int main(int argc, char *argv[]) {
char c;
int i, j, t, opt_idx, ntrees, nleaves = -1;
TreeNode *n, *node_i, *node_j, *lca, *nametree = NULL;
TreeNode **tree;
List *leaves, ***distance, *tree_fnames, *tot_dist;
int mod = FALSE;
char **leaf_name;
String *trees_arg;
FILE *F;
struct option long_opts[] = {
{"mod", 0, 0, 'm'},
{"tree", 1, 0, 't'},
{"help", 0, 0, 'h'},
{0, 0, 0, 0}
};
while ((c = getopt_long(argc, argv, "mt:h", long_opts, &opt_idx)) != -1) {
switch (c) {
case 'm':
mod = TRUE;
break;
case 't':
if (optarg[0] == '(')
nametree = tr_new_from_string(optarg);
else
nametree = tr_new_from_file(phast_fopen(optarg, "r"));
break;
case 'h':
usage(argv[0]);
case '?':
die("Bad argument. Try '%s -h'.\n", argv[0]);
}
}
if (optind > argc - 1)
die("Input filename required. Try '%s -h'.\n", argv[0]);
set_seed(-1);
/* build a comma-delimited list and pass to get_arg_list; allows
possibility of reading from file via '*' operator */
trees_arg = str_new(1000);
for (i = optind; i < argc; i++) {
str_append_charstr(trees_arg, argv[i]);
if (i < argc - 1) str_append_char(trees_arg, ',');
}
tree_fnames = get_arg_list(trees_arg->chars);
ntrees = lst_size(tree_fnames);
tree = smalloc(ntrees * sizeof(void*));
/* read trees */
for (t = 0; t < ntrees; t++) {
String *fname = lst_get_ptr(tree_fnames, t);
if (mod) {
TreeModel *m = tm_new_from_file(F = phast_fopen(fname->chars, "r"), 1);
tree[t] = tr_create_copy(m->tree);
tm_free(m);
phast_fclose(F);
}
else
tree[t] = tr_new_from_file(phast_fopen(fname->chars, "r"));
}
/* initialization */
nleaves = (tree[0]->nnodes + 1)/2;
leaves = lst_new_ptr(nleaves);
distance = smalloc(nleaves * sizeof(void*));
leaf_name = smalloc(nleaves * sizeof(void*));
for (i = 0; i < nleaves; i++) {
distance[i] = smalloc(nleaves * sizeof(void*));
for (j = i+1; j < nleaves; j++)
distance[i][j] = lst_new_dbl(ntrees);
}
if (nametree == NULL) nametree = tree[0];
for (i = 0, j = 0; i < lst_size(nametree->nodes); i++) {
n = lst_get_ptr(nametree->nodes, i);
if (n->lchild == NULL && n->rchild == NULL)
leaf_name[j++] = n->name;
}
tot_dist = lst_new_dbl(ntrees);
/* now compute distances */
for (t = 0; t < ntrees; t++) {
/* obtain list of leaves */
lst_clear(leaves);
for (i = 0; i < lst_size(tree[t]->nodes); i++) {
n = lst_get_ptr(tree[t]->nodes, i);
if (n->lchild == NULL && n->rchild == NULL)
lst_push_ptr(leaves, n);
}
if (lst_size(leaves) != nleaves)
die("ERROR: trees have different numbers of leaves.\n");
/* look at all pairs */
for (i = 0; i < nleaves; i++) {
node_i = lst_get_ptr(leaves, i);
for (j = i+1; j < nleaves; j++) {
double dist = 0;
node_j = lst_get_ptr(leaves, j);
/* because ids are assigned in pre-order, the first ancestor of
node j that has an id less than i is the LCA of i and j; we
seek the sum of distances from both i and j to this node */
for (n = node_j; n->id >= node_i->id; n = n->parent)
dist += n->dparent;
lca = n;
for (n = node_i; n != lca; n = n->parent)
dist += n->dparent;
lst_push_dbl(distance[i][j], dist);
}
}
lst_push_dbl(tot_dist, tr_total_len(tree[t]));
}
/* print distances and (optionally) stats */
if (ntrees == 1) {
for (i = 0; i < nleaves; i++) {
for (j = i+1; j < nleaves; j++) {
printf ("%s\t%s\t%f\n", leaf_name[i], leaf_name[j],
lst_get_dbl(distance[i][j], 0));
}
}
printf ("%s\t%s\t%f\n", "(total)", "-", lst_get_dbl(tot_dist, 0));
}
else {
double mean, stdev;
double quantiles[] = {0, 0.025, 0.05, 0.5, 0.95, 0.975, 1};
double quantile_vals[7];
printf("%-15s %-15s %9s %9s %9s %9s %9s %9s %9s %9s %9s\n", "leaf1",
"leaf2", "mean", "stdev", "median", "min", "max", "95%_min",
"95%_max", "90%_min", "90%_max");
for (i = 0; i < nleaves; i++) {
for (j = i+1; j < nleaves; j++) {
mean = lst_dbl_mean(distance[i][j]);
stdev = lst_dbl_stdev(distance[i][j]);
lst_qsort_dbl(distance[i][j], ASCENDING);
lst_dbl_quantiles(distance[i][j], quantiles, 7, quantile_vals);
printf("%-15s %-15s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n",
leaf_name[i], leaf_name[j], mean, stdev, quantile_vals[3], quantile_vals[0],
quantile_vals[6], quantile_vals[1], quantile_vals[5], quantile_vals[2],
quantile_vals[4]);
}
}
/* also do total branch len */
mean = lst_dbl_mean(tot_dist);
stdev = lst_dbl_stdev(tot_dist);
lst_qsort_dbl(tot_dist, ASCENDING);
lst_dbl_quantiles(tot_dist, quantiles, 7, quantile_vals);
printf("%-15s %-15s %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n",
"(total)", "-", mean, stdev, quantile_vals[3], quantile_vals[0],
quantile_vals[6], quantile_vals[1], quantile_vals[5], quantile_vals[2],
quantile_vals[4]);
}
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;
}
int main(int argc, char *argv[]) {
struct phastCons_struct *p = phastCons_struct_new(0);
struct option long_opts[] = {
{"states", 1, 0, 'S'},
{"hmm", 1, 0, 'H'},
{"viterbi", 1, 0, 'V'},
{"most-conserved", 1, 0, 'V'}, /* same as --viterbi */
{"no-post-probs", 0, 0, 'n'},
{"msa-format", 1, 0, 'i'},
{"FC", 0, 0, 'X'},
{"lambda", 1, 0, 'l'},
{"target-coverage", 1, 0, 'C'},
{"transitions", 1, 0, 't'},
{"expected-length", 1, 0, 'E'},
{"expected-lengths", 1, 0, 'E'}, /* for backward compatibility */
{"estimate-trees", 1, 0, 'T'},
{"estimate-rho", 1, 0, 'O'},
{"rho", 1, 0, 'R'},
{"gc", 1, 0, 'G'},
{"ignore-missing", 0, 0, 'z'},
{"nrates", 1, 0, 'k'},
{"log", 1, 0, 'g'},
{"refidx", 1, 0, 'r'},
{"suppress-missing", 0, 0, 'x'}, /* for backward compatibility */
{"reflect-strand", 1, 0, 'U'},
{"catmap", 1, 0, 'c'},
{"extrapolate", 1, 0, 'e'},
{"indels", 0, 0, 'I'},
{"max-micro-indel", 1, 0, 'Y'},
{"indel-params", 1, 0, 'D'},
{"min-informative-types", 1, 0, 'M'}, /* for backward compatibility */
{"require-informative", 1, 0, 'M'},
{"not-informative", 1, 0, 'F'},
{"lnl", 1, 0, 'L'},
{"seqname", 1, 0, 'N'},
{"idpref", 1, 0, 'P'},
{"score", 0, 0, 's'},
{"coding-potential", 0, 0, 'p'},
{"indels-only", 0, 0, 'J'},
{"alias", 1, 0, 'A'},
{"quiet", 0, 0, 'q'},
{"help", 0, 0, 'h'},
{0, 0, 0, 0}
};
/* other vars */
FILE *infile;
char *msa_fname;
char c;
int opt_idx, i, coding_potential=FALSE;
List *tmpl = NULL;
String *tmpstr;
char *mods_fname = NULL;
List *mod_fname_list;
msa_format_type msa_format = UNKNOWN_FORMAT;
while ((c = getopt_long(argc, argv,
"S:H:V:ni:k:l:C:G:zt:E:R:T:O:r:xL:sN:P:g:U:c:e:IY:D:JM:F:pA:Xqh",
long_opts, &opt_idx)) != -1) {
switch (c) {
case 'S':
p->states = get_arg_list(optarg);
break;
case 'H':
p->hmm = hmm_new_from_file(phast_fopen(optarg, "r"));
p->two_state = FALSE;
break;
case 'V':
p->viterbi_f = phast_fopen(optarg, "w+");
tmpstr = str_new_charstr(optarg);
if (str_ends_with_charstr(tmpstr, ".gff"))
p->gff = TRUE;
str_free(tmpstr);
break;
case 'n':
p->post_probs = FALSE;
break;
case 'i':
msa_format = msa_str_to_format(optarg);
if (msa_format == UNKNOWN_FORMAT)
die("ERROR: bad argument to --msa-format\n");
break;
case 'X':
p->FC = TRUE;
p->two_state = FALSE;
break;
case 'l':
if (optarg[0] != '~')
p->estim_lambda = FALSE;
else optarg = &optarg[1];
p->lambda = get_arg_dbl_bounds(optarg, 0, 1);
break;
case 'C':
p->gamma = get_arg_dbl_bounds(optarg, 0, 1);
break;
case 'G':
p->gc = get_arg_dbl_bounds(optarg, 0, 1);
break;
case 't':
p->set_transitions = TRUE;
if (optarg[0] != '~')
p->estim_transitions = FALSE;
else optarg = &optarg[1];
tmpl = get_arg_list_dbl(optarg);
if (lst_size(tmpl) != 2)
die("ERROR: bad argument to --transitions.\n");
p->mu = lst_get_dbl(tmpl, 0);
p->nu = lst_get_dbl(tmpl, 1);
if (p->mu <= 0 || p->mu >= 1 || p->nu <= 0 || p->nu >= 1)
die("ERROR: bad argument to --transitions.\n");
lst_free(tmpl);
break;
case 'E':
if (optarg[0] != '~')
p->estim_transitions = FALSE;
else optarg = &optarg[1];
p->omega = get_arg_dbl_bounds(optarg, 1, INFTY);
p->mu = 1/p->omega;
break;
case 'T':
p->estim_trees = TRUE;
p->estim_trees_fname_root = optarg;
break;
case 'O':
p->estim_rho = TRUE;
p->estim_trees_fname_root = optarg;
break;
case 'z':
p->ignore_missing = TRUE;
break;
case 'k':
tmpl = get_arg_list_int(optarg);
if (lst_size(tmpl) > 2)
die("ERROR: too many arguments with --nrates.\n");
p->nrates = lst_get_int(tmpl, 0);
if (p->nrates <= 0)
die("ERROR: bad argument to --nrates (%d).\n", p->nrates);
if (lst_size(tmpl) == 2) {
p->nrates2 = lst_get_int(tmpl, 1);
if (p->nrates2 <= 0)
die("ERROR: bad argument to --nrates (%d).\n", p->nrates2);
}
lst_free(tmpl);
break;
case 'R':
p->rho = get_arg_dbl_bounds(optarg, 0, 1);
break;
case 'g':
if (!strcmp(optarg, "-"))
p->log_f = stderr;
else p->log_f = phast_fopen(optarg, "w+");
break;
case 'r':
p->refidx = get_arg_int_bounds(optarg, 0, INFTY);
break;
case 'x':
/* do nothing; left in for backward compatibility */
break;
case 'U':
p->pivot_states = get_arg_list(optarg); /* we want strings not ints
for phmm_new */
break;
case 'e':
p->extrapolate_tree_fname = optarg;
break;
case 'I':
p->indels = TRUE;
break;
case 'Y':
p->max_micro_indel = get_arg_int_bounds(optarg, 1, INFTY);
break;
case 'D':
if (optarg[0] != '~')
p->estim_indels = FALSE;
else optarg = &optarg[1];
tmpl = get_arg_list_dbl(optarg);
if (lst_size(tmpl) != 6) die("ERROR: bad argument to --indel-params.\n");
p->alpha_0 = lst_get_dbl(tmpl, 0);
p->beta_0 = lst_get_dbl(tmpl, 1);
p->tau_0 = lst_get_dbl(tmpl, 2);
p->alpha_1 = lst_get_dbl(tmpl, 3);
p->beta_1 = lst_get_dbl(tmpl, 4);
p->tau_1 = lst_get_dbl(tmpl, 5);
if (p->alpha_0 < 0 || p->beta_0 < 0 || p->tau_0 < 0 ||
p->alpha_1 < 0 || p->beta_1 < 0 || p->tau_1 < 0)
die("ERROR: bad argument to --indel-params.\n");
lst_free(tmpl);
break;
case 'J':
p->indels_only = TRUE;
p->two_state = FALSE;
p->indels = TRUE;
p->post_probs = FALSE;
break;
case 'M':
p->inform_reqd = get_arg_list(optarg);
break;
case 'F':
p->not_informative = get_arg_list(optarg);
break;
case 'c':
p->cm = cm_new_string_or_file(optarg);
break;
case 'L':
p->lnl_f = phast_fopen(optarg, "w+");
break;
case 'N':
p->seqname = optarg;
break;
case 'P':
p->idpref = optarg;
break;
case 's':
p->score = TRUE;
break;
case 'p':
coding_potential = TRUE;
break;
case 'A':
p->alias_hash = make_name_hash(optarg);
break;
case 'q':
p->results_f = NULL;
break;
case 'h':
printf("%s", HELP);
exit(0);
case '?':
die("Bad argument. Try '%s -h'.\n", argv[0]);
}
}
if ((!coding_potential && optind != argc - 2) ||
(coding_potential && optind != argc - 2 && optind != argc - 1))
die("ERROR: extra or missing arguments. Try '%s -h'.\n", argv[0]);
set_seed(-1);
if (p->extrapolate_tree_fname != NULL &&
!strcmp(p->extrapolate_tree_fname, "default")) {
p->extrapolate_tree_fname = smalloc((strlen(PHAST_HOME)+100)*sizeof(char));
#if defined(__MINGW32__)
sprintf(p->extrapolate_tree_fname,
"%s\\data\\exoniphy\\mammals\\cftr25_hybrid.nh", PHAST_HOME);
#else
sprintf(p->extrapolate_tree_fname,
"%s/data/exoniphy/mammals/cftr25_hybrid.nh", PHAST_HOME);
#endif
}
if (p->extrapolate_tree_fname != NULL)
p->extrapolate_tree = tr_new_from_file(phast_fopen(p->extrapolate_tree_fname, "r"));
mods_fname = (optind == argc - 2 ? argv[argc - 1] : NULL);
/* if there are two args, mods are the second one; otherwise will
use default mods for coding potential (see below) */
/* set defaults for coding-potential mode */
if (coding_potential) {
char tmp[5000];
p->two_state = FALSE;
if (p->cm == NULL)
p->cm = cm_new_string_or_file("NCATS=4; CNS 1; CDS 2-4");
if (p->hmm == NULL) {
#if defined(__MINGW32__)
sprintf(tmp, "%s\\data\\phastCons\\%s", PHAST_HOME,
p->indels ? "simple-coding-indels.hmm" : "simple-coding.hmm");
#else
sprintf(tmp, "%s/data/phastCons/%s", PHAST_HOME,
p->indels ? "simple-coding-indels.hmm" : "simple-coding.hmm");
#endif
if (p->results_f!=NULL)
fprintf(p->results_f, "Reading HMM from %s...\n", tmp);
p->hmm = hmm_new_from_file(phast_fopen(tmp, "r"));
}
if (mods_fname == NULL) {
#if defined(__MINGW32__)
sprintf(tmp, "%s\\data\\exoniphy\\mammals\\r3.ncns.mod, %s\\data\\exoniphy\\mammals\\r3.cns.mod, %s\\data\\exoniphy\\mammals\\r3.cds-1.mod, %s\\data\\exoniphy\\mammals\\r3.cds-2.mod, %s\\data\\exoniphy\\mammals\\r3.cds-3.mod", PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME);
#else
sprintf(tmp, "\
%s/data/exoniphy/mammals/r3.ncns.mod,\
%s/data/exoniphy/mammals/r3.cns.mod,\
%s/data/exoniphy/mammals/r3.cds-1.mod,\
%s/data/exoniphy/mammals/r3.cds-2.mod,\
%s/data/exoniphy/mammals/r3.cds-3.mod",
PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME, PHAST_HOME);
#endif
mods_fname = tmp;
}
if (p->states == NULL)
p->states = get_arg_list("CDS");
if (p->pivot_states == NULL)
p->pivot_states = get_arg_list("background,CNS");
}
List *pwm_read(const char *filename) {
List *result;
Matrix *pwm = NULL;
int i, currBase, nBases = 0;
FILE * F;
// char *motifName;
String *line = str_new(STR_MED_LEN);
List *l = lst_new_ptr(3);
List *probabilitiesStr = lst_new_ptr(4);
List *probabilitiesDbl;
Regex *pssm_re = NULL;
Regex *motif_name_re = NULL;
int alphabetLength;
result = lst_new_ptr(1);
//letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.5e+004
pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)");
motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*");
//open PWM file
F = phast_fopen(filename, "r");
currBase = 0;
nBases = -1;
//For each line in the MEME file
while ((str_readline(line, F)) != EOF) {
//If line matches Motif name
if (str_re_match(line, motif_name_re, l, 1) > 0) {
// motifName = copy_charstr(((String*)lst_get_ptr(l, 1))->chars);
//printf("motifName=%s\n", motifName);
}
//If line matches beginning of a probability matrix
else if (str_re_match(line, pssm_re, l, 2) > 0) {
//Extract the alphabet size & number of bases in matrix
if (str_as_int((String*)lst_get_ptr(l, 1), &alphabetLength) != 0)
die("ERROR: Unable to parse 'alength=' from MEME file, expected integer, read %s", ((String*)lst_get_ptr(l, 1))->chars);
if (str_as_int((String*)lst_get_ptr(l, 2), &nBases) != 0)
die("ERROR: Unable to parse 'w=' from MEME file, expected integer, read %s ", ((String*)lst_get_ptr(l, 2))->chars);
currBase = 0;
if (nBases <= 0) //We must have at least one base in the PWM
die("ERROR: No Position Weight Matrices were detected in the provided PWM file");
if (alphabetLength <= 0) //We must have a positive alphabet length
die("ERROR: Alphabet lengh specified in PWM file must be greater than zero");
pwm = mat_new(nBases, alphabetLength);
mat_set_all(pwm, -1);
continue;
//If this row contains matrix data
} else if (currBase < nBases) {
//Parse row of probabilities
str_double_trim(line);
str_split(line, NULL, probabilitiesStr);
probabilitiesDbl = str_list_as_dbl(probabilitiesStr);
for (i = 0; i < lst_size(probabilitiesDbl); i++)
mat_set(pwm, currBase, i, log(lst_get_dbl(probabilitiesDbl, i)));
currBase++;
} else if ((currBase == nBases) && (pwm != NULL)) {
//Push full matrix
lst_push_ptr(result, pwm);
pwm = NULL;
}
}
if (currBase == nBases && pwm != NULL)
lst_push_ptr(result, pwm);
else if (pwm != NULL)
die("Premature end of PWM file\n");
str_re_free(motif_name_re);
str_re_free(pssm_re);
phast_fclose(F);
return result;
}
