static void write_model(GtStr *str, const char *model_cstr,
const GthBSSMModel *model)
{
GtUword i, j, k, l;
gt_assert(str && model_cstr && model);
gt_assert(model->hypothesis_num == 2 || model->hypothesis_num == 7);
gt_str_append_cstr(str, " ");
gt_str_append_cstr(str, model_cstr);
gt_str_append_cstr(str, " = {\n");
gt_str_append_cstr(str, " hypothesis_num = ");
gt_str_append_uword(str, model->hypothesis_num);
gt_str_append_cstr(str, ",\n");
gt_str_append_cstr(str, " window_size_left = ");
gt_str_append_uword(str, model->window_size_left);
gt_str_append_cstr(str, ",\n");
gt_str_append_cstr(str, " window_size_right = ");
gt_str_append_uword(str, model->window_size_right);
gt_str_append_cstr(str, ",\n");
for (i = 0; i < model->hypothesis_num; i++) {
gt_str_append_cstr(str, " {\n");
for (j = 0; j < WINSIZE + 2; j++) {
gt_str_append_cstr(str, " {\n");
for (k = 0; k < 4; k++) {
gt_str_append_cstr(str, " { ");
for (l = 0; l < 4; l++) {
if (l)
gt_str_append_cstr(str, ", ");
if (model->hypothesis_num == 2) {
gt_str_append_double(str, model->hypotables.hypo2table[i][j][k][l],
BSSM_PRECISION);
}
else {
gt_str_append_double(str, model->hypotables.hypo7table[i][j][k][l],
BSSM_PRECISION);
}
}
gt_str_append_cstr(str, " },\n");
}
gt_str_append_cstr(str, " },\n");
}
gt_str_append_cstr(str, " },\n");
}
gt_str_append_cstr(str, " }");
}
void gt_blast_process_call_set_xdrop_gap_final(GtBlastProcessCall *call,
double xdrop_gap_final)
{
gt_assert(!call->xdrop_gap_final);
call->xdrop_gap_final = true;
gt_assert(call->nucl);
if (call->all)
gt_str_append_cstr(call->str, " -Z ");
else
gt_str_append_cstr(call->str, " -xdrop_gap_final ");
gt_str_append_double(call->str, xdrop_gap_final, 2);
}
GtNodeVisitor* gt_ltrdigest_pdom_visitor_new(GtPdomModelSet *model,
double eval_cutoff,
unsigned int chain_max_gap_length,
GtPdomCutoff cutoff,
GtRegionMapping *rmap,
GtError *err)
{
GtNodeVisitor *nv;
GtLTRdigestPdomVisitor *lv;
GtStr *cmd;
int had_err = 0, i, rval;
gt_assert(model && rmap);
rval = system("hmmscan -h > /dev/null");
if (rval == -1) {
gt_error_set(err, "error executing system(hmmscan)");
return NULL;
}
#ifndef _WIN32
if (WEXITSTATUS(rval) != 0) {
gt_error_set(err, "cannot find the hmmscan executable in PATH");
return NULL;
}
#else
/* XXX */
gt_error_set(err, "hmmscan for Windows not implemented");
return NULL;
#endif
nv = gt_node_visitor_create(gt_ltrdigest_pdom_visitor_class());
lv = gt_ltrdigest_pdom_visitor_cast(nv);
lv->eval_cutoff = eval_cutoff;
lv->cutoff = cutoff;
lv->chain_max_gap_length = chain_max_gap_length;
lv->rmap = rmap;
lv->output_all_chains = false;
lv->tag = gt_str_new_cstr("GenomeTools");
lv->root_type = gt_symbol(gt_ft_LTR_retrotransposon);
for (i = 0; i < 3; i++) {
lv->fwd[i] = gt_str_new();
lv->rev[i] = gt_str_new();
}
if (!had_err) {
cmd = gt_str_new_cstr("hmmscan --cpu ");
gt_str_append_uint(cmd, gt_jobs);
gt_str_append_cstr(cmd, " ");
switch (cutoff) {
case GT_PHMM_CUTOFF_GA:
gt_str_append_cstr(cmd, "--cut_ga");
break;
case GT_PHMM_CUTOFF_TC:
gt_str_append_cstr(cmd, "--cut_tc");
break;
case GT_PHMM_CUTOFF_NONE:
gt_str_append_cstr(cmd, "--domE ");
gt_str_append_double(cmd, eval_cutoff, 50);
break;
}
gt_str_append_cstr(cmd, " ");
gt_str_append_cstr(cmd, gt_pdom_model_set_get_filename(model));
gt_str_append_cstr(cmd, " -");
lv->cmdline = cmd;
lv->args = gt_cstr_split(gt_str_get(lv->cmdline), ' ');
gt_log_log("HMMER cmdline: %s", gt_str_get(cmd));
}
return nv;
}
