int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL;
ESL_RANDOMNESS *r = NULL;
char **as = NULL; /* aligned character seqs (random, iid) */
int N,L; /* # of seqs, and their aligned lengths */
int seed;
int i,j;
int status;
double p[4]; /* ACGT probabilities */
#ifdef eslAUGMENT_ALPHABET
ESL_DSQ **ax = NULL; /* digitized alignment */
ESL_ALPHABET *abc = NULL;
#endif
/* Process command line
*/
go = esl_getopts_Create(options);
esl_opt_ProcessCmdline(go, argc, argv);
esl_opt_VerifyConfig(go);
if (esl_opt_GetBoolean(go, "-h") == TRUE) {
puts(usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2=indentation; 80=width */
return 0;
}
L = esl_opt_GetInteger(go, "-L");
N = esl_opt_GetInteger(go, "-N");
seed = esl_opt_GetInteger(go, "--seed");
if (esl_opt_ArgNumber(go) != 0) {
puts("Incorrect number of command line arguments.");
puts(usage);
return 1;
}
esl_getopts_Destroy(go);
/* Create a random DNA alignment;
* force it to obey the conventions of the unit tests:
* 0,1 are identical
* 0,2 are completely dissimilar
*/
r = esl_randomness_Create(seed);
for (i = 0; i < 4; i++) p[i] = 0.25;
ESL_ALLOC(as, sizeof(char *) * N);
for (i = 0; i < N; i++)
ESL_ALLOC(as[i], sizeof(char) * (L+1));
esl_rsq_IID(r, "ACGT", p, 4, L, as[0]);
strcpy(as[1], as[0]);
esl_rsq_IID(r, "ACGT", p, 4, L, as[2]);
for (j = 0; j < L; j++)
while (as[2][j] == as[0][j])
as[2][j] = "ACGT"[esl_rnd_Roll(r, 4)];
for (i = 3; i < N; i++)
esl_rsq_IID(r, "ACGT", p, 4, L, as[i]);
#ifdef eslAUGMENT_ALPHABET
abc = esl_alphabet_Create(eslDNA);
ESL_ALLOC(ax, sizeof(ESL_DSQ *) * N);
for (i = 0; i < N; i++)
esl_abc_CreateDsq(abc, as[i], &(ax[i]));
#endif /*eslAUGMENT_ALPHABET*/
/* Unit tests
*/
if (utest_CPairId(as, N) != eslOK) return eslFAIL;
if (utest_CJukesCantor(4, as, N) != eslOK) return eslFAIL;
#ifdef eslAUGMENT_ALPHABET
if (utest_XPairId(abc, as, ax, N) != eslOK) return eslFAIL;
if (utest_XJukesCantor(abc, as, ax, N) != eslOK) return eslFAIL;
#endif /*eslAUGMENT_ALPHABET*/
#ifdef eslAUGMENT_DMATRIX
if (utest_CPairIdMx(as, N) != eslOK) return eslFAIL;
if (utest_CDiffMx(as, N) != eslOK) return eslFAIL;
if (utest_CJukesCantorMx(4, as, N) != eslOK) return eslFAIL;
#endif /* eslAUGMENT_DMATRIX*/
#if defined (eslAUGMENT_ALPHABET) && defined (eslAUGMENT_DMATRIX)
if (utest_XPairIdMx(abc, as, ax, N) != eslOK) return eslFAIL;
if (utest_XDiffMx(abc, as, ax, N) != eslOK) return eslFAIL;
if (utest_XJukesCantorMx(abc, as, ax, N) != eslOK) return eslFAIL;
#endif
esl_randomness_Destroy(r);
esl_Free2D((void **) as, N);
#ifdef eslAUGMENT_ALPHABET
esl_alphabet_Destroy(abc);
esl_Free2D((void **) ax, N);
#endif
return eslOK;
ERROR:
return eslFAIL;
}
/* 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; /* application configuration */
ESL_ALPHABET *abc = NULL; /* biological alphabet */
char *alifile = NULL; /* alignment file name */
int fmt = eslMSAFILE_UNKNOWN; /* format code for alifile */
ESLX_MSAFILE *afp = NULL; /* open msa file */
ESL_MSAFILE2 *old_afp = NULL; /* open msa file, legacy (--small) */
ESL_MSA *msa = NULL; /* one multiple sequence alignment */
int nali; /* number of alignments read */
int i; /* counter over seqs */
int64_t alen; /* alignment length */
int nseq; /* number of sequences in the msa */
int64_t rlen; /* a raw (unaligned) seq length */
int64_t small, large; /* smallest, largest sequence */
int64_t nres; /* total # of residues in msa */
double avgid; /* average fractional pair id */
int max_comparisons; /* maximum # comparisons for avg id */
int do_stall; /* used to stall when debugging */
double **abc_ct = NULL; /* [0..msa->alen-1][0..abc->K] number of each residue at each position (abc->K is gap) */
double ***bp_ct = NULL; /* [0..msa->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. */
double **pp_ct = NULL; /* [0..msa->alen-1][0..11], count of each posterior probability (PP) code, over all sequences, gap is 11 */
int *i_am_rf = NULL; /* [0..i..msa->alen-1]: TRUE if pos i is non-gap RF posn, if msa->rf == NULL remains NULL */
int *rf2a_map = NULL; /* [0..rfpos..rflen-1] = apos,
* apos is the alignment position (0..msa->alen-1) that
* is non-gap RF position rfpos+1 (for rfpos in 0..rflen-1) */
int rflen = -1; /* nongap RF length */
char errbuf[eslERRBUFSIZE];
int status; /* easel return code */
/* optional output files */
FILE *iinfofp = NULL; /* output file for --iinfo */
FILE *pcinfofp = NULL; /* output file for --pcinfo */
FILE *psinfofp = NULL; /* output file for --psinfo */
FILE *rinfofp = NULL; /* output file for --rinfo */
FILE *icinfofp = NULL; /* output file for --icinfo */
FILE *listfp = NULL; /* output file for --list */
FILE *cinfofp = NULL; /* output file for --cinfo */
FILE *bpinfofp = NULL; /* output file for --bpinfo */
int use_weights; /* TRUE if --weight, reported weighted counts (using msa->wgt) to all output files */
int weights_exist; /* TRUE if at least one msa->wgt value differs from 1.0, FALSE if not (or if msa->wgt==NULL) */
/***********************************************
* 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);
puts("\n small memory mode, requires --amino,--dna, or --rna and --informat pfam:");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
puts("\n optional output files:");
esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) != 1)
{
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);
}
alifile = esl_opt_GetArg(go, 1);
if (esl_opt_IsOn(go, "--informat") &&
(fmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN)
esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
if (esl_opt_GetBoolean(go, "--small") && fmt != eslMSAFILE_PFAM) esl_fatal("--small requires --informat pfam\n");
max_comparisons = 1000;
do_stall = esl_opt_GetBoolean(go, "--stall"); /* a stall point for attaching gdb */
while (do_stall);
/***********************************************
* Open the MSA file; determine alphabet; set for digital input
***********************************************/
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);
/* We'd like to get rid of the legacy msafile interface, but it
* includes small memory functionality for Pfam format which we have
* to replace first. For now, use both interfaces, new and legacy
*/
if ( esl_opt_GetBoolean(go, "--small") )
{
if (! abc) esl_fatal("--small requires one of --amino, --dna, --rna be specified.");
status = esl_msafile2_OpenDigital(abc, alifile, NULL, &old_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);
}
else
{
if ( (status = eslx_msafile_Open(&abc, alifile, NULL, fmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
}
/**************************************
* Open optional output files, as nec *
**************************************/
/* determine name for first list file, if nec */
if( esl_opt_IsOn(go, "--list")) {
if ((listfp = fopen(esl_opt_GetString(go, "--list"), "w")) == NULL)
esl_fatal("Failed to open --list output file %s\n", esl_opt_GetString(go, "--list"));
}
if( esl_opt_IsOn(go, "--icinfo")) {
if ((icinfofp = fopen(esl_opt_GetString(go, "--icinfo"), "w")) == NULL)
esl_fatal("Failed to open --icinfo output file %s\n", esl_opt_GetString(go, "--icinfo"));
}
if( esl_opt_IsOn(go, "--rinfo")) {
if ((rinfofp = fopen(esl_opt_GetString(go, "--rinfo"), "w")) == NULL)
esl_fatal("Failed to open --rinfo output file %s\n", esl_opt_GetString(go, "--rinfo"));
}
if( esl_opt_IsOn(go, "--pcinfo")) {
if ((pcinfofp = fopen(esl_opt_GetString(go, "--pcinfo"), "w")) == NULL)
esl_fatal("Failed to open --pcinfo output file %s\n", esl_opt_GetString(go, "--pcinfo"));
}
if( esl_opt_IsOn(go, "--psinfo")) {
if ((psinfofp = fopen(esl_opt_GetString(go, "--psinfo"), "w")) == NULL)
esl_fatal("Failed to open --psinfo output file %s\n", esl_opt_GetString(go, "--psinfo"));
}
if( esl_opt_IsOn(go, "--iinfo")) {
if ((iinfofp = fopen(esl_opt_GetString(go, "--iinfo"), "w")) == NULL)
esl_fatal("Failed to open --iinfo output file %s\n", esl_opt_GetString(go, "--iinfo"));
}
if( esl_opt_IsOn(go, "--cinfo")) {
if ((cinfofp = fopen(esl_opt_GetString(go, "--cinfo"), "w")) == NULL)
esl_fatal("Failed to open --cinfo output file %s\n", esl_opt_GetString(go, "--cinfo"));
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if ((bpinfofp = fopen(esl_opt_GetString(go, "--bpinfo"), "w")) == NULL)
esl_fatal("Failed to open --bpinfo output file %s\n", esl_opt_GetString(go, "--bpinfo"));
}
/***********************************************
* Read MSAs one at a time.
***********************************************/
if (esl_opt_GetBoolean(go, "-1")) {
puts("#");
if(! esl_opt_GetBoolean(go, "--small")) {
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "idx", "name", "format", "nseq", "alen", "nres", "small", "large", "avlen", "%id");
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "------", "------", "----------", "---");
}
else {
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "idx", "name", "format", "nseq", "alen", "nres", "avlen");
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "----------");
}
}
nali = 0;
fmt = (esl_opt_GetBoolean(go, "--small") ? old_afp->format : afp->format);
while ( (status = ( esl_opt_GetBoolean(go, "--small") ?
esl_msafile2_ReadInfoPfam(old_afp, listfp, abc, -1, NULL, NULL, &msa, &nseq, &alen, NULL, NULL, NULL, NULL, NULL, &abc_ct, &pp_ct, NULL, NULL, NULL) :
eslx_msafile_Read (afp, &msa))) == eslOK)
{
nali++;
nres = 0;
if (! esl_opt_GetBoolean(go, "--small")) {
nseq = msa->nseq;
alen = msa->alen;
small = large = -1;
for (i = 0; i < msa->nseq; i++)
{
rlen = esl_abc_dsqrlen(msa->abc, msa->ax[i]);
nres += rlen;
if (small == -1 || rlen < small) small = rlen;
if (large == -1 || rlen > large) large = rlen;
}
esl_dst_XAverageId(abc, msa->ax, msa->nseq, max_comparisons, &avgid);
}
else { /* --small invoked */
for(i = 0; i < alen; i++) nres += (int) esl_vec_DSum(abc_ct[i], abc->K);
}
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-6d %-20s %10s %7d %7" PRId64 " %12" PRId64,
nali,
msa->name,
eslx_msafile_DecodeFormat(fmt),
nseq,
alen,
nres);
if (! esl_opt_GetBoolean(go, "--small")) {
printf(" %6" PRId64 " %6" PRId64 " %10.1f %3.0f\n",
small,
large,
(double) nres / (double) msa->nseq,
100.*avgid);
}
else {
printf(" %10.1f\n", (double) nres / (double) nseq);
}
}
else
{
printf("Alignment number: %d\n", nali);
if (msa->name != NULL)
printf("Alignment name: %s\n", msa->name);
printf("Format: %s\n", eslx_msafile_DecodeFormat(fmt));
printf("Number of sequences: %d\n", nseq);
printf("Alignment length: %" PRId64 "\n", alen);
printf("Total # residues: %" PRId64 "\n", nres);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Smallest: %" PRId64 "\n", small);
printf("Largest: %" PRId64 "\n", large);
}
printf("Average length: %.1f\n", (double) nres / (double) nseq);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Average identity: %.0f%%\n", 100.*avgid);
}
printf("//\n");
}
/* Dump data to optional output files, if nec */
if(esl_opt_IsOn(go, "--list")) {
if(! esl_opt_GetBoolean(go, "--small")) {
/* only print sequence name to list file if ! --small, else we already have in esl_msafile2_ReadInfoPfam() */
for(i = 0; i < msa->nseq; i++) fprintf(listfp, "%s\n", msa->sqname[i]);
}
}
/* if RF exists, get i_am_rf array[0..alen] which tells us which positions are non-gap RF positions
* and rf2a_map, a map of non-gap RF positions to overall alignment positions */
if(msa->rf != NULL) {
if((status = map_rfpos_to_apos(msa, abc, errbuf, alen, &i_am_rf, &rf2a_map, &rflen)) != eslOK) esl_fatal(errbuf);
}
else i_am_rf = NULL;
weights_exist = check_msa_weights(msa);
use_weights = (weights_exist && esl_opt_GetBoolean(go, "--weight")) ? TRUE : FALSE;
if( (! esl_opt_GetBoolean(go, "--small")) &&
(esl_opt_IsOn(go, "--icinfo") || esl_opt_IsOn(go, "--rinfo") || esl_opt_IsOn(go, "--pcinfo") ||
esl_opt_IsOn(go, "--cinfo") || esl_opt_IsOn(go, "--bpinfo"))) {
/* collect counts of each residue and PPs (if they exist) from the msa */
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = count_msa(msa, errbuf, nali,
esl_opt_GetBoolean(go, "--noambig"), /* ignore ambiguous residues? */
esl_opt_GetBoolean(go, "--weight"), /* use msa->wgt sequence weights? */
&abc_ct,
((bpinfofp != NULL && msa->ss_cons != NULL) ? &bp_ct : NULL), /* get basepair counts? */
(msa->pp != NULL ? &pp_ct : NULL))) /* get PP counts? */
!= eslOK) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--icinfo")) {
if((status = dump_infocontent_info(icinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--rinfo")) {
if((status = dump_residue_info(rinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--pcinfo")) {
if(pp_ct == NULL) esl_fatal("Error: --pcinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_column_info(pcinfofp, pp_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--psinfo")) {
if(msa->pp == NULL) esl_fatal("Error: --psinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_sequence_info(psinfofp, msa, nali, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--iinfo")) {
if(msa->rf == NULL) esl_fatal("--iinfo requires all alignments have #=GC RF annotation, but alignment %d does not", nali);
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = dump_insert_info(iinfofp, msa, use_weights, nali, i_am_rf, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--cinfo")) {
if((status = dump_column_residue_counts(cinfofp, abc, abc_ct, esl_opt_GetBoolean(go, "--noambig"), use_weights, nali, alen, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if(msa->ss_cons == NULL) esl_fatal("--bpinfo requires all alignments have #=GC SS_cons annotation, but alignment %d does not", nali);
if((status = dump_basepair_counts(bpinfofp, msa, abc, bp_ct, use_weights, nali, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
esl_msa_Destroy(msa);
if(abc_ct != NULL) { esl_Free2D((void **) abc_ct, alen); abc_ct = NULL; }
if(bp_ct != NULL) { esl_Free3D((void ***) bp_ct, alen, abc->Kp); bp_ct = NULL; }
if(pp_ct != NULL) { esl_Free2D((void **) pp_ct, alen); pp_ct = NULL; }
if(i_am_rf != NULL) { free(i_am_rf); i_am_rf = NULL; }
if(rf2a_map != NULL) { free(rf2a_map); rf2a_map = NULL; }
}
/* If an msa read failed, we've dropped out to here with an informative status code.
* we have to handle failures from new vs. legacy msa parsing differently
*/
if (esl_opt_GetBoolean(go, "--small"))
{
if (status == eslEFORMAT) esl_fatal("Alignment file parse error, line %d of file %s:\n%s\nOffending line is:\n%s\n", old_afp->linenumber, old_afp->fname, old_afp->errbuf, old_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);
}
else
{
if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status);
}
/* Cleanup, normal return
*/
if(listfp != NULL) {
fclose(listfp);
printf("# List of sequences in %d alignment(s) saved to file %s\n", nali, esl_opt_GetString(go, "--list"));
}
if(icinfofp != NULL) {
fclose(icinfofp);
printf("# Information content data saved to file %s.\n", esl_opt_GetString(go, "--icinfo"));
}
if(rinfofp != NULL) {
fclose(rinfofp);
printf("# Residue data saved to file %s.\n", esl_opt_GetString(go, "--rinfo"));
}
if(pcinfofp != NULL) {
fclose(pcinfofp);
printf("# Per-column posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--pcinfo"));
}
if(psinfofp != NULL) {
fclose(psinfofp);
printf("# Per-sequence posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--psinfo"));
}
if(iinfofp != NULL) {
printf("# Insert data saved to file %s.\n", esl_opt_GetString(go, "--iinfo"));
fclose(iinfofp);
}
if(cinfofp != NULL) {
printf("# Per-column counts data saved to file %s.\n", esl_opt_GetString(go, "--cinfo"));
fclose(cinfofp);
}
if(bpinfofp != NULL) {
printf("# Per-column basepair counts data saved to file %s.\n", esl_opt_GetString(go, "--bpinfo"));
fclose(bpinfofp);
}
if (afp) eslx_msafile_Close(afp);
if (old_afp) esl_msafile2_Close(old_afp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
/* 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;
}
