/* Construct consensus secondary structures from individually annotated * secondary structures * * EPN, Mon May 11 06:49:37 2009 * SVN $Id: esl-alimanip.c 270 2008-06-19 20:45:47Z nawrockie $ */ #include "esl_config.h" #include #include #include #include #include #include #include "easel.h" #include "esl_distance.h" #include "esl_fileparser.h" #include "esl_getopts.h" #include "esl_sq.h" #include "esl_sqio.h" #include "esl_msa.h" #include "esl_distance.h" #include "esl_dmatrix.h" #include "esl_vectorops.h" #include "esl_stack.h" #include "esl_tree.h" #include "esl_wuss.h" #define CONSOPTS "-x,--ffreq,--fmin,-r,-c,--indi" /* exclusive options for defining a new consensus structure */ static char banner[] = "describe or create a consensus secondary structure"; static char usage[] = "[options] \n\ must contain RNA or DNA sequences and be in Stockholm format."; static int get_gaps_per_column(ESL_MSA *msa, int **ret_ngaps); static ESL_OPTIONS options[] = { /* name type default env range togs reqs incomp help docgroup */ { "-h", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "help; show brief info on version and usage", 1}, { "-a", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, CONSOPTS, "print info on all conflicting bps in individual structures", 1}, { "-v", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,NULL, "be verbose", 1 }, /* options for defining new consensus structures */ { "-x", eslARG_NONE, NULL, NULL, NULL, NULL, "-o", CONSOPTS, "set SS_cons as max set of non-conflicting bps from indi SSs", 2 }, { "-r", eslARG_NONE, NULL, NULL, NULL, NULL, "-o", CONSOPTS, "remove SS_cons basepairs that conflicts with > 0 indi SS", 2 }, { "-c", eslARG_NONE, NULL, NULL, NULL, NULL, "-o", CONSOPTS, "set SS_cons as indi SS with max bps consistent with SS_cons", 2 }, { "--rfc", eslARG_NONE, NULL, NULL, NULL, NULL, "-c", NULL, "with -c, set RF annotation as seq SS_cons structure comes from", 2}, { "--indi", eslARG_STRING, NULL, NULL, NULL, NULL, "-o", CONSOPTS, "define SS_cons as individual SS for sequence ", 2 }, { "--rfindi", eslARG_NONE, NULL, NULL, NULL, NULL, "--indi",NULL, "with --indi , define RF annotation as ", 2 }, { "--ffreq", eslARG_REAL, NULL, NULL,"0.<=x<=1", NULL,"-o", CONSOPTS, "aln cols i:j become SS_cons bps if paired in > indi SS", 2}, { "--fmin", eslARG_NONE, NULL, NULL, NULL, NULL, "-o", CONSOPTS, "same as --ffreq but find min that gives consistent SS_cons", 2}, { "-o", eslARG_OUTFILE,NULL, NULL, NULL, NULL, NULL, "-a", "output a new alignment to file ", 2 }, { "--pfam", eslARG_NONE, FALSE, NULL, NULL, NULL, "-o", NULL, "output alignment in Pfam (non-interleaved, 1 line/seq) format", 2 }, /* options for listing sequences based on structural properties */ { "-l", eslARG_OUTFILE,NULL, NULL, NULL, NULL, NULL, NULL, "list seqs w/> 0 indi bp that conflicts w/a SS_cons bp to file ", 3}, { "--lmax", eslARG_INT, "0", NULL, "n>=0", NULL, NULL, NULL, "with -l, change maximum allowed conflicts of 0 to ", 3}, /* options for specifying alphabet */ { "--dna", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL,"--rna", " contain DNA alignments", 4 }, { "--rna", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL,"--dna", " contain RNA alignments", 4 }, { 0,0,0,0,0,0,0,0,0,0 }, }; 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 */ ESLX_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.; /* from -f */ int do_remove_bps = FALSE; /* TRUE if -r */ int do_consistent = FALSE; /* TRUE if -c */ int do_indi2cons = FALSE; /* TRUE if --indi */ char *indi2cons; 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 from --indi */ 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 from -l */ 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] = , i < nmate_l2r[i], there are different right mates j for i */ int *nmates_r2l; /* half matrix, nmate_r2l[j] = , j < nmate_r2l[j], there are 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 = eslx_msafile_Open(&abc, alifile, NULL, fmt, NULL, &afp)) != eslOK) eslx_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; indi2cons = esl_opt_GetString(go, "--indi"); } 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 = eslx_msafile_Read(afp, &msa)) != eslEOF) { if (status != eslOK) eslx_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 */ nbps = 0; 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 > individual SS contain i:j as a pair\n"); printf("# We'll search for minimal 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", "", "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 fraction of indi structures */ if(do_ffreq || do_fmin) { if(do_fmin) { printf("#\n# 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 from --indi */ 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 = eslx_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); } eslx_msafile_Close(afp); esl_getopts_Destroy(go); return 0; ERROR: if(afp) eslx_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; } /* get_gaps_per_column * * Given an MSA, determine the number of gaps per * column, and return a newly allocated array with this * into in *ret_ngaps. */ static int get_gaps_per_column(ESL_MSA *msa, int **ret_ngaps) { int status; int i, apos; int *ngaps = NULL; /* contract check */ if(! (msa->flags & eslMSA_DIGITAL)) { status = eslEINVAL; goto ERROR; } ESL_ALLOC(ngaps, sizeof(int) * (msa->alen+1)); esl_vec_ISet(ngaps, msa->alen+1, 0); for(i = 0; i < msa->nseq; i++) { for(apos = 1; apos <= msa->alen; apos++) ngaps[apos] += esl_abc_XIsGap(msa->abc, msa->ax[i][apos]); } *ret_ngaps = ngaps; return eslOK; ERROR: if(ngaps != NULL) free(ngaps); return status; }