static int
profillic_esl_msafile_profile_Read(ESLX_MSAFILE *afp, ESL_MSA **ret_msa, ProfileType * profile_ptr )
{
/// \note Right now this isn't actually using the open file pointer; for convenience I just use the profile.fromFile( <filename> ) method.
/// \todo Use convenience fns in esl_buffer.h; see eg hmmer-3.1/easel/esl_msafile_stockholm.c for examples...
ESL_MSA *msa = NULL;
string profile_string;
char *buf;
long len;
int seqidx;
int status;
char errmsg2[eslERRBUFSIZE];
ESL_DASSERT1((afp->format == eslMSAFILE_PROFILLIC));
const char * const seqname = "Galosh Profile Consensus";
const char * const msaname = "Galosh Profile";
uint32_t profile_length;
galosh::Sequence<typename ProfileType::ProfileResidueType> consensus_sequence;
stringstream tmp_consensus_output_stream;
uint32_t pos_i;
if (profile_ptr == NULL) { ESL_EXCEPTION(eslEINCONCEIVABLE, "profile_ptr is NULL in profillic_esl_msafile_profile_Read(..)!"); }
//if (feof(afp->bf->fp)) { status = eslEOF; goto ERROR; }
afp->errmsg[0] = '\0';
// Read in the galosh profile (from profillic)
//fseek( afp->bf->fp, 0, SEEK_END ); // go to the end
//len = afp->bf->ftell( afp->bf->fp ); // get the position at the end (length)
//fseek( afp->bf->fp, 0, SEEK_SET ); // go to the beginning again.
//ESL_ALLOC_CPP( char, buf, sizeof( char ) * len ); //malloc buffer
//fread( buf, len, 1, afp->bf->fp ); //read into buffer
//profile_string = buf;
//profile_ptr->fromString( profile_string );
profile_ptr->fromFile( afp->bf->filename );
//if (buf) free(buf);
// \todo WHY WON'T THIS WORK? See HACKs in profillic-hmmbuild.cpp to work around it.
//fseek( afp->bf->fp, 0, SEEK_END ); // go to the end (to signal there's no more profiles in the file, the next time we come to this function)
// Calculate the consensus sequence.
profile_length = profile_ptr->length();
consensus_sequence.reinitialize( profile_length );
for( pos_i = 0; pos_i < profile_length; pos_i++ ) {
consensus_sequence[ pos_i ] =
( *profile_ptr )[ pos_i ][ galosh::Emission::Match ].maximumValueType();
}
tmp_consensus_output_stream << consensus_sequence;
/* Allocate a growable MSA, and auxiliary parse data coupled to the MSA allocation */
#ifdef eslAUGMENT_ALPHABET
if (afp->abc && (msa = esl_msa_CreateDigital(afp->abc, 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
#endif
if (! afp->abc && (msa = esl_msa_Create( 16, -1)) == NULL) { status = eslEMEM; goto ERROR; }
// Set first-and-only seq to the consensus. This should set sqlen[0] to the profile's length and set ax to have length 1 and ax[0] to be the sequence itself. Also msa->sqname[0] to the "name" of that consensus sequence.
/* if nec, make room for the new seq */
if (msa->nseq >= msa->sqalloc && (status = esl_msa_Expand(msa)) != eslOK) return status;
seqidx = msa->nseq; // 0
msa->nseq++; // = 1
status = esl_strdup(seqname, -1, &(msa->sqname[seqidx]));
// NOTE: Could add description of this "sequence" here, using esl_msa_SetSeqDescription(msa, seqidx, desc).
#ifdef eslAUGMENT_ALPHABET
if (msa->flags & eslMSA_DIGITAL)
{
// NOTE (profillic): There was a bug in this; it had said .."esl_abc_dsqcat(msa->abc, " where it should have said .."esl_abc_dsqcat(msa->abc->inmap, "
if((status = esl_abc_dsqcat(msa->abc->inmap, &(msa->ax[seqidx]), &(msa->sqlen[seqidx]), tmp_consensus_output_stream.str().c_str(), profile_length)) != eslOK) {
/* invalid char(s), get informative error message */
if (esl_abc_ValidateSeq(msa->abc, tmp_consensus_output_stream.str().c_str(), profile_length, afp->errmsg) != eslOK)
ESL_XFAIL(eslEFORMAT, errmsg2, "%s (line %d): %s", msa->sqname[0], afp->linenumber, afp->errmsg);
}
}
#endif
if (! (msa->flags & eslMSA_DIGITAL))
{
status = esl_strcat(&(msa->aseq[seqidx]), 0, tmp_consensus_output_stream.str().c_str(), profile_length);
msa->sqlen[seqidx] = profile_length;
}
msa->alen = profile_length;
/// \todo OR read in a fasta file of sequences too.
/// \todo (Optional?) Set msa->name to the name of the profile (file?)
esl_strdup(msaname, -1, &(msa->name));
/// \todo make sure eslMSA_HASWGTS is FALSE .. OR set it to TRUE and set msa->wgt[idx] to 1.0.
/// \note Could have secondary structure (per sequence) too. msa->ss[0]. msa->sslen[0] should be the same as msa->sqlen[0].
/// \todo Investigate what msa->sa and msa->pp are for.
/* Give the newly parsed MSA a good
* going-over, and finalize the fields of the MSA data structure.
* verify_parse will fill in errmsg if it sees a problem.
*/
//if (verify_parse(msa, afp->errmsg) != eslOK) { status = eslEFORMAT; goto ERROR; }
if (( status = esl_msa_SetDefaultWeights(msa)) != eslOK) goto ERROR;
if (ret_msa != NULL) *ret_msa = msa; else esl_msa_Destroy(msa);
return eslOK;
ERROR:
if (msa != NULL) esl_msa_Destroy(msa);
if (ret_msa != NULL) *ret_msa = NULL;
return status;
}
P7_HMM * constructHMM(ESL_MSA *msa, ESL_ALPHABET *abc, int ali_hmm, int frag, P7_HMM **ret_hmm, char *errbuf){
int status;
ESL_GETOPTS *go = esl_getopts_Create(options);
P7_BUILDER *bld = NULL;
P7_BG *bg = NULL;
char *args = NULL;
esl_strcat(&args, -1, "X ", -1);
status = esl_msa_SetName(msa, "Query", -1);
/* Now take this alignment and make an HMM from it */
if(status != eslOK){
ESL_XFAIL(status, errbuf, "Easel MSA SetNAME returned an error %d\n", status);
}
bg = p7_bg_Create(abc);
if(bg == NULL){
ESL_XFAIL(status, errbuf, "Error generating bg\n");
}
if (frag == 1) {
// add --fragthresh 0
esl_strcat(&args, -1, "--fragthresh 0 ", -1);
}
// if these flags are set, then we want a non standard hmm out. Used by the logo server.
if (ali_hmm == 1) {
// observed counts
// arguments "X --pnone --wnone --enone"
esl_strcat(&args, -1, "--pnone --wnone --enone --symfrac 0 ", -1);
}
else if (ali_hmm == 2) {
// weighted counts
// arguments "X --pnone");
esl_strcat(&args, -1, "--pnone --symfrac 0 ", -1);
}
else if (ali_hmm == 3) {
// Create HMM - keep all columns
esl_strcat(&args, -1, "--symfrac 0 ", -1);
}
else {
// no arguments ?
}
// pass in arguments to hmm builder
esl_opt_ProcessSpoof(go, args);
if (args != NULL) free(args);
bld = p7_builder_Create(go, abc);
if(bld == NULL){
ESL_XFAIL(eslEMEM, errbuf, "Error creating builder\n");
}
status = p7_Builder(bld, msa, bg, ret_hmm, NULL, NULL, NULL, NULL);
if (status != eslOK) {
strcpy( errbuf, bld->errbuf );
goto ERROR;
}
p7_bg_Destroy(bg);
p7_builder_Destroy(bld);
esl_getopts_Destroy(go);
return status;
ERROR:
if (bg != NULL) p7_bg_Destroy(bg);
if (bld != NULL) p7_builder_Destroy(bld);
if (go != NULL) esl_getopts_Destroy(go);
return status;
}
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; /* format code for alifiles */
ESL_MSAFILE *afp = NULL; /* open alignment file */
ESL_MSA *msa = NULL; /* multiple sequence alignment */
int status; /* easel return code */
int do_info = TRUE; /* TRUE if -i */
int do_max = FALSE; /* TRUE if -x */
int do_ffreq = FALSE; /* TRUE if --ffreq */
int do_fmin = FALSE; /* TRUE if --fmin */
float fthresh = 0.; /* <x> from -f <x> */
int do_remove_bps = FALSE; /* TRUE if -r */
int do_consistent = FALSE; /* TRUE if -c */
int do_indi2cons = FALSE; /* TRUE if --indi <x> */
int have_cons; /* TRUE if first alignment has consensus sequence */
int do_newcons = FALSE; /* TRUE if we're creating a new consensus structure
* and outputing a new alignment (if -x -f -c or --indi)
*/
int do_a = FALSE; /* TRUE if -a */
char *indi; /* for <x> from --indi <x> */
int nindi_read; /* number of individual sequence SS lines we've read for current alignment */
int a; /* counter over seqs */
int i, i2; /* counter over residues */
int j, j2; /* counter over residues */
int nali; /* counter over alignments */
int **bp = NULL; /* bp[i][j] is number of individual bps exist between aln cols i and j */
int *cur_ct = NULL; /* ct array of basepairs for current sequence */
int *cons_ct = NULL; /* ct array of basepairs for SS_cons being created */
int *xcons_ct = NULL; /* ct array of basepairs for existing SS_cons */
int *ngaps = NULL; /* number of gaps in each alignment position */
FILE *ofp; /* output file (default is stdout) */
int be_verbose = FALSE; /* TRUE to print extra info */
int seqthresh; /* sequence number threshold for defining a bp as consensus (int) ((fthresh * nseq) + 0.5)*/
char *sscons = NULL; /* the new SS_cons line */
FILE *lfp = NULL; /* file to list sequences with conflicting bps to */
int nlist = 0; /* number of sequences listed to list file */
int *nconflictsA; /* number of conflicting bps in seq a's individual structure annotation */
int nconflicts_total = 0; /* total number of conflicts */
int nconflicts_list = 0; /* total number of conflicts in sequences listed to file <x> from -l <x> */
int noverlaps_total = 0; /* total number of overlaps */
int nconsistent_total = 0; /* total number of consistent bps */
int nbps_total = 0; /* total number of bps */
int *nconsistentA; /* number of consistent bps in seq a's individual structure annotation */
int *noverlapsA; /* number of bps in seq a's indi structure that overlap with consensus structure */
int *nbpsA; /* number of bps in seq a's indi structure that overlap with consensus structure */
int ncons_bps = 0; /* number of bps in consensus structure */
int max_noverlaps_aidx;
int max_nconsistent_aidx;
int max_nbps_aidx;
int *removebp; /* removebp[i] is TRUE remove consensus bp [i]:xcons_ct[i] */
int *has_conflict;
int *nmates_l2r; /* half matrix, nmate_l2r[i] = <x>, i < nmate_l2r[i], there are <x> different right mates j for i */
int *nmates_r2l; /* half matrix, nmate_r2l[j] = <x>, j < nmate_r2l[j], there are <x> different left mates i for j */
int lmax; /* with -l, maximum number of conflicts to allow */
int namewidth = 18; /* length of 'SS_cons(consensus)' */
char *namedashes = NULL; /* to store underline for seq name */
/* --fmin related variables */
int nbps = 0;
int prev_nbps = -1;
float fmin;
int inconsistent_flag;
int pknot_flag;
int k,l;
/***********************************************
* 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("\nwhere basic options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
puts("\noptions for defining a new consensus structure (all of these require -o):");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
puts("\noptions for listing sequences based on structure:");
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);
fmt = eslMSAFILE_STOCKHOLM;
/***********************************************
* Open the MSA file; determine alphabet; set for digital input
***********************************************/
if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
if ( (status = esl_msafile_Open(&abc, alifile, NULL, fmt, NULL, &afp)) != eslOK)
esl_msafile_OpenFailure(afp, status);
/* open output file */
if (esl_opt_GetString(go, "-o") != NULL) {
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
esl_fatal("Failed to open -o output file %s\n", esl_opt_GetString(go, "-o"));
} else ofp = NULL;
if (esl_opt_GetString(go, "-l") != NULL) {
if ((lfp = fopen(esl_opt_GetString(go, "-l"), "w")) == NULL)
esl_fatal("Failed to open -l output file %s\n", esl_opt_GetString(go, "-l"));
}
/* determine if we're creating a structure */
do_max = esl_opt_GetBoolean(go, "-x");
if(!(esl_opt_IsDefault(go, "--ffreq"))) {
do_ffreq = TRUE;
fthresh = esl_opt_GetReal(go, "--ffreq");
}
if(!(esl_opt_IsDefault(go, "--fmin"))) {
do_fmin = TRUE;
}
do_remove_bps = esl_opt_GetBoolean(go, "-r");
do_consistent = esl_opt_GetBoolean(go, "-c");
if(!(esl_opt_IsDefault(go, "--indi"))) {
do_indi2cons = TRUE;
}
if(do_max || do_ffreq || do_fmin || do_remove_bps || do_consistent || do_indi2cons) {
do_newcons = TRUE;
}
do_a = esl_opt_GetBoolean(go, "-a");
if(do_a || do_max || do_ffreq || do_fmin || do_remove_bps || do_consistent || do_indi2cons) {
do_info = FALSE;
}
/***********************************************
* Read MSAs one at a time.
***********************************************/
nali = 0;
have_cons = FALSE;
lmax = esl_opt_GetInteger(go, "--lmax");
if(esl_opt_GetBoolean(go, "-v")) be_verbose = TRUE;
while ((status = esl_msafile_Read(afp, &msa)) != eslEOF)
{
if (status != eslOK) esl_msafile_ReadFailure(afp, status);
nali++;
/* determine max length name */
namewidth = 18; /* length of 'SS_cons(consensus)' */
for(i = 0; i < msa->nseq; i++) namewidth = ESL_MAX(namewidth, strlen(msa->sqname[i]));
if(namedashes != NULL) { free(namedashes); }
ESL_ALLOC(namedashes, sizeof(char) * namewidth+1);
namedashes[namewidth] = '\0';
for(i = 0; i < namewidth; i++) namedashes[i] = '-';
ESL_ALLOC(sscons, sizeof(char) * (msa->alen+1));
ESL_ALLOC(cur_ct, sizeof(int) * (msa->alen+1));
ESL_ALLOC(cons_ct, sizeof(int) * (msa->alen+1));
ESL_ALLOC(xcons_ct, sizeof(int) * (msa->alen+1));
ESL_ALLOC(bp, sizeof(int *) * (msa->alen+1));
ESL_ALLOC(removebp, sizeof(int) * (msa->alen+1));
ESL_ALLOC(has_conflict, sizeof(int) * (msa->alen+1));
ESL_ALLOC(nmates_l2r, sizeof(int) * (msa->alen+1));
ESL_ALLOC(nmates_r2l, sizeof(int) * (msa->alen+1));
esl_vec_ISet(cur_ct, (msa->alen+1), 0);
esl_vec_ISet(cons_ct, (msa->alen+1), 0);
esl_vec_ISet(xcons_ct, (msa->alen+1), 0);
esl_vec_ISet(removebp, (msa->alen+1), FALSE);
esl_vec_ISet(has_conflict, (msa->alen+1), FALSE);
esl_vec_ISet(nmates_l2r, (msa->alen+1), 0);
esl_vec_ISet(nmates_r2l, (msa->alen+1), 0);
ESL_ALLOC(nconflictsA, sizeof(int) * msa->nseq);
ESL_ALLOC(noverlapsA, sizeof(int) * msa->nseq);
ESL_ALLOC(nconsistentA, sizeof(int) * msa->nseq);
ESL_ALLOC(nbpsA, sizeof(int) * msa->nseq);
esl_vec_ISet(nconflictsA, msa->nseq, 0);
esl_vec_ISet(noverlapsA, msa->nseq, 0);
esl_vec_ISet(nconsistentA, msa->nseq, 0);
esl_vec_ISet(nbpsA, msa->nseq, 0);
max_noverlaps_aidx = max_nconsistent_aidx = max_nbps_aidx = 0;
nconsistent_total = nbps_total = noverlaps_total = nconflicts_total = nconflicts_list = 0;
for(i = 1; i <= msa->alen; i++) {
ESL_ALLOC(bp[i], sizeof(int) * (msa->alen+1));
esl_vec_ISet(bp[i], (msa->alen+1), 0);
}
/* make sure we have ss_cons and indi ss if we need it */
if(msa->ss_cons == NULL && do_remove_bps) esl_fatal("-r requires all alignments have SS_cons annotation, alignment %d does not.", nali);
if(msa->ss == NULL && do_max) esl_fatal("-x requires all alignments have individual SS annotation, alignment %d does not.", nali);
if(msa->ss == NULL && do_consistent) esl_fatal("-c requires all alignments have individual SS annotation, alignment %d does not.", nali);
if(msa->ss == NULL && do_indi2cons) esl_fatal("--indi requires all alignments have individual SS annotation, alignment %d does not.", nali);
if(msa->ss == NULL && do_ffreq) esl_fatal("--ffreq requires all alignments have individual SS annotation, alignment %d does not.", nali);
if(msa->ss == NULL && do_fmin) esl_fatal("--fmin requires all alignments have individual SS annotation, alignment %d does not.", nali);
if(msa->ss_cons != NULL) {
if((status = esl_wuss2ct(msa->ss_cons, msa->alen, xcons_ct)) != eslOK) {
esl_fatal("Existing SS_cons for alignment %d is invalid.", nali);
}
ncons_bps = 0;
for(i = 1; i <= msa->alen; i++)
if(xcons_ct[i] != 0 && i < xcons_ct[i])
ncons_bps++;
if(nali > 1 && !have_cons)
esl_fatal("the first aln has SS_cons but aln %d lacks it, if one has it, they all must.", nali);
if(nali == 1) have_cons = TRUE;
}
else if (lfp != NULL) {
esl_fatal("the -l option requires existing SS_cons annotation, aln %d lacks it.", nali);
}
else if (do_remove_bps) {
esl_fatal("the -r option requires existing SS_cons annotation, aln %d lacks it.", nali);
}
else if (do_consistent) {
esl_fatal("the -c option requires existing SS_cons annotation, aln %d lacks it.", nali);
}
else {
if(nali > 1 && have_cons)
esl_fatal("the first aln does not have SS_cons but aln %d does, if one has it, they all must.", nali);
}
if(do_info) {
printf("# Per-sequence basepair information:\n");
printf("# Alignment file: %s\n", alifile);
printf("# Alignment idx: %d\n", nali);
if(msa->name != NULL) { printf("# Alignment name: %s\n", msa->name); }
if(have_cons) {
printf("#\n");
printf("# indibp: number of basepairs in the individual sequence SS annotation\n");
printf("# ovrlap: number of indibp basepairs that also exist as consensus basepairs\n");
printf("# cnsist: number of indibp basepairs that do not conflict with any consensus basepairs\n");
printf("# cnflct: number of indibp basepairs that conflict with >= 1 consensus basepairs\n");
printf("#\n");
printf("# A conflict exists between two basepairs in different structures, one between columns i and j\n");
printf("# and the other between columns k and l, if (i == k and j != l) or (j == l and i != k).\n");
printf("#\n");
printf("# %-*s %6s %6s %6s %6s\n", namewidth, "seqname", "indibp", "ovrlap", "cnsist", "cnflct");
printf("# %-*s %6s %6s %6s %6s\n", namewidth, namedashes, "------", "------", "-----", "------");
}
else {
printf("# %-*s %6s\n", namewidth, "seqname", "nbp");
printf("# %-*s %6s\n", namewidth, namedashes, "------");
}
}
nindi_read = 0;
for (a = 0; a < msa->nseq; a++) {
if(msa->ss != NULL && msa->ss[a] != NULL) {
if((status = esl_wuss2ct(msa->ss[a], msa->alen, cur_ct)) != eslOK) {
esl_fatal("SS annotation for sequence %d, aln %d is invalid.\n", (a+1), nali);
}
nindi_read++;
for(i = 1; i <= msa->alen; i++) {
if(i < cur_ct[i]) {
bp[i][cur_ct[i]]++;
if(bp[i][cur_ct[i]] == 1) {
nmates_l2r[i]++;
nmates_r2l[cur_ct[i]]++;
}
}
}
for(i = 1; i <= msa->alen; i++) {
if(cur_ct[i] != 0 && i < cur_ct[i]) {
if(xcons_ct[i] == cur_ct[i]) noverlapsA[a]++;
if((xcons_ct[i] != 0) && (xcons_ct[i] != cur_ct[i])) {
if(be_verbose) { printf("ali: %2d seq %3d (%s) bp %4d:%4d conflicts with consensus bp %4d:%4d\n", nali, a, msa->sqname[a], i, cur_ct[i], i, xcons_ct[i]); }
nconflictsA[a]++;
/* indi bp i:cur_ct[i] conflicts with i:xcons_ct[i] */
removebp[i] = TRUE;
removebp[xcons_ct[i]] = TRUE;
}
else if((xcons_ct[cur_ct[i]] != 0) && (xcons_ct[cur_ct[i]] != i) && (cur_ct[xcons_ct[cur_ct[i]]] == 0)) {
if(be_verbose) { printf("ali: %2d seq %3d (%s) bp %4d:%4d conflicts with consensus bp %4d:%4d\n", nali, a, msa->sqname[a], xcons_ct[i], cur_ct[xcons_ct[i]], xcons_ct[cur_ct[i]], cur_ct[i]); }
nconflictsA[a]++;
/* indi bp i:cur_ct[i] conflicts with xcons_ct[cur_ct[i]]:cur_ct[i] */
removebp[cur_ct[i]] = TRUE;
removebp[xcons_ct[cur_ct[i]]] = TRUE;
}
else nconsistentA[a]++;
}
}
if(nconflictsA[a] > lmax) {
if(lfp != NULL) fprintf(lfp, "%s\n", msa->sqname[a]);
nconflicts_list += nconflictsA[a];
nlist++;
}
nbpsA[a] = nconflictsA[a] + nconsistentA[a];
nconflicts_total += nconflictsA[a];
nconsistent_total += nconsistentA[a];
noverlaps_total += noverlapsA[a];
nbps_total += nbpsA[a];
if(do_info && have_cons) printf(" %-*s %6d %6d %6d %6d\n", namewidth, msa->sqname[a], nbpsA[a], noverlapsA[a], nconsistentA[a], nconflictsA[a]);
if(do_info && !have_cons) printf(" %-*s %6d\n", namewidth, msa->sqname[a], nbpsA[a]);
if(nbpsA[a] > nbpsA[max_nbps_aidx]) max_nbps_aidx = a;
if((noverlapsA[a] > noverlapsA[max_noverlaps_aidx]) || ((noverlapsA[a] == noverlapsA[max_noverlaps_aidx]) && (nbpsA[a] > nbpsA[max_noverlaps_aidx]))) max_noverlaps_aidx = a;
if((nconsistentA[a] > nconsistentA[max_nconsistent_aidx]) || ((nconsistentA[a] == nconsistentA[max_nconsistent_aidx]) && (nbpsA[a] > nbpsA[max_nconsistent_aidx]))) max_nconsistent_aidx = a;
}
else if(do_newcons || esl_opt_GetBoolean(go, "-a")) { esl_fatal("No SS annotation for sequence %d, aln %d.\n", (a+1), nali); }
}
if(do_info && have_cons) {
if(nindi_read > 0) printf("\n");
printf(" %-*s %6d %6d %6d %6d\n", namewidth, "SS_cons(consensus)", ncons_bps, ncons_bps, ncons_bps, 0);
if(nindi_read > 0) {
printf("\n# %6d/%6d (%.3f) overlap\n", noverlaps_total, nbps_total, nbps_total > 0 ? (float) noverlaps_total / (float) nbps_total : 0.);
printf("# %6d/%6d (%.3f) consistent\n", nconsistent_total, nbps_total, nbps_total > 0 ? (float) nconsistent_total / (float) nbps_total: 0.);
printf("# %6d/%6d (%.3f) conflict\n", nconflicts_total, nbps_total, nbps_total > 0 ? (float) nconflicts_total / (float) nbps_total: 0.);
}
else {
printf("# No sequences in the alignment have GR SS annotation.\n");
}
}
if(lfp != NULL) {
printf("# %d/%d sequences with %.3f individual bps on avg that conflict with SS_cons written to %s\n", nlist, msa->nseq, (float) nconflicts_list / (float) nlist, esl_opt_GetString(go, "-l"));
}
/* determine number of gaps per alignment column */
if((status = get_gaps_per_column(msa, &ngaps)) != eslOK) goto ERROR;
/* -x: determine max bp structure OR
* -a: list all conflicts in individual structures */
if(do_max || do_a) {
for(i = 1; i <= msa->alen; i++) {
if(nmates_l2r[i] > 1) {/* list the conflicts */
has_conflict[i] = TRUE;
for(j = 1; j <= msa->alen; j++) {
if(bp[i][j] > 0) {
if(do_a) printf("More than 1 right mates for left mate %4d %4d:%4d bp exists in %4d/%4d seqs (%.3f)\n", i, i, j, bp[i][j], msa->nseq - ngaps[i], (float) bp[i][j] / (float) (msa->nseq - ngaps[i]));
has_conflict[j] = TRUE;
}
}
}
}
for(i = 1; i <= msa->alen; i++) {
if(nmates_r2l[i] > 1) {/* list the conflicts */
has_conflict[i] = TRUE;
for(j = 1; j <= msa->alen; j++) {
if(bp[j][i] > 0) {
if(do_a) printf("More than 1 left mates for right mate %4d %4d:%4d bp exists in %4d/%4d seqs (%.3f)\n", i, j, i, bp[j][i], msa->nseq - ngaps[i], (float) bp[j][i] / (float) (msa->nseq - ngaps[i]));
has_conflict[j] = TRUE;
}
}
}
}
for(i = 1; i <= msa->alen; i++) {
/*printf("conflict[%4d]: %d\n", i, has_conflict[i]);*/
if(nmates_l2r[i] == 1 && (!(has_conflict[i]))) {
j = i+1;
while(bp[i][j] == 0) j++;
cons_ct[i] = j;
cons_ct[j] = i;
}
}
/* remove pseudoknotted bps greedily */
for(i = 1; i <= msa->alen; i++) {
j = cons_ct[i];
if(j != 0 && i < j) {
for(i2 = i+1; i2 <= msa->alen; i2++) {
j2 = cons_ct[i2];
if(j2 != 0 && i2 < j2) {
if((i2 < j) && (j < j2)) {
/*printf("KNOT %4d:%4d (%4d) %4d:%4d (%4d)\n", i, j, bp[i][j], i2, j2, bp[i2][j2]);*/
/* note: remove both if they have equal number of sequences */
if(bp[i][j] <= bp[i2][j2]) {
/*printf("rm %4d:%4d\n", i, j);*/
cons_ct[cons_ct[i]] = 0;
cons_ct[i] = 0;
}
if(bp[i][j] >= bp[i2][j2]) {
/*printf("rm %4d:%4d\n", i2, j2);*/
cons_ct[cons_ct[i2]] = 0;
cons_ct[i2] = 0;
}
}
}
}
}
}
}
/***************************************/
/*PARANOID, second check for knots
for(i = 1; i <= msa->alen; i++) {
j = cons_ct[i];
if(j != 0 && i < j) {
printf("BP: %4d:%4d\n", i, j);
for(i2 = 1; i2 <= msa->alen; i2++) {
j2 = cons_ct[i2];
if(j2 != 0 && i2 < j2) {
if((i2 < j) && (j < j2)) {
if((i < i2)) {
printf("KNOT %4d:%4d (%4d) %4d:%4d (%4d)\n", i, j, bp[i][j], i2, j2, bp[i2][j2]);
}
}
}
}
}
}
******************************************/
/***************************************/
/*PARANOID, check cons_ct for consistency
for(i = 1; i <= msa->alen; i++) {
if(cons_ct[i] != 0) {
if(cons_ct[cons_ct[i]] != i) { printf("ERROR: i: %4d cons_ct[i]: %4d cons_ct[cons_ct[i]]: %4d\n", i, cons_ct[i], cons_ct[cons_ct[i]]); }
}
}
*/
/*PARANOID, write out SS_cons
for(i = 1; i <= msa->alen; i++) {
if(i < cons_ct[i]) printf("<");
else if(cons_ct[i] != 0) { printf(">"); }
else printf(".");
}
printf("\n");
*/
/***************************************/
/* textize alignment */
if((status = esl_msa_Textize(msa)) != eslOK) esl_fatal("ERROR textizing alignment %d\n", nali);
/* --fmin */
if(do_fmin) {
/* define ss_cons */
prev_nbps = -1;
fthresh = 0.99;
inconsistent_flag = pknot_flag = FALSE;
printf("# Defining consensus structure:\n");
printf("# indi SS basepair aln columns i:j (from at least 1 indi SS) will become consensus basepair\n");
printf("# if > <x> individual SS contain i:j as a pair\n");
printf("# We'll search for minimal <x> that gives a consistent consensus structure.\n");
printf("# A consistent structure has each position involved in 0 or 1 basepairs.\n");
printf("#\n");
printf("# Alignment file: %s\n", alifile);
printf("# Alignment idx: %d\n", nali);
printf("# Number of seqs: %d\n", msa->nseq);
printf("#\n");
printf("# %5s %23s %6s\n", "<x>", "nseq-required-with-bp", "numbps");
printf("# %5s %23s %6s\n", "-----", "-----------------------", "------");
while(fthresh >= 0.00 && (inconsistent_flag == FALSE) && (pknot_flag == FALSE)) {
nbps = 0;
seqthresh = (int) (fthresh * msa->nseq);
/*printf("fthresh: %f seqthresh: %d nseq: %d\n", fthresh, seqthresh, msa->nseq);*/
esl_vec_ISet(cons_ct, msa->alen+1, 0);
for(i = 1; i <= msa->alen; i++) {
for(j = i+1; j <= msa->alen; j++) {
if(bp[i][j] > seqthresh) {
if(cons_ct[i] != 0 || cons_ct[j] != 0) {
inconsistent_flag = TRUE;
}
/* check for pseudoknots */
for(k = i+1; k < j; k++) {
l = cons_ct[k];
if((k < l) && (l > j)) {
pknot_flag = TRUE;
}
if((k > l) && (l != 0) && (l < i)) {
pknot_flag = TRUE;
}
}
cons_ct[i] = j;
cons_ct[j] = i;
nbps++;
}
}
}
if(inconsistent_flag)
printf(" %.3f %23d %s\n", fthresh, seqthresh+1, "inconsistent");
else if(pknot_flag)
printf(" %.3f %23d %s\n", fthresh, seqthresh+1, "pseudoknotted");
else {
if(nbps != prev_nbps) {
printf(" %.3f %23d %6d\n", fthresh, seqthresh+1, nbps);
}
fmin = fthresh;
}
fthresh -= 0.01;
prev_nbps = nbps;
}
fthresh = fmin;
esl_vec_ISet(cons_ct, msa->alen+1, 0);
}
/* --ffreq: determine structure by defining consensus bps that occur in <x> fraction of indi structures */
if(do_ffreq || do_fmin) {
if(do_fmin) { printf("#\n# <x> determined to be %.3f\n", fthresh); }
if(do_ffreq) {
printf("# Defining consensus structure:\n");
printf("# indi SS basepair aln columns i:j (from at least 1 indi SS) will become consensus basepair\n");
printf("# if > %f individual SS contain i:j as a pair\n", fthresh);
}
esl_vec_ISet(cons_ct, msa->alen+1, 0);
/* define ss_cons */
seqthresh = (int) (fthresh * msa->nseq);
/*printf("fthresh: %f seqthresh: %d nseq: %d\n", fthresh, seqthresh, msa->nseq);*/
for(i = 1; i <= msa->alen; i++) {
for(j = i+1; j <= msa->alen; j++) {
if(bp[i][j] > seqthresh) {
if(cons_ct[i] != 0) {
esl_fatal("ERROR, two base pairs including position %d satisfy threshold (%d:%d and %d:%d)!\n", i, i, cons_ct[i], i, j);
}
if(cons_ct[j] != 0) {
esl_fatal("ERROR, two base pairs including position %d satisfy threshold (%d:%d and %d:%d)!\n", j, j, cons_ct[j], i, j);
}
cons_ct[i] = j;
cons_ct[j] = i;
}
}
}
}
/* -r: redefine consensus struct by removing any bps that conflict with individual structures */
if(do_remove_bps) {
for(i = 1; i <= msa->alen; i++) {
if(!(removebp[i])) {
cons_ct[i] = xcons_ct[i];
cons_ct[cons_ct[i]] = i;
}
else {
printf("# Removing consensus bp: %d:%d\n", i, xcons_ct[i]);
cons_ct[xcons_ct[i]] = 0;
cons_ct[i] = 0;
}
}
}
/* -c: define consensus structure as indi sequence with highest number of consistent bps with structure OR */
/* --indi: define consensus structure as indi sequence <x> from --indi <x> */
if(do_consistent || do_indi2cons) {
if(do_indi2cons) {
indi = esl_opt_GetString(go, "--indi");
for(a = 0; a < msa->nseq; a++) {
if(strcmp(indi, msa->sqname[a]) == 0) break;
}
if(a == msa->nseq) esl_fatal("ERROR, could not find a sequence named %s in the alignment.\n", indi);
}
else { /* do_consistent */
a = max_nconsistent_aidx;
}
if(msa->ss == NULL || msa->ss[a] == NULL) esl_fatal("ERROR, no individual SS annotation for %s in the alignment.\n", msa->sqname[a]);
if((status = esl_wuss2ct(msa->ss[a], msa->alen, cons_ct)) != eslOK) {
esl_fatal("Second pass... SS annotation for sequence %d, aln %d is invalid.\n", (a), nali);
}
printf("# Defined new SS_cons as SS annotation for %s (%d basepairs)\n", msa->sqname[a], nbpsA[a]);
if(esl_opt_GetBoolean(go, "--rfc") || esl_opt_GetBoolean(go, "--rfindi")) {
if(msa->rf != NULL) { free(msa->rf); msa->rf = NULL; }
if((status = esl_strcat(&(msa->rf), -1, msa->aseq[a], msa->alen)) != eslOK) goto ERROR;
printf("# Defined new RF as %s sequence\n", msa->sqname[a]);
}
}
/* write out alignment with new SS_cons */
if(do_newcons) {
if((status = esl_ct2wuss(cons_ct, msa->alen, sscons)) != eslOK) goto ERROR;
if(msa->ss_cons != NULL) { free(msa->ss_cons); msa->ss_cons = NULL; }
if((status = esl_strcat(&(msa->ss_cons), -1, sscons, msa->alen)) != eslOK) goto ERROR;
status = esl_msafile_Write(ofp, msa, (esl_opt_GetBoolean(go, "--pfam") ? eslMSAFILE_PFAM : eslMSAFILE_STOCKHOLM));
if (status == eslEMEM) esl_fatal("Memory error when outputting alignment\n");
else if (status != eslOK) esl_fatal("Writing alignment file failed with error %d\n", status);
}
free(sscons);
free(cur_ct);
free(cons_ct);
free(xcons_ct);
for(i = 1; i <= msa->alen; i++) free(bp[i]);
free(bp);
esl_msa_Destroy(msa);
}
if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
/* Cleanup, normal return
*/
if(lfp != NULL) fclose(lfp);
if(ofp != NULL) {
printf("# Alignment(s) saved to file %s\n", esl_opt_GetString(go, "-o"));
fclose(ofp);
}
esl_msafile_Close(afp);
esl_getopts_Destroy(go);
return 0;
ERROR:
if(afp) esl_msafile_Close(afp);
if(go) esl_getopts_Destroy(go);
if(msa) esl_msa_Destroy(msa);
if(lfp) fclose(lfp);
if(ofp) fclose(ofp);
esl_fatal("ERROR\n");
return 1;
}
/* Create an SSI index file for open sequence file <sqfp>.
* Both name and accession of sequences are stored as keys.
*/
static void
create_ssi_index(ESL_GETOPTS *go, ESL_SQFILE *sqfp)
{
ESL_NEWSSI *ns = NULL;
ESL_SQ *sq = esl_sq_Create();
int nseq = 0;
char *ssifile = NULL;
uint16_t fh;
int status;
esl_strdup(sqfp->filename, -1, &ssifile);
esl_strcat(&ssifile, -1, ".ssi", 4);
status = esl_newssi_Open(ssifile, TRUE, &ns); /* TRUE is for allowing overwrite. */
if (status == eslENOTFOUND) esl_fatal("failed to open SSI index %s", ssifile);
else if (status == eslEOVERWRITE) esl_fatal("SSI index %s already exists; delete or rename it", ssifile); /* won't happen, see TRUE above... */
else if (status != eslOK) esl_fatal("failed to create a new SSI index");
if (esl_newssi_AddFile(ns, sqfp->filename, sqfp->format, &fh) != eslOK)
esl_fatal("Failed to add sequence file %s to new SSI index\n", sqfp->filename);
printf("Creating SSI index for %s... ", sqfp->filename);
fflush(stdout);
while ((status = esl_sqio_ReadInfo(sqfp, sq)) == eslOK)
{
nseq++;
if (sq->name == NULL) esl_fatal("Every sequence must have a name to be indexed. Failed to find name of seq #%d\n", nseq);
if (esl_newssi_AddKey(ns, sq->name, fh, sq->roff, sq->doff, sq->L) != eslOK)
esl_fatal("Failed to add key %s to SSI index", sq->name);
if (sq->acc[0] != '\0') {
if (esl_newssi_AddAlias(ns, sq->acc, sq->name) != eslOK)
esl_fatal("Failed to add secondary key %s to SSI index", sq->acc);
}
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
/* Determine if the file was suitable for fast subseq lookup. */
if (sqfp->data.ascii.bpl > 0 && sqfp->data.ascii.rpl > 0) {
if ((status = esl_newssi_SetSubseq(ns, fh, sqfp->data.ascii.bpl, sqfp->data.ascii.rpl)) != eslOK)
esl_fatal("Failed to set %s for fast subseq lookup.");
}
/* Save the SSI file to disk */
if (esl_newssi_Write(ns) != eslOK) esl_fatal("Failed to write keys to ssi file %s\n", ssifile);
/* Done - output and exit. */
printf("done.\n");
if (ns->nsecondary > 0)
printf("Indexed %d sequences (%ld names and %ld accessions).\n", nseq, (long) ns->nprimary, (long) ns->nsecondary);
else
printf("Indexed %d sequences (%ld names).\n", nseq, (long) ns->nprimary);
printf("SSI index written to file %s\n", ssifile);
free(ssifile);
esl_sq_Destroy(sq);
esl_newssi_Close(ns);
return;
}
