int main(int argc, char *argv[]) { FILE *infile; char c; int opt_idx; msa_format_type msa_format; struct bgchmm_struct *b = bgchmm_struct_new(0); struct option long_opts[] = { {"bgc", 1, 0, 'B'}, {"estimate-bgc", 1, 0, 'b'}, {"bgc-exp-length", 1, 0, 'L'}, {"estimate-bgc-exp-length", 1, 0, 'l'}, {"bgc-target-coverage", 1, 0, 'C'}, {"estimate-bgc-target-coverage", 1, 0, 'c'}, {"rho", 1, 0, 'R'}, {"cons-exp-length", 1, 0, 'E'}, {"cons-target-coverage", 1, 0, 'T'}, {"scale", 1, 0, 'S'}, {"estimate-scale", 1, 0, 's'}, {"eqfreqs-from-msa", 1, 0, 'f'}, {"output-tracts", 1, 0, 'g'}, {"posteriors", 1, 0, 'p'}, {"output-mods", 1, 0, 'm'}, {"help", 0, 0, 'h'}, {0,0,0,0}}; while ((c = getopt_long(argc, argv, "B:b:L:l:C:c:R:E:T:S:s:f:g:p:m:Wh", long_opts, &opt_idx)) != -1) { switch (c) { case 'B': b->bgc = get_arg_dbl_bounds(optarg, 0, INFTY); break; case 'b': b->estimate_bgc = get_arg_int_bounds(optarg, 0, 1); break; case 'L': b->bgc_expected_length = get_arg_dbl_bounds(optarg, 0, INFTY); break; case 'l': b->estimate_bgc_expected_length = get_arg_int_bounds(optarg, 0, 1); break; case 'C': b->bgc_target_coverage = get_arg_dbl_bounds(optarg, 0, 1); break; case 'c': b->estimate_bgc_target_coverage = get_arg_int_bounds(optarg, 0, 1); break; case 'R': b->rho = get_arg_dbl_bounds(optarg, 0, INFTY); if (b->rho > 1.0) phast_warning("Warning: rho is a scale for conserved states and is usually less than 1, got %f", b->rho); break; case 'E': b->cons_expected_length = get_arg_dbl_bounds(optarg, 0, INFTY); break; case 'T': b->cons_target_coverage = get_arg_dbl_bounds(optarg, 0, 1); break; case 'S': b->scale = get_arg_dbl_bounds(optarg, 0, INFTY); break; case 's': b->estimate_scale = get_arg_int_bounds(optarg, 0, 1); break; case 'f': b->eqfreqs_from_msa = get_arg_int_bounds(optarg, 0, 1); break; case 'g': b->tract_fn = optarg; break; case 'p': if (strcasecmp(optarg, "none")==0) b->post_probs = NONE; else if (strcasecmp(optarg, "wig")==0) b->post_probs = WIG; else if (strcasecmp(optarg, "full")==0) b->post_probs = FULL; else die("--posteriors option expects either none, wig, or full, got %s", optarg); break; case 'm': b->mods_fn = optarg; break; case 'W': b->post_probs = NONE; break; case 'h': printf("%s", HELP); exit(0); case '?': default: die("Bad argument. Try '%s -h'.\n", argv[0]); } } if (optind != argc - 3) die("ERROR: extra or missing arguments. Try '%s -h'.\n", argv[0]); /* read the MSA and make sure there are no sufficient stats (we want to get these later depending on whether coding/noncoding, tuple size will be 3 or 1) */ infile = phast_fopen(argv[optind], "r"); msa_format = msa_format_for_content(infile, 1); if (msa_format == MAF) b->msa = maf_read(infile, NULL, 1, NULL, NULL, NULL, 0, 1, NULL, NO_STRIP, 0); else b->msa = msa_new_from_file_define_format(infile, msa_format, NULL); fclose(infile); infile = phast_fopen(argv[optind+1], "r"); b->mod = tm_new_from_file(infile, 1); fclose(infile); b->foregd_branch = argv[optind+2]; bgcHmm(b); return 0; }
int main(int argc, char *argv[]) { int check_start = 0, check_stop = 0, check_splice = 0, check_nonsense = 0, offset5 = 0, offset3 = 0, opt_idx, i, j, indel_strict = 0, no_output = 0, check_alignment = 0, splice_strict = 0; int ncons_tested, nkept, nconserved_exons; int nce_gap_type[NGAP_TYPES], nconsid[NTYPES], nfail[NTYPES]; double Nfrac = 0.05; char c; MSA *msa; GFF_Set *gff; msa_format_type msa_format = UNKNOWN_FORMAT; List *keepers, *problems = lst_new_ptr(10), *ends_adjusted = lst_new_ptr(1), *starts_adjusted = lst_new_ptr(1), *discards=NULL, *intron_splice = lst_new_ptr(10); char *rseq_fname = NULL; FILE *logf = NULL, *mlogf = NULL, *statsf = NULL, *discardf = NULL; cds_gap_type fshift_mode = FSHIFT_BAD; char *groupby = "transcript_id"; msa_coord_map *map; int *countNs, *countCDSs; FILE *infile; char *msa_fname; struct option long_opts[] = { {"start", 0, 0, 's'}, {"stop", 0, 0, 't'}, {"splice", 0, 0, 'l'}, {"nonsense", 0, 0, 'n'}, {"fshift", 0, 0, 'f'}, {"conserved", 0, 0, 'c'}, {"N-limit", 1, 0, 'N'}, {"clean-gaps", 0, 0, 'e'}, {"indel-strict", 0, 0, 'I'}, {"splice-strict", 0, 0, 'C'}, {"groupby", 1, 0, 'g'}, {"msa-format", 1, 0, 'i'}, {"refseq", 1, 0, 'r'}, {"offset5", 1, 0, 'o'}, {"offset3", 1, 0, 'p'}, {"no-output", 0, 0, 'x'}, {"discards", 1, 0, 'd'}, {"log", 1, 0, 'L'}, {"machine-log", 1, 0, 'M'}, {"stats", 1, 0, 'S'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; while ((c = (char)getopt_long(argc, argv, "N:i:r:L:M:S:g:d:stlnfceICxh", long_opts, &opt_idx)) != -1) { switch(c) { case 's': check_alignment = check_start = 1; break; case 't': check_alignment = check_stop = 1; break; case 'l': check_alignment = check_splice = 1; break; case 'n': check_alignment = check_nonsense = 1; break; case 'f': check_alignment = 1; fshift_mode = FSHIFT_OK; break; case 'c': check_alignment = check_start = check_stop = check_splice = check_nonsense = 1; if (fshift_mode < FSHIFT_OK) fshift_mode = FSHIFT_OK; break; case 'N': Nfrac = get_arg_dbl_bounds(optarg, 0, 1); break; case 'e': check_alignment = 1; if (fshift_mode < CLN_GAPS) fshift_mode = CLN_GAPS; break; case 'I': check_alignment = 1; fshift_mode = NOVRLP_CLN_GAPS; indel_strict = 1; break; case 'C': check_alignment = check_splice = splice_strict = 1; break; case 'g': groupby = optarg; break; case 'i': msa_format = msa_str_to_format(optarg); if (msa_format == UNKNOWN_FORMAT) die("Bad alignment format.\n"); break; case 'r': rseq_fname = optarg; break; case 'o': offset5 = get_arg_int(optarg); break; case 'p': offset3 = get_arg_int(optarg); break; case 'L': logf = phast_fopen(optarg, "w+"); break; case 'M': mlogf = phast_fopen(optarg, "w+"); break; case 'S': statsf = phast_fopen(optarg, "w+"); break; case 'd': discardf = phast_fopen(optarg, "w+"); break; case 'x': no_output = 1; break; case 'h': printf("%s", HELP); exit(0); case '?': die("ERROR: Bad argument. Try the --help option.\n"); } } if (optind + 1 >= argc ) { die("ERROR: Missing required arguments. Try the --help option.\n"); } set_seed(-1); gff = gff_read_set(phast_fopen(argv[optind], "r")); msa_fname = argv[optind+1]; infile = phast_fopen(msa_fname, "r"); if (msa_format == UNKNOWN_FORMAT) msa_format = msa_format_for_content(infile, 1); if (msa_format == MAF) { msa = maf_read(infile, rseq_fname == NULL ? NULL : phast_fopen(rseq_fname, "r"), 1, NULL, NULL, NULL, -1, TRUE, NULL, NO_STRIP, FALSE); } else { msa = msa_new_from_file_define_format(infile, msa_format, NULL); if (msa->ss == NULL) ss_from_msas(msa, 1, 1, NULL, NULL, NULL, -1, 0); } if (!msa->ss->tuple_idx) die("ERROR: need ordered tuples\n"); msa_remove_N_from_alph(msa); /* for backward compatibility (old SS files) */ if (msa->idx_offset != 0) { /* avoids offset problem */ for (i = 0; i < lst_size(gff->features); i++) { GFF_Feature *f = lst_get_ptr(gff->features, i); f->start -= msa->idx_offset; f->end -= msa->idx_offset; } } /* set up coordinate map; assume GFF is for sequence 1 */ map = msa_build_coord_map(msa, 1); /* convert all features */ for (i = 0; i < lst_size(gff->features); i++) { GFF_Feature *f = lst_get_ptr(gff->features, i); int newstart, newend; if (f->start < 0 || f->end < f->start) die("ERROR: bad feature in GFF (start=%d, end=%d).\n", f->start, f->end); newstart = msa_map_seq_to_msa(map, f->start); newend = msa_map_seq_to_msa(map, f->end); if (newstart < 0 || newend < newstart) die("ERROR: unable to map coordinates for feature (start=%d, end=%d).\n", f->start, f->end); f->start = newstart; f->end = newend; } gff_group(gff, groupby); /* do this after coord conversion, or group coords and feature coords will be out of sync */ keepers = lst_new_ptr(lst_size(gff->features)); if (discardf != NULL) discards = lst_new_ptr(lst_size(gff->features)); ncons_tested = nkept = nconserved_exons = 0; for (i = 0; i < NTYPES; i++) nconsid[i] = 0; for (i = 0; i < NTYPES; i++) nfail[i] = 0; for (i = 0; i < NGAP_TYPES; i++) nce_gap_type[i] = 0; countNs = smalloc(msa->nseqs * sizeof(int)); countCDSs = smalloc(msa->nseqs * sizeof(int)); for (i = 0; i < lst_size(gff->groups); i++) { GFF_FeatureGroup *group = lst_get_ptr(gff->groups, i); List *gfeatures = group->features; GFF_Feature *feat; status_type status = OKAY; cds_gap_type gt = FSHIFT_BAD; problems_clear(problems); /* make sure have frame info for CDSs */ for (j = 0; j < lst_size(gfeatures); j++) { feat = lst_get_ptr(gfeatures, j); if (str_equals_charstr(feat->feature, GFF_CDS_TYPE) && feat->frame == GFF_NULL_FRAME) die("ERROR: Missing frame info for CDS.\n"); } /* First, exclude stop codons from cds's, if necessary (simplifies the detection of nonsense mutations). */ exclude_stops(group, starts_adjusted, ends_adjusted); /* In all cases, discard any group for which the reference sequence doesn't have valid splice sites or start/stop codons, or has a premature stop codon */ if (!ref_seq_okay(gfeatures, msa, offset3, indel_strict, splice_strict, problems)) { status = BAD_REF; nfail[BAD_REF]++; } else /* Everything else counts as a potentially valid group */ ncons_tested++; if (status == OKAY && check_alignment) { /* only bother with below if interested in cross-species conservation */ /* Check first to make sure there's alignment across species in the cds; if not, there's no need to look at individual features. */ for (j = 0; j < lst_size(gfeatures); j++) { feat = lst_get_ptr(gfeatures, j); if (str_equals_charstr(feat->feature, GFF_CDS_TYPE) && is_incomplete_alignment(feat, msa)) { status = NO_ALN; nfail[NO_ALN]++; problem_add(problems, feat, NO_ALN, -1, -1); break; } } if (status == OKAY) { /* we have alignment and agreement with the ref seq; now check feature by feature */ lst_clear(intron_splice); for (j = 0; j < msa->nseqs; j++) countNs[j] = countCDSs[j] = 0; for (j = 0; j < lst_size(gfeatures); j++) { feat = lst_get_ptr(gfeatures, j); if (feat->end - 1 >= msa->length) die("ERROR: feature extends beyond alignment (%d >= %d).\n", feat->end - 1, msa->length); if (check_start && str_equals_charstr(feat->feature, GFF_START_TYPE)) { nconsid[BAD_START]++; if (!is_conserved_start(feat, msa)) { status = BAD_START; problem_add(problems, feat, BAD_START, -1, -1); } } else if (check_stop && str_equals_charstr(feat->feature, GFF_STOP_TYPE)) { nconsid[BAD_STOP]++; if (!is_conserved_stop(feat, msa)) { status = BAD_STOP; problem_add(problems, feat, BAD_STOP, -1, -1); } } else if (check_splice && str_equals_charstr(feat->feature, SPLICE_5)) { nconsid[BAD_5_SPLICE]++; if (!is_conserved_5splice(feat, msa, offset5, splice_strict)) { status = BAD_5_SPLICE; problem_add(problems, feat, BAD_5_SPLICE, -1, -1); } else lst_push_ptr(intron_splice, feat); } else if (check_splice && str_equals_charstr(feat->feature, SPLICE_5_UTR)) { nconsid[BAD_5_SPLICE_UTR]++; if (!is_conserved_5splice(feat, msa, offset5, splice_strict)) { status = BAD_5_SPLICE_UTR; problem_add(problems, feat, BAD_5_SPLICE_UTR, -1, -1); } else lst_push_ptr(intron_splice, feat); } else if (check_splice && str_equals_charstr(feat->feature, SPLICE_3)) { nconsid[BAD_3_SPLICE]++; if (!is_conserved_3splice(feat, msa, offset3, splice_strict)) { status = BAD_3_SPLICE; problem_add(problems, feat, BAD_3_SPLICE, -1, -1); } else lst_push_ptr(intron_splice, feat); } else if (check_splice && str_equals_charstr(feat->feature, SPLICE_3)) { nconsid[BAD_3_SPLICE_UTR]++; if (!is_conserved_3splice(feat, msa, offset3, splice_strict)) { status = BAD_3_SPLICE_UTR; problem_add(problems, feat, BAD_3_SPLICE_UTR, -1, -1); } else lst_push_ptr(intron_splice, feat); } else if (str_equals_charstr(feat->feature, GFF_CDS_TYPE)) { if (fshift_mode > FSHIFT_BAD && (gt = get_cds_gap_type(feat, msa, problems)) < fshift_mode) { if (status == OKAY || status == NONSENSE) status = FSHIFT; } if (check_nonsense && !is_nonsense_clean(feat, msa, problems)) { if (status == OKAY) status = NONSENSE; } if (Nfrac < 1) get_N_counts(countNs, countCDSs, feat, msa); } } /* end loop through features in group */ /* still have to make sure splice sites are paired correctly (GT-AG, GC-AG, AT-AC) */ if (status == OKAY && !splice_strict && lst_size(intron_splice) >= 2 && !are_introns_okay(intron_splice, msa, problems, offset5, offset3)) status = BAD_INTRON; /* also check fraction of Ns */ if (Nfrac < 1) { enum {MY_OKAY, MY_FAIL, MY_WARN} Nstatus = MY_OKAY; for (j = 0; j < msa->nseqs; j++) { if ((double)countNs[j] / countCDSs[j] > Nfrac) Nstatus = MY_FAIL; if (Nstatus == MY_OKAY && countNs[j] > 0) Nstatus = MY_WARN; } if (Nstatus == MY_FAIL) { problem_add(problems, NULL, TOO_MANY_Ns, -1, -1); if (status == OKAY) status = TOO_MANY_Ns; } else if (Nstatus == MY_WARN) problem_add(problems, NULL, WARN_Ns, -1, -1); } /* if collecting stats, record counts for failures */ if (statsf != NULL) { if (status != OKAY) { for (j = 0; j < lst_size(problems); j++) { struct Problem *problem = lst_get_ptr(problems, j); status_type ftype = problem->status; if ((ftype == FSHIFT || ftype == NONSENSE) && status != FSHIFT && status != NONSENSE) continue; /* don't count secondary frame shifts and nonsense mutations */ if (ftype == BAD_INTRON && j % 2 == 0) continue; /* only count one of every pair of these */ nfail[ftype]++; } } /* also keep track of the total number of "conserved exons", and the number having each kind of gap */ if ((status == OKAY || (status == FSHIFT && gt >= FSHIFT_OK))) { nconserved_exons++; nce_gap_type[gt]++; /* number of conserved exons having given type of gaps */ } } } /* end if (status == OKAY) [checks for conserved features] */ } /* end if (status == OKAY && check_alignment) [all cross-species checks] */ /* now we have looked at the whole group; we just need to do some final accounting and logging */ if (status == OKAY) { nkept++; if (!no_output) { restore_stops(group, starts_adjusted, ends_adjusted); for (j = 0; j < lst_size(gfeatures); j++) lst_push_ptr(keepers, lst_get_ptr(gfeatures, j)); } if (logf != NULL && lst_size(problems) > 0) /* warnings only */ write_log(logf, group, status, problems, msa, map); if (mlogf != NULL) { /* no problem, need to add an okay status to log */ problem_add(problems, NULL, OKAY, -1, -1); write_machine_log(mlogf, group, problems, map); /* may include warnings */ } } else { if (discardf != NULL) { restore_stops(group, starts_adjusted, ends_adjusted); for (j = 0; j < lst_size(gfeatures); j++) lst_push_ptr(discards, lst_get_ptr(gfeatures, j)); } if (logf != NULL) write_log(logf, group, status, problems, msa, map); if (mlogf != NULL) write_machine_log(mlogf, group, problems, map); } } /* end loop over groups */ /* write main output and discards */ if (!no_output || discardf != NULL) { /* first map features back to coord frame of reference seq. */ for (i = 0; i < lst_size(gff->features); i++) { GFF_Feature *f = lst_get_ptr(gff->features, i); f->start = msa_map_msa_to_seq(map, f->start) + msa->idx_offset; f->end = msa_map_msa_to_seq(map, f->end) + msa->idx_offset; } if (!no_output) { gff->features = keepers; gff_print_set(stdout, gff); } if (discardf != NULL) { gff->features = discards; gff_print_set(discardf, gff); } } /* dump counts to stats file */ if (statsf != NULL) { fprintf(statsf, "#%11s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s %12s\n", "total", "nbad_ref", "nconsid", "nkept", "nno_aln", "nbad_starts", "(out of)", "nbad_stops", "(out of)", "nbad_5spl", "(out of)", "nbad_3spl", "(out of)", "nbad_5utr", "(out of)", "nbad_3utr", "(out of)", "nbad_intron", "nnons", "nfshifts", "nNs", "ncons_exons", "nce_ngaps", "nce_nov_cln", "nce_clean", "nce_fshftok"); fprintf(statsf, "%12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d %12d\n", nfail[BAD_REF]+ncons_tested, nfail[BAD_REF], ncons_tested, nkept, nfail[NO_ALN], nfail[BAD_START], nconsid[BAD_START], nfail[BAD_STOP], nconsid[BAD_STOP], nfail[BAD_5_SPLICE], nconsid[BAD_5_SPLICE], nfail[BAD_3_SPLICE], nconsid[BAD_3_SPLICE], nfail[BAD_5_SPLICE_UTR], nconsid[BAD_5_SPLICE_UTR], nfail[BAD_3_SPLICE_UTR], nconsid[BAD_3_SPLICE_UTR], nfail[BAD_INTRON], nfail[NONSENSE], nfail[FSHIFT], nfail[TOO_MANY_Ns], nconserved_exons, nce_gap_type[NGAPS], nce_gap_type[NOVRLP_CLN_GAPS], nce_gap_type[CLN_GAPS], nce_gap_type[FSHIFT_OK]); fprintf(statsf, "%s", STATS_DESCRIPTION); } if (logf != NULL) phast_fclose(logf); if (mlogf != NULL) phast_fclose(mlogf); if (statsf != NULL) phast_fclose(statsf); if (discardf != NULL) phast_fclose(discardf); return 0; }
int main(int argc, char *argv[]) { char c; int opt_idx, node; FILE *out_f = NULL, *msa_f, *mod_f; char *out_root; TreeModel *mod; MSA *msa; char out_fname[STR_MED_LEN]; struct option long_opts[] = { {"refseq", 1, 0, 'r'}, {"msa-format", 1, 0, 'i'}, {"seqs", 1, 0, 's'}, {"exclude", 0, 0, 'x'}, {"no-probs", 0, 0, 'n'}, {"suff-stats", 0, 0, 'S'}, {"encode", 1, 0, 'e'}, {"keep-gaps", 0, 0, 'k'}, {"gibbs", 1, 0, 'G'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; /* arguments and defaults for options */ FILE *refseq_f = NULL; msa_format_type msa_format = UNKNOWN_FORMAT; int suff_stats = FALSE, exclude = FALSE, keep_gaps = FALSE, do_probs = TRUE; List *seqlist = NULL; PbsCode *code = NULL; int gibbs_nsamples = -1; while ((c = (char)getopt_long(argc, argv, "r:i:s:e:knxSh", long_opts, &opt_idx)) != -1) { switch (c) { case 'r': refseq_f = phast_fopen(optarg, "r"); break; case 'i': msa_format = msa_str_to_format(optarg); if (msa_format == UNKNOWN_FORMAT) die("ERROR: unrecognized alignment format.\n"); break; case 'S': suff_stats = TRUE; break; case 'e': code = pbs_new_from_file(phast_fopen(optarg, "r")); break; case 's': seqlist = get_arg_list(optarg); break; case 'x': exclude = TRUE; break; case 'n': do_probs = FALSE; break; case 'k': keep_gaps = TRUE; break; case 'G': gibbs_nsamples = get_arg_int_bounds(optarg, 1, INFTY); break; case 'h': printf("%s", HELP); exit(0); case '?': die("Bad argument. Try 'prequel -h'.\n"); } } if (optind != argc - 3) die("Three arguments required. Try 'prequel -h'.\n"); set_seed(-1); if (!do_probs && (suff_stats || code != NULL)) die("ERROR: --no-probs can't be used with --suff-stats or --encode.\n"); msa_f = phast_fopen(argv[optind], "r"); if (msa_format == UNKNOWN_FORMAT) msa_format = msa_format_for_content(msa_f, 1); fprintf(stderr, "Reading alignment from %s...\n", argv[optind]); if (msa_format == MAF) { msa = maf_read(msa_f, refseq_f, 1, NULL, NULL, NULL, -1, !suff_stats, NULL, NO_STRIP, FALSE); /* (no need to store order if suff_stats mode) */ } else msa = msa_new_from_file_define_format(msa_f, msa_format, NULL); if (msa->ss == NULL) { fprintf(stderr, "Extracting sufficient statistics...\n"); ss_from_msas(msa, 1, TRUE, NULL, NULL, NULL, -1, 0); } else if (msa->ss->tuple_idx == NULL && !suff_stats) die("ERROR: ordered representation of alignment required unless --suff-stats.\n"); mod_f = phast_fopen(argv[optind+1], "r"); out_root = argv[optind+2]; mod = tm_new_from_file(mod_f, 1); /* MH prune just like in phastcons */ int old_nnodes = mod->tree->nnodes; List *pruned_names = lst_new_ptr(msa->nseqs); tm_prune(mod, msa, pruned_names); if (lst_size(pruned_names) == (old_nnodes + 1) / 2) die("ERROR: no match for leaves of tree in alignment (leaf names must match alignment names).\n"); if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves of tree with no match in alignment ("); int j; for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); tr_name_ancestors(mod->tree); if (mod->order != 0) die("ERROR: Only single nucleotide models are supported.\n"); if (mod->nratecats > 1) die("ERROR: Rate variation not supported.\n"); mod->tree_posteriors = tl_new_tree_posteriors(mod, msa, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE); fprintf(stderr, "Computing posterior probabilities...\n"); if (gibbs_nsamples > 0) die("ERROR: --gibbs not implemented yet."); /* gb_sample_ancestral_seqs(mod, msa, mod->tree_posteriors, gibbs_nsamples); */ else tl_compute_log_likelihood(mod, msa, NULL, NULL, -1, mod->tree_posteriors); fprintf(stderr, "Reconstructing indels by parsimony...\n"); do_indels(msa, mod); for (node = 0; node < mod->tree->nnodes; node++) { int i, j; TreeNode *n = lst_get_ptr(mod->tree->nodes, node); if (n->lchild == NULL || n->rchild == NULL) continue; if (seqlist != NULL) { int in_list = str_in_list_charstr(n->name, seqlist); if ((in_list && exclude) || (!in_list && !exclude)) continue; } fprintf(stderr, "Writing output for ancestral node '%s'...\n", n->name); if (suff_stats) { if (out_f == NULL) { sprintf(out_fname, "%s.stats", out_root); out_f = phast_fopen(out_fname, "w+"); fprintf(out_f, "#count\t"); for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "p(%c)%c", mod->rate_matrix->states[j], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } for (i = 0; i < msa->ss->ntuples; i++) { if (mod->tree_posteriors->base_probs[0][0][node][i] == -1) continue; /* no base this node */ fprintf(out_f, "%.0f\t", msa->ss->counts[i]); for (j = 0; j < mod->rate_matrix->size; j++) { fprintf(out_f, "%f%c", mod->tree_posteriors->base_probs[0][j][node][i], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } } } else if (code == NULL && do_probs) { /* ordinary sequence-by-sequence output */ sprintf(out_fname, "%s.%s.probs", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); fprintf(out_f, "#"); for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "p(%c)%c", mod->rate_matrix->states[j], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); for (i = 0; i < msa->length; i++) { if (mod->tree_posteriors->base_probs[0][0][node][msa->ss->tuple_idx[i]] == -1) { /* no base */ if (keep_gaps) fprintf(out_f, "-\n"); /* otherwise do nothing */ } else for (j = 0; j < mod->rate_matrix->size; j++) fprintf(out_f, "%f%c", mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]], j == mod->rate_matrix->size - 1 ? '\n' : '\t'); } phast_fclose(out_f); } else if (code == NULL && !do_probs) { /* write point estimates to FASTA file */ char *outseq = smalloc((msa->length + 1) * sizeof(char)); int len = 0; for (i = 0; i < msa->length; i++) { if (mod->tree_posteriors->base_probs[0][0][node][msa->ss->tuple_idx[i]] == -1) { /* no base */ if (keep_gaps) outseq[len++] = GAP_CHAR; /* otherwise do nothing */ } else { double maxprob = 0; int maxidx = -1; for (j = 0; j < mod->rate_matrix->size; j++) { if (mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]] > maxprob) { maxprob = mod->tree_posteriors->base_probs[0][j][node][msa->ss->tuple_idx[i]]; maxidx = j; } } outseq[len++] = mod->rate_matrix->states[maxidx]; } } outseq[len] = '\0'; /* print in FASTA format */ sprintf(out_fname, "%s.%s.fa", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); print_seq_fasta(out_f, outseq, n->name, len); phast_fclose(out_f); sfree(outseq); } else { /* encoded sequence-by-sequence output */ double error, tot_error = 0; int ngaps = 0; Vector *v; unsigned *encoded; /* first encode tuple by tuple */ v = vec_new(mod->rate_matrix->size); encoded = smalloc(msa->ss->ntuples * sizeof(unsigned)); for (i = 0; i < msa->ss->ntuples; i++) { if (mod->tree_posteriors->base_probs[0][0][node][i] == -1) { encoded[i] = code->gap_code; ngaps += msa->ss->counts[i]; } else { for (j = 0; j < mod->rate_matrix->size; j++) vec_set(v, j, mod->tree_posteriors->base_probs[0][j][node][i]); encoded[i] = pbs_get_index(code, v, &error); tot_error += error * msa->ss->counts[i]; } } vec_free(v); /* now write site by site */ sprintf(out_fname, "%s.%s.bin", out_root, n->name); out_f = phast_fopen(out_fname, "w+"); for (i = 0; i < msa->length; i++) { if (keep_gaps || encoded[msa->ss->tuple_idx[i]] != code->gap_code) pbs_write_binary(code, encoded[msa->ss->tuple_idx[i]], out_f); } fprintf(stderr, "Average approximation error ('%s'): %f bits\n", n->name, tot_error/(msa->length - ngaps)); sfree(encoded); } } fprintf(stderr, "Done.\n"); return 0; }
int main(int argc, char *argv[]) { char *msa_fname = NULL, *alph = "ACGT"; msa_format_type input_format = UNKNOWN_FORMAT; char c; int opt_idx, seed=-1; String *optstr; List *tmplist = NULL; struct phyloFit_struct *pf; FILE *infile; struct option long_opts[] = { {"msa", 1, 0, 'm'}, {"tree", 1, 0, 't'}, {"subst-mod", 1, 0, 's'}, {"msa-format", 1, 0, 'i'}, {"nrates", 1, 0, 'k'}, {"alpha", 1, 0, 'a'}, {"features", 1, 0, 'g'}, {"catmap", 1, 0, 'c'}, {"log", 1, 0, 'l'}, {"out-root", 1, 0, 'o'}, {"EM", 0, 0, 'E'}, {"error", 1, 0, 'e'}, {"precision", 1, 0, 'p'}, {"do-cats", 1, 0, 'C'}, {"non-overlapping", 0, 0, 'V'}, {"markov", 0, 0, 'N'}, {"reverse-groups", 1, 0, 'R'}, {"init-model", 1, 0, 'M'}, {"init-random", 0, 0, 'r'}, {"init-parsimony", 0, 0, 'y'}, {"print-parsimony", 1, 0, 'Y'}, {"lnl", 0, 0, 'L'}, {"scale-only", 0, 0, 'B'}, {"scale-subtree", 1, 0, 'S'}, {"estimate-freqs", 0, 0, 'F'}, {"sym-freqs", 0, 0, 'W'}, {"no-freqs", 0, 0, 'f'}, {"no-rates", 0, 0, 'n'}, {"no-opt", 1, 0, 'O'}, {"min-informative", 1, 0, 'I'}, {"gaps-as-bases", 0, 0, 'G'}, {"quiet", 0, 0, 'q'}, {"help", 0, 0, 'h'}, {"windows", 1, 0, 'w'}, {"windows-explicit", 1, 0, 'v'}, {"ancestor", 1, 0, 'A'}, {"post-probs", 0, 0, 'P'}, {"expected-subs", 0, 0, 'X'}, {"expected-total-subs", 0, 0, 'Z'}, {"expected-subs-col", 0, 0, 'J'}, {"column-probs", 0, 0, 'U'}, {"rate-constants", 1, 0, 'K'}, {"ignore-branches", 1, 0, 'b'}, {"clock", 0, 0, 'z'}, {"alt-model", 1, 0, 'd'}, {"label-branches", 1, 0, 0}, {"label-subtree", 1, 0, 0}, {"selection", 1, 0, 0}, {"bound", 1, 0, 'u'}, {"seed", 1, 0, 'D'}, {0, 0, 0, 0} }; // NOTE: remaining shortcuts left: HjQx pf = phyloFit_struct_new(0); while ((c = (char)getopt_long(argc, argv, "m:t:s:g:c:C:i:o:k:a:l:w:v:M:p:A:I:K:S:b:d:O:u:Y:e:D:GVENRqLPXZUBFfnrzhWyJ", long_opts, &opt_idx)) != -1) { switch(c) { case 'm': msa_fname = optarg; break; case 't': if (optarg[0] == '(') /* in this case, assume topology given at command line */ pf->tree = tr_new_from_string(optarg); else pf->tree = tr_new_from_file(phast_fopen(optarg, "r")); break; case 's': pf->subst_mod = tm_get_subst_mod_type(optarg); if (pf->subst_mod == UNDEF_MOD) die("ERROR: illegal substitution model. Type \"phyloFit -h\" for usage.\n"); break; case 'g': pf->gff = gff_read_set(phast_fopen(optarg, "r")); break; case 'c': pf->cm = cm_new_string_or_file(optarg); break; case 'C': pf->cats_to_do_str = get_arg_list(optarg); break; case 'V': pf->nonoverlapping = TRUE; break; case 'o': pf->output_fname_root = optarg; break; case 'k': pf->nratecats = get_arg_int_bounds(optarg, 0, INFTY); break; case 'a': pf->alpha = get_arg_dbl(optarg); break; case 'R': pf->reverse_group_tag = optarg; break; case 'i': input_format = msa_str_to_format(optarg); if (input_format == UNKNOWN_FORMAT) die("ERROR: unrecognized alignment format. Type 'phyloFit -h' for usage.\n"); break; case 'l': if (!strcmp(optarg, "-")) pf->logf = stderr; else pf->logf = phast_fopen(optarg, "w+"); break; case 'N': pf->use_conditionals = 1; break; case 'w': tmplist = get_arg_list(optarg); if (lst_size(tmplist) != 2 || str_as_int(lst_get_ptr(tmplist, 0), &(pf->window_size)) != 0 || str_as_int(lst_get_ptr(tmplist, 1), &(pf->window_shift)) != 0) die("ERROR: illegal arguments to --windows.\n"); lst_free_strings(tmplist); lst_free(tmplist); break; case 'v': tmplist = get_arg_list(optarg); if (lst_size(tmplist) % 2 != 0) die("ERROR: argument to --windows-explicit must be a list of even length.\n"); pf->window_coords = str_list_as_int(tmplist); lst_free(tmplist); break; case 'E': pf->use_em = TRUE; break; case 'e': pf->error_fname=optarg; break; case 'p': if (!strcmp(optarg, "LOW")) pf->precision = OPT_LOW_PREC; else if (!strcmp(optarg, "MED")) pf->precision = OPT_MED_PREC; else if (!strcmp(optarg, "HIGH")) pf->precision = OPT_HIGH_PREC; else if (!strcmp(optarg, "VERY_HIGH")) pf->precision = OPT_VERY_HIGH_PREC; else die("ERROR: --precision must be LOW, MED, or HIGH.\n\n"); break; case 'M': pf->input_mod = tm_new_from_file(phast_fopen(optarg, "r"), 1); break; case 'r': pf->random_init = TRUE; break; case 'y': pf->init_parsimony = TRUE; break; case 'Y': pf->init_parsimony = TRUE; pf->parsimony_cost_fname = optarg; pf->parsimony_only=TRUE; break; case 'L': pf->likelihood_only = TRUE; break; case 'q': pf->quiet = TRUE; break; case 'P': pf->do_bases = TRUE; break; case 'X': pf->do_expected_nsubst = TRUE; break; case 'Z': pf->do_expected_nsubst_tot = TRUE; break; case 'J': pf->do_expected_nsubst_col = TRUE; break; case 'U': pf->likelihood_only = TRUE; /* force -L */ pf->nsites_threshold = 0; /* also force this; typical use is with small number of tuples, no tuple_idx */ pf->do_column_probs = TRUE; break; case 'A': pf->root_seqname = optarg; break; case 'I': pf->nsites_threshold = get_arg_int(optarg); break; case 'G': pf->gaps_as_bases = TRUE; alph = "ACGT-"; break; case 'B': pf->estimate_scale_only = TRUE; break; case 'S': pf->subtree_name = optarg; break; case 'F': pf->estimate_backgd = TRUE; break; case 'W': pf->estimate_backgd = TRUE; pf->symfreq = TRUE; break; case 'f': pf->no_freqs = TRUE; break; case 'n': pf->no_rates = TRUE; break; case 'K': tmplist = get_arg_list(optarg); pf->rate_consts = str_list_as_dbl(tmplist); pf->nratecats = lst_size(pf->rate_consts); pf->use_em = 1; lst_free_strings(tmplist); lst_free(tmplist); break; case 'b': pf->ignore_branches = get_arg_list(optarg); break; case 'z': pf->assume_clock = TRUE; break; case 'O': if (pf->nooptstr == NULL) pf->nooptstr = str_new_charstr(optarg); else die("ERROR: no-opt argument can only be used once! parameters can be comma-separated list."); break; case 'd': if (pf->alt_mod_str == NULL) { pf->alt_mod_str = lst_new_ptr(1); } optstr = str_new_charstr(optarg); lst_push_ptr(pf->alt_mod_str, optstr); break; case 0: if (strcmp(long_opts[opt_idx].name, "label-branches") == 0 || strcmp(long_opts[opt_idx].name, "label-subtree") == 0) { optstr = str_new_charstr(optarg); if (pf->label_str == NULL) { pf->label_str = lst_new_ptr(3); pf->label_type = lst_new_int(3); } lst_push_ptr(pf->label_str, optstr); lst_push_int(pf->label_type, strcmp(long_opts[opt_idx].name, "label-branches") == 0 ? BRANCH_TYPE : SUBTREE_TYPE); } else if (strcmp(long_opts[opt_idx].name, "selection") == 0) { pf->selection = get_arg_dbl(optarg); pf->use_selection = TRUE; } else { die("ERROR: unknown option. Type 'phyloFit -h' for usage.\n"); } break; case 'u': if (pf->bound_arg == NULL) pf->bound_arg = lst_new_ptr(1); optstr = str_new_charstr(optarg); lst_push_ptr(pf->bound_arg, optstr); break; case 'D': seed = get_arg_int_bounds(optarg, 1, INFTY); break; case 'h': printf("%s", HELP); exit(0); case '?': die("ERROR: illegal argument. Type 'phyloFit -h' for usage.\n"); } } set_seed(seed); if (msa_fname == NULL) { if (optind >= argc) die("ERROR: missing alignment filename. Type 'phyloFit -h' for usage.\n"); msa_fname = argv[optind]; pf->msa_fname = msa_fname; } infile = phast_fopen(msa_fname, "r"); if (input_format == UNKNOWN_FORMAT) input_format = msa_format_for_content(infile, 1); if (pf->nonoverlapping && (pf->use_conditionals || pf->gff != NULL || pf->cats_to_do_str || input_format == SS)) die("ERROR: cannot use --non-overlapping with --markov, --features,\n--msa-format SS, or --do-cats.\n"); /* read alignment */ if (!pf->quiet) fprintf(stderr, "Reading alignment from %s ...\n", msa_fname); if (input_format == MAF) { pf->msa = maf_read(infile, NULL, tm_order(pf->subst_mod) + 1, NULL, pf->gff, pf->cm, pf->nonoverlapping ? tm_order(pf->subst_mod) + 1 : -1, FALSE, pf->reverse_group_tag, NO_STRIP, FALSE); if (pf->gaps_as_bases) msa_reset_alphabet(pf->msa, alph); } else pf->msa = msa_new_from_file_define_format(infile, input_format, alph); /* set up for categories */ /* first label sites, if necessary */ pf->label_categories = (input_format != MAF); run_phyloFit(pf); if (pf->logf != NULL && pf->logf != stderr && pf->logf != stdout) phast_fclose(pf->logf); if (!pf->quiet) fprintf(stderr, "Done.\n"); sfree(pf); return 0; }
int main(int argc, char *argv[]) { char c; List *l; int i, j, strand, bed_output = 0, backgd_nmods = -1, feat_nmods = -1, winsize = -1, verbose = 0, max_nmods, memblocksize, old_nleaves, refidx = 1, base_by_base = FALSE, windowWig = FALSE; TreeModel **backgd_mods = NULL, **feat_mods = NULL; HMM *backgd_hmm = NULL, *feat_hmm = NULL; msa_format_type inform = UNKNOWN_FORMAT; GFF_Set *features = NULL; MSA *msa, *msa_compl=NULL; double **backgd_emissions, **feat_emissions, **mem, **dummy_emissions, *winscore_pos=NULL, *winscore_neg=NULL; int *no_alignment=NULL; List *pruned_names; char *msa_fname; FILE *infile; int opt_idx; struct option long_opts[] = { {"background-mods", 1, 0, 'b'}, {"background-hmm", 1, 0, 'B'}, {"feature-mods", 1, 0, 'f'}, {"feature-hmm", 1, 0, 'F'}, {"features", 1, 0, 'g'}, {"window", 1, 0, 'w'}, {"window-wig", 1, 0, 'W'}, {"base-by-base", 0, 0, 'y'}, {"msa-format", 1, 0, 'i'}, {"refidx", 1, 0, 'r'}, {"output-bed", 0, 0, 'd'}, {"verbose", 0, 0, 'v'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; while ((c = getopt_long(argc, argv, "B:b:F:f:r:g:w:W:i:ydvh", long_opts, &opt_idx)) != -1) { switch (c) { case 'B': backgd_hmm = hmm_new_from_file(phast_fopen(optarg, "r")); break; case 'b': l = get_arg_list(optarg); backgd_nmods = lst_size(l); backgd_mods = smalloc(backgd_nmods * sizeof(void*)); for (i = 0; i < backgd_nmods; i++) backgd_mods[i] = tm_new_from_file(phast_fopen(((String*)lst_get_ptr(l, i))->chars, "r"), 1); lst_free_strings(l); lst_free(l); break; case 'F': feat_hmm = hmm_new_from_file(phast_fopen(optarg, "r")); break; case 'f': l = get_arg_list(optarg); feat_nmods = lst_size(l); feat_mods = smalloc(feat_nmods * sizeof(void*)); for (i = 0; i < feat_nmods; i++) feat_mods[i] = tm_new_from_file(phast_fopen(((String*)lst_get_ptr(l, i))->chars, "r"), 1); lst_free_strings(l); lst_free(l); break; case 'g': features = gff_read_set(phast_fopen(optarg, "r")); break; case 'w': winsize = get_arg_int(optarg); if (winsize <= 0) die("ERROR: window size must be positive.\n"); break; case 'W': winsize = get_arg_int(optarg); if (winsize <= 0) die("ERROR: window size must be positive.\n"); windowWig = TRUE; break; case 'y': base_by_base = TRUE; break; case 'i': inform = msa_str_to_format(optarg); if (inform == UNKNOWN_FORMAT) die("Bad argument to -i.\n"); break; case 'r': refidx = get_arg_int_bounds(optarg, 0, INFTY); break; case 'd': bed_output = 1; break; case 'h': printf("%s", HELP); exit(0); case 'v': verbose = 1; break; case '?': die("Bad argument. Try '%s -h'.\n", argv[0]); } } set_seed(-1); if (backgd_mods == NULL || feat_mods == NULL) die("ERROR: -b and -f required. Try '%s -h'.\n", argv[0]); if (backgd_nmods == 1 && backgd_hmm == NULL) backgd_hmm = hmm_create_trivial(); else if (backgd_hmm == NULL) die("ERROR: -B required. Try '%s -h'.\n", argv[0]); if (feat_nmods == 1 && feat_hmm == NULL) feat_hmm = hmm_create_trivial(); else if (feat_hmm == NULL) die("ERROR: -F required. Try '%s -h'.\n", argv[0]); if ((winsize == -1 && features == NULL && !base_by_base) || (winsize != -1 && features != NULL) || (winsize != -1 && base_by_base) || (features != NULL && base_by_base)) die("ERROR: must specify exactly one of -g, -w, and -y. Try '%s -h'.\n", argv[0]); if (backgd_hmm->nstates != backgd_nmods) die("ERROR: number of states must equal number of tree models for background.\n"); if (feat_hmm->nstates != feat_nmods) die("ERROR: number of states must equal number of tree models for features.\n"); if (features != NULL && lst_size(features->features) == 0) die("ERROR: empty features file.\n"); if (base_by_base && (backgd_nmods > 1 || feat_nmods > 1)) die("ERROR: only single phylogenetic models (not HMMs) are supported with --base-by-base.\n"); if (optind != argc - 1) die("ERROR: too few arguments. Try '%s -h'.\n", argv[0]); if (verbose) fprintf(stderr, "Reading alignment ...\n"); msa_fname = argv[optind]; infile = phast_fopen(msa_fname, "r"); if (inform == UNKNOWN_FORMAT) inform = msa_format_for_content(infile, 1); if (inform == MAF) msa = maf_read(infile, NULL, 1, NULL, NULL, NULL, -1, TRUE, NULL, NO_STRIP, FALSE); else msa = msa_new_from_file_define_format(infile, inform, NULL); if (msa_alph_has_lowercase(msa)) msa_toupper(msa); msa_remove_N_from_alph(msa); /* need ordered representation of alignment */ if (msa->seqs == NULL && (msa->ss == NULL || msa->ss->tuple_idx == NULL) ) die("ERROR: ordered sufficient statistics are required.\n"); pruned_names = lst_new_ptr(msa->nseqs); for (i = 0; i < backgd_nmods; i++) { old_nleaves = (backgd_mods[i]->tree->nnodes + 1) / 2; tm_prune(backgd_mods[i], msa, pruned_names); if (lst_size(pruned_names) >= old_nleaves) die("ERROR: no match for leaves of tree in alignment (background model #%d)\n", i+1); else if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves in background model (#%d) with no match in alignment (", i+1); for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); } for (i = 0; i < feat_nmods; i++) { old_nleaves = (feat_mods[i]->tree->nnodes + 1) / 2; tm_prune(feat_mods[i], msa, pruned_names); if (lst_size(pruned_names) >= old_nleaves) die("ERROR: no match for leaves of tree in alignment (features model #%d)\n", i+1); else if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves in features model (#%d) with no match in alignment (", i+1); for (j = 0; j < lst_size(pruned_names); j++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, j))->chars, j < lst_size(pruned_names) - 1 ? ", " : ").\n"); } lst_free_strings(pruned_names); } lst_free(pruned_names); /* first have to subtract offset from features, if necessary */ if (msa->idx_offset != 0 && features != NULL) { for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); f->start -= msa->idx_offset; f->end -= msa->idx_offset; } } /* convert to coord frame of alignment */ if (features != NULL && refidx != 0) { if (verbose) fprintf(stderr, "Mapping coordinates ...\n"); msa_map_gff_coords(msa, features, refidx, 0, 0); if (lst_size(features->features) == 0) die("ERROR: no features within coordinate range of alignment.\n"); } /* Make a reverse complemented copy of the alignment. The two strands will be processed separately, to avoid problems with overlapping features, etc. */ if (!base_by_base) { /* skip in base by base case */ if (verbose) fprintf(stderr, "Creating reverse complemented alignment ...\n"); msa_compl = msa_create_copy(msa, 0); /* temporary workaround: make sure reverse complement not based on sufficient stats */ if (msa_compl->seqs == NULL) ss_to_msa(msa_compl); if (msa_compl->ss != NULL) { ss_free(msa_compl->ss); msa_compl->ss = NULL; } msa_reverse_compl(msa_compl); } /* allocate memory for computing scores */ backgd_emissions = smalloc(backgd_nmods * sizeof(void*)); for (i = 0; i < backgd_nmods; i++) backgd_emissions[i] = smalloc(msa->length * sizeof(double)); feat_emissions = smalloc(feat_nmods * sizeof(void*)); for (i = 0; i < feat_nmods; i++) feat_emissions[i] = smalloc(msa->length * sizeof(double)); max_nmods = max(backgd_nmods, feat_nmods); dummy_emissions = smalloc(max_nmods * sizeof(void*)); mem = smalloc(max_nmods * sizeof(void*)); /* memory for forward algorithm -- each block must be as large as the largest feature */ if (features != NULL) { for (i = 0, memblocksize = -1; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); if (f->end - f->start + 1 > memblocksize) memblocksize = f->end - f->start + 1; } } else memblocksize = winsize; /* -1 if base-by-base mode */ if (memblocksize > 0) for (i = 0; i < max_nmods; i++) mem[i] = smalloc(memblocksize * sizeof(double)); if (winsize != -1) { winscore_pos = smalloc(msa->length * sizeof(double)); winscore_neg = smalloc(msa->length * sizeof(double)); no_alignment = smalloc(msa->length * sizeof(int)); for (i = 0; i < msa->length; i++) { winscore_pos[i] = winscore_neg[i] = NEGINFTY; if (refidx == 0) no_alignment[i] = FALSE; else no_alignment[i] = msa_missing_col(msa, refidx, i); } } /* the rest will be repeated for each strand */ for (strand = 1; strand <= 2; strand++) { MSA *thismsa = strand == 1 ? msa : msa_compl; double *winscore = strand == 1 ? winscore_pos : winscore_neg; if (base_by_base && strand == 2) break; /* don't do second pass in base_by_base case */ if (verbose) fprintf(stderr, "Processing %c strand ...\n", strand == 1 ? '+' : '-'); /* set up dummy categories array, so that emissions are only computed where needed */ thismsa->categories = smalloc(thismsa->length * sizeof(int)); thismsa->ncats = 1; if (winsize != -1) { if (strand == 1) for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = no_alignment[i] ? 0 : 1; else for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = no_alignment[thismsa->length - i - 1] ? 0 : 1; } else if (features != NULL) { for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = 0; for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); if (f->start <= 0 || f->end <= 0) { fprintf(stderr, "WARNING: feature out of range ('"); gff_print_feat(stderr, f); fprintf(stderr, "')\n"); continue; } if (strand == 1 && f->strand != '-') for (j = f->start - 1; j < f->end; j++) thismsa->categories[j] = 1; else if (strand == 2 && f->strand == '-') for (j = thismsa->length - f->end; j < thismsa->length - f->start + 1; j++) thismsa->categories[j] = 1; } } else { /* base-by-base scores */ for (i = 0; i < thismsa->length; i++) thismsa->categories[i] = 1; } if (thismsa->ss != NULL) ss_update_categories(thismsa); /* compute emissions */ for (i = 0; i < backgd_nmods; i++) { if (verbose) fprintf(stderr, "Computing emissions for background model #%d ...\n", i+1); tl_compute_log_likelihood(backgd_mods[i], thismsa, backgd_emissions[i], NULL, 1, NULL); } for (i = 0; i < feat_nmods; i++) { if (verbose) fprintf(stderr, "Computing emissions for features model #%d ...\n", i+1); tl_compute_log_likelihood(feat_mods[i], thismsa, feat_emissions[i], NULL, 1, NULL); } /* now compute scores */ if (winsize != -1) { /* windows case */ int winstart; if (verbose) fprintf(stderr, "Computing scores ...\n"); for (winstart = 0; winstart <= thismsa->length - winsize; winstart++) { int centeridx = winstart + winsize/2; if (strand == 2) centeridx = thismsa->length - centeridx - 1; if (no_alignment[centeridx]) continue; for (j = 0; j < feat_nmods; j++) dummy_emissions[j] = &(feat_emissions[j][winstart]); winscore[centeridx] = hmm_forward(feat_hmm, dummy_emissions, winsize, mem); if (winscore[centeridx] <= NEGINFTY) { winscore[centeridx] = NEGINFTY; continue; } for (j = 0; j < backgd_nmods; j++) dummy_emissions[j] = &(backgd_emissions[j][winstart]); winscore[centeridx] -= hmm_forward(backgd_hmm, dummy_emissions, winsize, mem); if (winscore[centeridx] < NEGINFTY) winscore[centeridx] = NEGINFTY; } } else if (features != NULL) { /* features case */ if (verbose) fprintf(stderr, "Computing scores ...\n"); for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); int s, e; if ((strand == 1 && f->strand == '-') || (strand == 2 && f->strand != '-') || f->start <= 0 || f->end <= 0 || f->end - f->start < 0) continue; /* effective coords */ if (f->strand == '-') { s = thismsa->length - f->end + 1; e = thismsa->length - f->start + 1; } else { s = f->start; e = f->end; } f->score_is_null = 0; for (j = 0; j < feat_nmods; j++) dummy_emissions[j] = &(feat_emissions[j][s-1]); f->score = hmm_forward(feat_hmm, dummy_emissions, e - s + 1, mem); if (f->score <= NEGINFTY) { f->score = NEGINFTY; continue; } for (j = 0; j < backgd_nmods; j++) dummy_emissions[j] = &(backgd_emissions[j][s-1]); f->score -= hmm_forward(backgd_hmm, dummy_emissions, e - s + 1, mem); if (f->score < NEGINFTY) f->score = NEGINFTY; } } } if (verbose) fprintf(stderr, "Generating output ...\n"); if (winsize != -1 && windowWig == FALSE) { /* standard windows output */ for (i = 0, j = 0; i < msa->length; i++) { if (no_alignment[i] == FALSE) printf("%d\t%.3f\t%.3f\n", j + msa->idx_offset + 1, winscore_pos[i], winscore_neg[i]); if (ss_get_char_pos(msa, i, 0, 0) != GAP_CHAR) j++; } } else if (windowWig == TRUE) { /* windows with wig output */ int last = NEGINFTY; for (i = 0, j = 0; i < msa->length; i++) { if (refidx == 0 || msa_get_char(msa, refidx-1, i) != GAP_CHAR) { if (no_alignment[i] == FALSE && winscore_pos[i] > NEGINFTY) { if (j > last + 1) printf("fixedStep chrom=%s start=%d step=1\n", refidx > 0 ? msa->names[refidx-1] : "alignment", j + msa->idx_offset + 1); printf("%.3f\n", winscore_pos[i]); last = j; } j++; } } } else if (features != NULL) { /* features output */ /* return to coord frame of reference seq (also, replace offset) */ if (refidx != 0) msa_map_gff_coords(msa, features, 0, refidx, msa->idx_offset); else if (msa->idx_offset != 0) { for (i = 0; i < lst_size(features->features); i++) { GFF_Feature *f = lst_get_ptr(features->features, i); f->start += msa->idx_offset; f->end += msa->idx_offset; } } if (bed_output) gff_print_bed(stdout, features, FALSE); else gff_print_set(stdout, features); } else { /* base-by-base scores */ /* in this case, we can just output the difference between the emissions */ printf("fixedStep chrom=%s start=%d step=1\n", refidx > 0 ? msa->names[refidx-1] : "alignment", msa->idx_offset + 1); for (i = 0, j = 0; i < msa->length; i++) { if (refidx == 0 || msa_get_char(msa, refidx-1, i) != GAP_CHAR) { printf("%.3f\n", feat_emissions[0][i] - backgd_emissions[0][i]); j++; } } } if (verbose) fprintf(stderr, "\nDone.\n"); return 0; }
int main(int argc, char *argv[]) { char c; char *msa_fname = NULL; int opt_idx, i, old_nnodes; MSA *msa; List *pruned_names = lst_new_ptr(5), *tmpl; BDPhyloHmm *bdphmm; GFF_Set *predictions; int found = FALSE; List *ignore_types = lst_new_ptr(1); struct option long_opts[] = { {"refseq", 1, 0, 'M'}, {"msa-format", 1, 0, 'i'}, {"refidx", 1, 0, 'r'}, {"rho", 1, 0, 'R'}, {"phi", 1, 0, 'p'}, {"transitions", 1, 0, 't'}, {"expected-length", 1, 0, 'E'}, {"target-coverage", 1, 0, 'C'}, {"seqname", 1, 0, 'N'}, {"idpref", 1, 0, 'P'}, {"indel-model", 1, 0, 'I'}, {"indel-history", 1, 0, 'H'}, {"help", 0, 0, 'h'}, {0, 0, 0, 0} }; /* arguments and defaults for options */ FILE *refseq_f = NULL, *msa_f = NULL; msa_format_type msa_format = UNKNOWN_FORMAT; TreeModel *source_mod; double rho = DEFAULT_RHO, mu = DEFAULT_MU, nu = DEFAULT_NU, phi = DEFAULT_PHI, gamma = -1, omega = -1, alpha_c = -1, beta_c = -1, tau_c = -1, alpha_n = -1, beta_n = -1, tau_n = -1; int set_transitions = FALSE, refidx = 1, estim_phi = TRUE, estim_gamma = TRUE, estim_omega = TRUE; char *seqname = NULL, *idpref = NULL; IndelHistory *ih = NULL; while ((c = getopt_long(argc, argv, "R:t:p:E:C:r:M:i:N:P:I:H:h", long_opts, &opt_idx)) != -1) { switch (c) { case 'R': rho = get_arg_dbl_bounds(optarg, 0, 1); break; case 't': if (optarg[0] != '~') estim_gamma = estim_omega = FALSE; else optarg = &optarg[1]; set_transitions = TRUE; tmpl = get_arg_list_dbl(optarg); if (lst_size(tmpl) != 2) die("ERROR: bad argument to --transitions.\n"); mu = lst_get_dbl(tmpl, 0); nu = lst_get_dbl(tmpl, 1); if (mu <= 0 || mu >= 1 || nu <= 0 || nu >= 1) die("ERROR: bad argument to --transitions.\n"); lst_free(tmpl); break; case 'p': if (optarg[0] != '~') estim_phi = FALSE; else optarg = &optarg[1]; phi = get_arg_dbl_bounds(optarg, 0, 1); break; case 'E': if (optarg[0] != '~') estim_omega = FALSE; else optarg = &optarg[1]; omega = get_arg_dbl_bounds(optarg, 1, INFTY); mu = 1/omega; break; case 'C': if (optarg[0] != '~') estim_gamma = FALSE; else optarg = &optarg[1]; gamma = get_arg_dbl_bounds(optarg, 0, 1); break; case 'r': refidx = get_arg_int_bounds(optarg, 0, INFTY); break; case 'M': refseq_f = phast_fopen(optarg, "r"); break; case 'i': msa_format = msa_str_to_format(optarg); if (msa_format == UNKNOWN_FORMAT) die("ERROR: unrecognized alignment format.\n"); break; case 'N': seqname = optarg; break; case 'P': idpref = optarg; break; case 'I': tmpl = get_arg_list_dbl(optarg); if (lst_size(tmpl) != 3 && lst_size(tmpl) != 6) die("ERROR: bad argument to --indel-model.\n"); alpha_n = lst_get_dbl(tmpl, 0); beta_n = lst_get_dbl(tmpl, 1); tau_n = lst_get_dbl(tmpl, 2); if (lst_size(tmpl) == 6) { alpha_c = lst_get_dbl(tmpl, 3); beta_c = lst_get_dbl(tmpl, 4); tau_c = lst_get_dbl(tmpl, 5); } else { alpha_c = alpha_n; beta_c = beta_n; tau_c = tau_n; } if (alpha_c <= 0 || alpha_c >= 1 || beta_c <= 0 || beta_c >= 1 || tau_c <= 0 || tau_c >= 1 || alpha_n <= 0 || alpha_n >= 1 || beta_n <= 0 || beta_n >= 1 || tau_n <= 0 || tau_n >= 1) die("ERROR: bad argument to --indel-model.\n"); break; case 'H': fprintf(stderr, "Reading indel history from %s...\n", optarg); ih = ih_new_from_file(phast_fopen(optarg, "r")); break; case 'h': printf("%s", HELP); exit(0); case '?': die("Bad argument. Try 'dless -h'.\n"); } } if (optind != argc - 1) die("Missing alignment file or model file. Try 'dless -h'.\n"); if (set_transitions && (gamma != -1 || omega != -1)) die("ERROR: --transitions and --target-coverage/--expected-length cannot be used together.\n"); if ((gamma != -1 && omega == -1) || (gamma == -1 && omega != -1)) die("ERROR: --target-coverage and --expecteed-length must be used together.\n"); set_seed(-1); if (gamma != -1) nu = gamma/(1-gamma) * mu; fprintf(stderr, "Reading tree model from %s...\n", argv[optind]); source_mod = tm_new_from_file(phast_fopen(argv[optind], "r"), 1); if (source_mod->nratecats > 1) die("ERROR: rate variation not currently supported.\n"); if (source_mod->order > 0) die("ERROR: only single nucleotide models are currently supported.\n"); if (!tm_is_reversible(source_mod)) phast_warning("WARNING: p-value computation assumes reversibility and your model is non-reversible.\n"); /* read alignment */ msa_f = phast_fopen(argv[optind], "r"); fprintf(stderr, "Reading alignment from %s...\n", argv[optind]); if (msa_format == UNKNOWN_FORMAT) msa_format = msa_format_for_content(msa_f, 1); if (msa_format == MAF) { msa = maf_read(msa_f, refseq_f, 1, NULL, NULL, NULL, -1, TRUE, NULL, NO_STRIP, FALSE); } else msa = msa_new_from_file_define_format(msa_f, msa_format, NULL); if (msa_alph_has_lowercase(msa)) msa_toupper(msa); msa_remove_N_from_alph(msa); if (msa->ss == NULL) { fprintf(stderr, "Extracting sufficient statistics...\n"); ss_from_msas(msa, 1, TRUE, NULL, NULL, NULL, -1, 0); } else if (msa->ss->tuple_idx == NULL) die("ERROR: ordered representation of alignment required unless --suff-stats.\n"); /* prune tree, if necessary */ old_nnodes = source_mod->tree->nnodes; tm_prune(source_mod, msa, pruned_names); if (lst_size(pruned_names) == (old_nnodes + 1) / 2) die("ERROR: no match for leaves of tree in alignment (leaf names must match alignment names).\n"); if (lst_size(pruned_names) > 0) { fprintf(stderr, "WARNING: pruned away leaves of tree with no match in alignment ("); for (i = 0; i < lst_size(pruned_names); i++) fprintf(stderr, "%s%s", ((String*)lst_get_ptr(pruned_names, i))->chars, i < lst_size(pruned_names) - 1 ? ", " : ").\n"); } /* this has to be done after pruning tree */ tr_name_ancestors(source_mod->tree); /* also make sure match for reference sequence in tree */ if (refidx > 0) { for (i = 0, found = FALSE; !found && i < source_mod->tree->nnodes; i++) { TreeNode *n = lst_get_ptr(source_mod->tree->nodes, i); if (!strcmp(n->name, msa->names[refidx-1])) found = TRUE; } if (!found) die("ERROR: no match for reference sequence in tree.\n"); } /* checks for indel model */ if (alpha_c > 0) { if (ih == NULL) { fprintf(stderr, "Reconstructing indel history by parsimony...\n"); ih = ih_reconstruct(msa, source_mod->tree); } else { if (ih->ncols != msa->length) die("ERROR: indel history doesn't seem to match alignment.\n"); if (ih->tree->nnodes != source_mod->tree->nnodes) die("ERROR: indel history doesn't seem to match tree model.\n"); } } bdphmm = bd_new(source_mod, rho, mu, nu, phi, alpha_c, beta_c, tau_c, alpha_n, beta_n, tau_n, estim_gamma, estim_omega, estim_phi); /* compute emissions */ phmm_compute_emissions(bdphmm->phmm, msa, FALSE); /* add emissions for indel model, if necessary */ if (alpha_c > 0) { fprintf(stderr, "Adjusting emissions for indels...\n"); bd_add_indel_emissions(bdphmm, ih); } /* postprocess for missing data (requires special handling) */ fprintf(stderr, "Adjusting emissions for missing data...\n"); bd_handle_missing_data(bdphmm, msa); if (estim_gamma || estim_omega || estim_phi) { fprintf(stderr, "Estimating free parameters...\n"); bd_estimate_transitions(bdphmm, msa); } /* set seqname and idpref, if necessary */ if (seqname == NULL || idpref == NULL) { /* derive default from file name root */ String *tmp = str_new_charstr(msa_fname); if (!str_equals_charstr(tmp, "-")) { str_remove_path(tmp); str_root(tmp, '.'); if (idpref == NULL) idpref = copy_charstr(tmp->chars); str_root(tmp, '.'); /* apply one more time for double suffix */ if (seqname == NULL) seqname = tmp->chars; } else if (seqname == NULL) seqname = "refseq"; } /* obtain predictions */ fprintf(stderr, "Running Viterbi algorithm...\n"); predictions = phmm_predict_viterbi(bdphmm->phmm, seqname, NULL, idpref, NULL); lst_push_ptr(ignore_types, str_new_charstr("nonconserved")); gff_filter_by_type(predictions, ignore_types, TRUE, NULL); /* score predictions */ fprintf(stderr, "Scoring predictions...\n"); bd_score_predictions(bdphmm, predictions); /* can free emissions now */ for (i = 0; i < bdphmm->phmm->hmm->nstates; i++) sfree(bdphmm->phmm->emissions[i]); sfree(bdphmm->phmm->emissions); bdphmm->phmm->emissions = NULL; /* convert GFF to coord frame of reference sequence and adjust coords by idx_offset, if necessary */ if (refidx != 0 || msa->idx_offset != 0) msa_map_gff_coords(msa, predictions, 0, refidx, msa->idx_offset); if (refidx != 0) gff_flatten(predictions); /* necessary because coord conversion might create overlapping features (can happen in deletions in reference sequence) */ /* now output predictions */ fprintf(stderr, "Writing GFF to stdout...\n"); gff_print_set(stdout, predictions); fprintf(stderr, "Done.\n"); return 0; }