, if nec */
if (esl_opt_IsOn(go, "--c2dfile")) {
if ((dfp = fopen(esl_opt_GetString(go, "--c2dfile"), "w")) == NULL) esl_fatal("Failed to open --c2dfile output file %s\n", esl_opt_GetString(go, "--c2dfile"));
}
/***********************************************
* Do alignment comparisons, one seq at a time;
* this means looping over all seqs in all alignments.
***********************************************/
nali = 0;
while ( (kstatus = esl_msafile_Read(kfp, &ka)) != eslEOF)
{
if ( kstatus != eslOK) esl_msafile_ReadFailure(kfp, kstatus);
if ( (tstatus = esl_msafile_Read(tfp, &ta)) != eslOK) esl_msafile_ReadFailure(tfp, tstatus);
nali++;
if((nali > 1) && (esl_opt_IsOn(go, "--c2dfile"))) esl_fatal("--c2dfile is only meant for msafiles with single alignments");
/* Sanity check on alignment
*/
if (ka->nseq != ta->nseq)
esl_fatal("trusted, test alignments don't have same seq #\n");
if (ka->rf == NULL)
esl_fatal("trusted alignment has no reference annotation\n");
if (ta->rf == NULL)
esl_fatal("test alignment has no reference annotation\n");
/* make sure the sequences are all identical */
ESL_ALLOC(seqlen, sizeof(int) * ka->nseq);
for(i = 0; i < ka->nseq; i++) {
if(strcmp(ka->sqname[i], ta->sqname[i]) != 0) esl_fatal("sequence %d of trusted alignment %s has different name than seq %d of predicted alignment %s\n", (i+1), ka->sqname[i], (i+1), ta->sqname[i]);
ESL_ALLOC(ks, sizeof(ESL_DSQ) * (ka->alen+2));
memcpy(ks, ka->ax[i], (ka->alen+2) * sizeof(ESL_DSQ));
esl_abc_XDealign(ka->abc, ks, ka->ax[i], &klen);
ESL_ALLOC(ts, sizeof(ESL_DSQ) * (ta->alen+2));
memcpy(ts, ta->ax[i], (ta->alen+2) * sizeof(ESL_DSQ));
esl_abc_XDealign(ta->abc, ts, ta->ax[i], &tlen);
if (tlen != klen)
esl_fatal("dealigned sequence mismatch, seq %d, when dealigned, is %d residues in the known alignment, but %d residues in the trusted alignment.", (i+1), klen, tlen);
if (memcmp(ks, ts, sizeof(ESL_DSQ) * klen) != 0)
esl_fatal("dealigned sequence mismatch, seq %d %s, when dealigned, are not identical.", (i+1), ka->sqname[i]);
seqlen[i] = tlen;
free(ks);
free(ts);
}
/* determine non-gap RF length */
rflen = 0;
for(apos = 1; apos <= ka->alen; apos++) {
if((! esl_abc_CIsGap (ka->abc, ka->rf[apos-1])) &&
(! esl_abc_CIsMissing(ka->abc, ka->rf[apos-1]))) rflen++;
}
t_rflen = 0;
for(apos = 1; apos <= ta->alen; apos++) {
if((! esl_abc_CIsGap (ta->abc, ta->rf[apos-1])) &&
(! esl_abc_CIsMissing (ta->abc, ta->rf[apos-1]))) t_rflen++;
}
if(t_rflen != rflen) esl_fatal("Trusted alignment non-gap RF length (%d) != predicted alignment non-gap RF length (%d).\n", rflen, t_rflen);
/* if -p, make sure the test alignment has posterior probabilities, and allocate our counters for correct/incorrect per post value */
if(do_post) {
if(! esl_opt_IsDefault(go, "--p-mask")) {
if(masklen != rflen) {
esl_fatal("Length of mask in %s (%d) not equal to non-gap RF len of alignments (%d)\n", esl_opt_GetString(go, "--p-mask"), masklen, rflen);
}
}
if(ta->pp == NULL) esl_fatal("-p requires \"#=GR PP\" annotation in the test alignment, but none exists");
ESL_ALLOC(ptm, sizeof(int) * npostvals);
ESL_ALLOC(pti, sizeof(int) * npostvals);
ESL_ALLOC(cor_ptm, sizeof(int) * npostvals);
ESL_ALLOC(cor_pti, sizeof(int) * npostvals);
esl_vec_ISet(ptm, npostvals, 0);
esl_vec_ISet(pti, npostvals, 0);
esl_vec_ISet(cor_ptm, npostvals, 0);
esl_vec_ISet(cor_pti, npostvals, 0);
}
/* allocate and initialize our counters */
ESL_ALLOC(kp, sizeof(int *) * ka->nseq);
ESL_ALLOC(tp, sizeof(int *) * ta->nseq);
for(i = 0; i < ka->nseq; i++) {
ESL_ALLOC(kp[i], sizeof(int) * (seqlen[i]+1));
ESL_ALLOC(tp[i], sizeof(int) * (seqlen[i]+1));
esl_vec_ISet(kp[i], seqlen[i]+1, -987654321);
esl_vec_ISet(tp[i], seqlen[i]+1, -987654321);
}
ESL_ALLOC(km_pos, sizeof(int) * (rflen+1));
ESL_ALLOC(ki_pos, sizeof(int) * (rflen+1));
ESL_ALLOC(tm_pos, sizeof(int) * (rflen+1));
ESL_ALLOC(ti_pos, sizeof(int) * (rflen+1));
ESL_ALLOC(cor_tm_pos, sizeof(int) * (rflen+1));
ESL_ALLOC(cor_ti_pos, sizeof(int) * (rflen+1));
esl_vec_ISet(km_pos, rflen+1, 0);
esl_vec_ISet(ki_pos, rflen+1, 0);
esl_vec_ISet(tm_pos, rflen+1, 0);
esl_vec_ISet(ti_pos, rflen+1, 0);
esl_vec_ISet(cor_tm_pos, rflen+1, 0);
esl_vec_ISet(cor_ti_pos, rflen+1, 0);
ESL_ALLOC(km_seq, sizeof(int) * ka->nseq);
ESL_ALLOC(ki_seq, sizeof(int) * ka->nseq);
ESL_ALLOC(tm_seq, sizeof(int) * ka->nseq);
ESL_ALLOC(ti_seq, sizeof(int) * ka->nseq);
ESL_ALLOC(cor_tm_seq, sizeof(int) * ka->nseq);
ESL_ALLOC(cor_ti_seq, sizeof(int) * ka->nseq);
esl_vec_ISet(km_seq, ka->nseq, 0);
esl_vec_ISet(ki_seq, ka->nseq, 0);
esl_vec_ISet(tm_seq, ka->nseq, 0);
esl_vec_ISet(ti_seq, ka->nseq, 0);
esl_vec_ISet(cor_tm_seq, ka->nseq, 0);
esl_vec_ISet(cor_ti_seq, ka->nseq, 0);
/* determine non-gap RF location of each residue in known alignment */
for(i = 0; i < ka->nseq; i++) {
uapos = rfpos = 0;
for(apos = 1; apos <= ka->alen; apos++) {
is_rfpos = FALSE;
if((! esl_abc_CIsGap (ka->abc, ka->rf[apos-1])) &&
(! esl_abc_CIsMissing (ka->abc, ka->rf[apos-1]))) {
rfpos++; is_rfpos = TRUE;
}
if(esl_abc_XIsResidue(ka->abc, ka->ax[i][apos])) {
uapos++;
kp[i][uapos] = (is_rfpos) ? rfpos : (-1 * rfpos);
if(is_rfpos) { km_pos[rfpos]++; km_seq[i]++; }
else { ki_pos[rfpos]++; ki_seq[i]++; }
}
}
}
/* determine non-gap RF location of each residue in predicted alignment */
for(i = 0; i < ta->nseq; i++) {
uapos = rfpos = 0;
for(apos = 1; apos <= ta->alen; apos++) {
is_rfpos = FALSE;
if((! esl_abc_CIsGap (abc, ta->rf[apos-1])) &&
(! esl_abc_CIsMissing (abc, ta->rf[apos-1]))) {
rfpos++; is_rfpos = TRUE;
if(do_post) {
do_post_for_this_rfpos = (mask != NULL && mask[rfpos-1] == '0') ? FALSE : TRUE;
}
}
if(esl_abc_XIsResidue(ta->abc, ta->ax[i][apos])) {
uapos++;
tp[i][uapos] = (is_rfpos) ? rfpos : (-1 * rfpos);
if(do_post) {
if(esl_abc_CIsGap(abc, ta->pp[i][(apos-1)])) esl_fatal("gap PP value for nongap residue: ali: %d seq: %d apos: %d\n", nali, i, apos);
ppidx = get_pp_idx(abc, ta->pp[i][(apos-1)]);
if(ppidx == -1) esl_fatal("unrecognized PP value (%c) for nongap residue: ali: %d seq: %d apos: %d\n", ta->pp[i][(apos-1)], nali, i, apos);
}
if(is_rfpos) {
tm_pos[rfpos]++; tm_seq[i]++;
if(do_post_for_this_rfpos) ptm[ppidx]++;
}
else {
ti_pos[rfpos]++; ti_seq[i]++;
if(do_post) pti[ppidx]++;
}
if(kp[i][uapos] == tp[i][uapos]) { /* correctly predicted this residue */
if(is_rfpos) {
cor_tm_seq[i]++; cor_tm_pos[rfpos]++;
if(do_post_for_this_rfpos) cor_ptm[ppidx]++;
}
else {
cor_ti_seq[i]++; cor_ti_pos[rfpos]++;
if(do_post) cor_pti[ppidx]++;
}
}
}
}
}
if((! (esl_opt_GetBoolean(go, "-c"))) && (! esl_opt_GetBoolean(go, "-p"))) {
/* print per sequence statistics */
/* determine the longest name in msa */
for(ni = 0; ni < ka->nseq; ni++) namewidth = ESL_MAX(namewidth, strlen(ka->sqname[ni]));
ESL_ALLOC(namedashes, sizeof(char) * namewidth+1);
namedashes[namewidth] = '\0';
for(ni = 0; ni < namewidth; ni++) namedashes[ni] = '-';
printf("# %-*s %6s %28s %28s %28s\n", namewidth, "seq name", "len", "match columns", "insert columns", "all columns");
printf("# %-*s %6s %28s %28s %28s\n", namewidth, namedashes, "------", "----------------------------", "----------------------------", "----------------------------");
for(i = 0; i < ta->nseq; i++) {
printf(" %-*s %6d %8d / %8d (%.3f) %8d / %8d (%.3f) %8d / %8d (%.3f)\n", namewidth, ka->sqname[i], seqlen[i],
cor_tm_seq[i], km_seq[i], (km_seq[i] == 0) ? 0. : ((float) cor_tm_seq[i] / (float) km_seq[i]),
cor_ti_seq[i], ki_seq[i], (ki_seq[i] == 0) ? 0. : ((float) cor_ti_seq[i] / (float) ki_seq[i]),
(cor_tm_seq[i] + cor_ti_seq[i]), (km_seq[i] + ki_seq[i]), ((float) (cor_tm_seq[i] + cor_ti_seq[i]) / ((float) km_seq[i] + ki_seq[i])));
}
cor_tm = esl_vec_ISum(cor_tm_seq, ka->nseq);
cor_ti = esl_vec_ISum(cor_ti_seq, ka->nseq);
km = esl_vec_ISum(km_seq, ka->nseq);
ki = esl_vec_ISum(ki_seq, ka->nseq);
printf("# %-*s %6s %28s %28s %28s\n", namewidth, namedashes, "-----", "----------------------------", "----------------------------", "----------------------------");
printf("# %-*s %6s %8d / %8d (%.3f) %8d / %8d (%.3f) %8d / %8d (%.3f)\n",
namewidth, "*all*", "-",
cor_tm, km, ((float) cor_tm / (float) km),
cor_ti, ki, ((float) cor_ti / (float) ki),
(cor_tm+cor_ti), (km+ki), (((float) (cor_tm + cor_ti))/ ((float) (km + ki))));
free(namedashes);
for(i = 0; i < ka->nseq; i++) {
free(kp[i]);
free(tp[i]);
}
}
else if(esl_opt_GetBoolean(go, "-c")) { /* print per column statistics */
printf("# %5s %20s %20s %20s\n", "rfpos", "match", "insert", "both");
printf("# %5s %20s %20s %20s\n", "-----", "--------------------", "--------------------", "--------------------");
for(rfpos = 0; rfpos <= rflen; rfpos++) {
printf(" %5d %4d / %4d (%.3f) %4d / %4d (%.3f) %4d / %4d (%.3f)\n", rfpos,
cor_tm_pos[rfpos], km_pos[rfpos], (km_pos[rfpos] == 0) ? 0. : ((float) cor_tm_pos[rfpos] / (float) km_pos[rfpos]),
cor_ti_pos[rfpos], ki_pos[rfpos], (ki_pos[rfpos] == 0) ? 0. : ((float) cor_ti_pos[rfpos] / (float) ki_pos[rfpos]),
(cor_tm_pos[rfpos] + cor_ti_pos[rfpos]), (km_pos[rfpos] + ki_pos[rfpos]), ((float) (cor_tm_pos[rfpos] + cor_ti_pos[rfpos]) / ((float) km_pos[rfpos] + ki_pos[rfpos])));
}
}
else if(do_post) { /* do posterior output */
if(mask == NULL) {
printf("# %2s %29s %29s\n", "", " match columns ", " insert columns ");
printf("# %2s %29s %29s\n", "", "-----------------------------", "-----------------------------") ;
printf("# %2s %8s %8s %9s %8s %8s %9s\n", "PP", "ncorrect", "ntotal", "fractcor", "ncorrect", "ntotal", "fractcor");
printf("# %2s %8s %8s %9s %8s %8s %9s\n", "--", "--------", "--------", "---------", "--------", "--------", "---------");
}
else {
printf("# %2s %29s %29s\n", "", " match columns within mask ", " insert columns ");
printf("# %2s %29s %29s\n", "", "-----------------------------", "-----------------------------") ;
printf("# %2s %8s %8s %9s %8s %8s %9s\n", "PP", "ncorrect", "ntotal", "fractcor", "ncorrect", "ntotal", "fractcor");
printf("# %2s %8s %8s %9s %8s %8s %9s\n", "--", "--------", "--------", "---------", "--------", "--------", "---------");
}
cm_ptm = cm_pti = cm_cor_ptm = cm_cor_pti = cm_incor_ptm = cm_incor_pti = 0;
//tot_ptm = esl_vec_ISum(ptm, npostvals);
//tot_pti = esl_vec_ISum(pti, npostvals);
//tot_cor_ptm = esl_vec_ISum(cor_ptm, npostvals);
//tot_cor_pti = esl_vec_ISum(cor_pti, npostvals);
//tot_incor_ptm = tot_ptm - tot_cor_ptm;
//tot_incor_pti = tot_pti - tot_cor_pti;
for(p = (npostvals-1); p >= 0; p--) {
cm_cor_ptm += cor_ptm[p];
cm_cor_pti += cor_pti[p];
cm_ptm += ptm[p];
cm_pti += pti[p];
cm_incor_ptm += ptm[p] - cor_ptm[p];
cm_incor_pti += pti[p] - cor_pti[p];
printf(" %2c %8d / %8d (%.5f) %8d / %8d (%.5f)\n",
ppchars[p], cor_ptm[p], ptm[p],
(ptm[p] == 0) ? 0. : (float) cor_ptm[p] / (float) ptm[p],
cor_pti[p], pti[p],
(pti[p] == 0) ? 0. : (float) cor_pti[p] / (float) pti[p]);
}
}
/* handle --c2dfile */
if (dfp != NULL) {
/* match stats, 4 fields, CMYK color values */
for(rfpos = 1; rfpos <= rflen; rfpos++) {
if(km_pos[rfpos] == 0) { /* special case, no known alignment residues, a blank position */
fprintf(dfp, "%.3f %.3f %.3f %.3f\n", 0., 0., 0., 0.);
}
else {
fprintf(dfp, "%.3f %.3f %.3f %.3f\n",
0., /* cyan */
1. - ((float) cor_tm_pos[rfpos] / (float) km_pos[rfpos]), /* magenta, fraction incorrect */
1. - ((float) km_pos[rfpos] / ta->nseq), /* yellow, 1 - fraction of seqs with residue in column */
0.);
}
}
fprintf(dfp, "//\n");
/* insert stats, 4 fields, CMYK color values */
rfpos = 0; /* special case, combine insert posn 0 and 1 together */
if(ki_pos[rfpos] == 0) { /* special case, no known alignment residues, a blank position */
fprintf(dfp, "%.3f %.3f %.3f %.3f\n", 0., 0., 0., 0.);
}
else {
fprintf(dfp, "%.3f %.3f %.3f %.3f\n",
0., /* cyan */
1. - ((float) (cor_ti_pos[0] + cor_ti_pos[1]) / ((float) (ki_pos[0] + ki_pos[1]))), /* magenta, fraction correct */
0.,
0.);
}
/* insert stats posn 2..rflen */
for(rfpos = 2; rfpos <= rflen; rfpos++) {
if(ki_pos[rfpos] == 0) { /* special case, no known alignment residues, a blank position */
fprintf(dfp, "%.3f %.3f %.3f %.3f\n", 0., 0., 0., 0.);
}
else {
fprintf(dfp, "%.3f %.3f %.3f %.3f\n",
0., /* cyan */
1. - ((float) cor_ti_pos[rfpos] / (float) ki_pos[rfpos]), /* magenta, fraction correct */
0.,
0.);
}
}
fprintf(dfp, "//\n");
}
if(ptm != NULL) free(ptm);
if(pti != NULL) free(pti);
if(cor_ptm != NULL) free(cor_ptm);
if(cor_ptm != NULL) free(cor_pti);
free(kp);
free(tp);
free(km_seq);
free(ki_seq);
free(tm_seq);
free(ti_seq);
free(cor_tm_seq);
free(cor_ti_seq);
free(km_pos);
free(ki_pos);
free(tm_pos);
free(ti_pos);
free(cor_tm_pos);
free(cor_ti_pos);
free(seqlen);
esl_msa_Destroy(ka);
esl_msa_Destroy(ta);
}
if(mask != NULL) free(mask);
if(dfp != NULL) {
fclose(dfp);
printf("# Draw file of per-column stats saved to file: %s\n", esl_opt_GetString(go, "--c2dfile"));
}
if(abc) esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
esl_msafile_Close(tfp);
esl_msafile_Close(kfp);
return 0;
ERROR:
return status;
}
/* Function: esl_msafile_a2m_Write()
* Synopsis: Write an A2M (UCSC SAM) dotless format alignment to a stream.
*
* Purpose: Write alignment <msa> in dotless UCSC A2M format to a
* stream <fp>.
*
* The <msa> should have a valid reference line <msa->rf>,
* with alphanumeric characters marking consensus (match)
* columns, and non-alphanumeric characters marking
* nonconsensus (insert) columns. If it does not,
* then as a fallback, the first sequence in the alignment is
* considered to be the consensus.
*
* In "dotless" A2M format, gap characters (.) in insert
* columns are omitted; therefore sequences can be of
* different lengths, but each sequence has the same number
* of consensus columns (residue or -).
*
* A2M format cannot represent missing data symbols
* (Easel's ~). Any missing data symbols are converted to
* gaps.
*
* A2M format cannot represent pyrrolysine residues in
* amino acid sequences, because it treats 'O' symbols
* specially, as indicating a position at which a
* free-insertion module (FIM) should be created. Any 'O'
* in the <msa> is written instead as an unknown
* residue ('X', in protein sequences).
*
* Args: fp - open output stream
* msa - MSA to write
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
* <eslEWRITE> on any system write error, such as filled disk.
*/
int
esl_msafile_a2m_Write(FILE *fp, const ESL_MSA *msa)
{
char *buf = NULL;
int cpl = 60;
int bpos;
int pos;
int is_consensus;
int is_residue;
int do_dotless = TRUE; /* just changing this to FALSE makes it write dots too */
int i;
int sym;
int status;
ESL_ALLOC(buf, sizeof(char) * (cpl+1));
for (i = 0; i < msa->nseq; i++)
{
/* Construct the name/description line */
if (fprintf(fp, ">%s", msa->sqname[i]) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed");
if (msa->sqacc != NULL && msa->sqacc[i] != NULL) { if (fprintf(fp, " %s", msa->sqacc[i]) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed"); }
if (msa->sqdesc != NULL && msa->sqdesc[i] != NULL) { if (fprintf(fp, " %s", msa->sqdesc[i]) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed"); }
if (fputc('\n', fp) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed");
#ifdef eslAUGMENT_ALPHABET
if (msa->abc)
{
pos = 0;
while (pos < msa->alen)
{
for (bpos = 0; pos < msa->alen && bpos < cpl; pos++)
{
sym = msa->abc->sym[msa->ax[i][pos+1]]; /* note off-by-one in digitized aseq: 1..alen */
is_residue = esl_abc_XIsResidue(msa->abc, msa->ax[i][pos+1]);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos]) ? TRUE : FALSE);
else is_consensus = (esl_abc_XIsResidue(msa->abc, msa->ax[0][pos+1]) ? TRUE : FALSE);
if (sym == 'O') sym = esl_abc_XGetUnknown(msa->abc); /* watch out: O means "insert a FIM" in a2m format, not pyrrolysine */
if (is_consensus) { buf[bpos++] = (is_residue ? toupper(sym) : '-'); }
else if (is_residue) { buf[bpos++] = tolower(sym); }
else if (! do_dotless) { buf[bpos++] = '.'; }
}
buf[bpos] = '\0';
if (bpos) { if (fprintf(fp, "%s\n", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed");}
}
}
#endif
if (! msa->abc)
{
pos = 0;
while (pos < msa->alen)
{
for (bpos = 0; pos < msa->alen && bpos < cpl; pos++)
{
sym = msa->aseq[i][pos];
is_residue = isalpha(msa->aseq[i][pos]);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos]) ? TRUE : FALSE);
else is_consensus = (isalnum(msa->aseq[0][pos]) ? TRUE : FALSE);
if (sym == 'O') sym = 'X';
if (is_consensus) { buf[bpos++] = ( is_residue ? toupper(sym) : '-'); }
else if (is_residue) { buf[bpos++] = tolower(sym); }
else if (! do_dotless) { buf[bpos++] = '.'; }
}
buf[bpos] = '\0';
if (bpos) { if (fprintf(fp, "%s\n", buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "a2m msa file write failed"); }
}
}
} /* end, loop over sequences in the MSA */
free(buf);
return eslOK;
ERROR:
if (buf) free(buf);
return status;
}
/* Function: esl_msafile_psiblast_Write()
* Synopsis: Write an MSA to a stream in PSI-BLAST format
*
* Purpose: Write alignment <msa> in NCBI PSI-BLAST format to
* stream <fp>.
*
* The <msa> should have a valid reference line <msa->rf>,
* with alphanumeric characters marking consensus (match)
* columns, and non-alphanumeric characters marking
* nonconsensus (insert) columns. If it does not have RF
* annotation, then the first sequence in the <msa>
* defines the "consensus".
*
* PSI-BLAST format allows only one symbol ('-') for gaps,
* and cannot represent missing data symbols (Easel's
* '~'). Any missing data symbols are converted to gaps.
*
* Args: fp - open output stream
* msa - MSA to write
*
* Returns: <eslOK> on success.
*
* Throws: <eslEMEM> on allocation failure.
* <eslEWRITE> on any system write failure, such as filled disk.
*/
int
esl_msafile_psiblast_Write(FILE *fp, const ESL_MSA *msa)
{
char *buf = NULL;
int cpl = 60;
int acpl;
int i;
int sym;
int64_t pos, bpos;
int maxnamewidth = esl_str_GetMaxWidth(msa->sqname, msa->nseq);
int is_consensus;
int is_residue;
int status;
ESL_ALLOC(buf, sizeof(char) * (cpl+1));
for (pos = 0; pos < msa->alen; pos += cpl)
{
for (i = 0; i < msa->nseq; i++)
{
acpl = (msa->alen - pos > cpl)? cpl : msa->alen - pos;
#ifdef eslAUGMENT_ALPHABET
if (msa->abc)
{
for (bpos = 0; bpos < acpl; bpos++)
{
sym = msa->abc->sym[msa->ax[i][pos + bpos + 1]];
is_residue = esl_abc_XIsResidue(msa->abc, msa->ax[i][pos+bpos+1]);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos + bpos]) ? TRUE : FALSE);
else is_consensus = (esl_abc_XIsResidue(msa->abc, msa->ax[0][pos+bpos+1]) ? TRUE : FALSE);
if (is_consensus) { buf[bpos] = (is_residue ? toupper(sym) : '-'); }
else { buf[bpos] = (is_residue ? tolower(sym) : '-'); }
}
}
#endif
if (! msa->abc)
{
for (bpos = 0; bpos < acpl; bpos++)
{
sym = msa->aseq[i][pos + bpos];
is_residue = isalnum(sym);
if (msa->rf) is_consensus = (isalnum(msa->rf[pos + bpos]) ? TRUE : FALSE);
else is_consensus = (isalnum(msa->aseq[0][pos+bpos]) ? TRUE : FALSE);
if (is_consensus) { buf[bpos] = (is_residue ? toupper(sym) : '-'); }
else { buf[bpos] = (is_residue ? tolower(sym) : '-'); }
}
}
buf[acpl] = '\0';
if (fprintf(fp, "%-*s %s\n", maxnamewidth, msa->sqname[i], buf) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "psiblast msa write failed");
} /* end loop over sequences */
if (pos + cpl < msa->alen)
{ if (fputc('\n', fp) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "psiblast msa write failed"); }
}
free(buf);
return eslOK;
ERROR:
if (buf) free(buf);
return status;
}
/* Function: scoredata_GetSSVScoreArrays()
* Synopsis: Get compact representation of substitution scores and maximal extensions
*
* Purpose: Extract 8-bit (MSV-style) substitution scores from optimized
* matrix. These scores will be used in both standard MSV diagonal
* recovery and FM-MSV diagonal scoring.
*
* Optionally, for each position in the model, capture the maximum
* possible score that can be added to a diagonal's score (in both
* directions) by extending lengths 1..10. These extension scores
* are used in FM-MSV's pruning step.
*
* Once a hit passes the SSV filter, and the prefix/suffix
* values of P7_SCOREDATA are required (to establish windows
* around SSV diagonals), p7_hmm_ScoreDataComputeRest()
* must be called.
*
*
* Args: om - P7_OPROFILE containing scores used to produce SCOREDATA contents
* data - where scores and will be stored
* do_opt_ext - boolean, TRUE if optimal-extension scores are required (for FM-MSV)
* scale - used to produce 8-bit extracted scores
* bias - used to produce 8-bit extracted scores
*
* Returns: data->scores and possibly ->opt_ext_(fwd|rev) are filled in;
* return eslEMEM on allocation failure, eslOK otherwise.
*/
static int
scoredata_GetSSVScoreArrays(P7_OPROFILE *om, P7_PROFILE *gm, P7_SCOREDATA *data ) {
int i, j, status;
//gather values from gm->rsc into a succinct 2D array
float *max_scores;
float sc_fwd, sc_rev;
int K = om->abc->Kp;
data->M = om->M;
if (!gm) { // get values for the standard pipeline
data->type = p7_sd_std;
ESL_ALLOC(data->ssv_scores, (om->M + 1) * K * sizeof(uint8_t));
p7_oprofile_GetSSVEmissionScoreArray(om, data->ssv_scores);
} else {// need float, unscaled scores, and other stuff used in the FMindex-based SSV pipeline,
data->type = p7_sd_fm;
ESL_ALLOC(data->ssv_scores_f, (om->M + 1) * K * sizeof(float));
ESL_ALLOC(max_scores, (om->M + 1) * sizeof(float));
for (i = 1; i <= om->M; i++) {
max_scores[i] = 0;
for (j=0; j<K; j++) {
if (esl_abc_XIsResidue(om->abc,j)) {
data->ssv_scores_f[i*K + j] = gm->rsc[j][(i) * p7P_NR + p7P_MSC];
if (data->ssv_scores_f[i*K + j] > max_scores[i]) max_scores[i] = data->ssv_scores_f[i*K + j];
}
}
}
//for each position in the query, what's the highest possible score achieved by extending X positions, for X=1..10
ESL_ALLOC(data->opt_ext_fwd, (om->M + 1) * sizeof(float*));
ESL_ALLOC(data->opt_ext_rev, (om->M + 1) * sizeof(float*));
for (i=1; i<om->M; i++) {
ESL_ALLOC(data->opt_ext_fwd[i], 10 * sizeof(float));
ESL_ALLOC(data->opt_ext_rev[i], 10 * sizeof(float));
}
for (i=1; i<om->M; i++) {
sc_fwd = 0;
sc_rev = 0;
for (j=0; j<10 && i+j+1<=om->M; j++) {
sc_fwd += max_scores[i+j+1];
data->opt_ext_fwd[i][j] = sc_fwd;
sc_rev += max_scores[om->M-i-j];
data->opt_ext_rev[om->M-i][j] = sc_rev;
}
for ( ; j<10; j++) { //fill in empty values
data->opt_ext_fwd[i][j] = data->opt_ext_fwd[i][j-1];
data->opt_ext_rev[om->M-i][j] = data->opt_ext_rev[om->M-i][j-1];
}
}
free(max_scores);
}
return eslOK;
ERROR:
return eslEMEM;
}
/* 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;
}
