void gt_gff3_output_leading_str(GtFeatureNode *fn, GtStr *outstr)
{
GtGenomeNode *gn;
gt_assert(fn && outstr);
gn = (GtGenomeNode*) fn;
gt_str_append_str(outstr, gt_genome_node_get_seqid(gn));
gt_str_append_char(outstr, '\t');
gt_str_append_cstr(outstr, gt_feature_node_get_source(fn));
gt_str_append_char(outstr, '\t');
gt_str_append_cstr(outstr, gt_feature_node_get_type(fn));
gt_str_append_char(outstr, '\t');
gt_str_append_uword(outstr, gt_genome_node_get_start(gn));
gt_str_append_char(outstr, '\t');
gt_str_append_uword(outstr, gt_genome_node_get_end(gn));
gt_str_append_char(outstr, '\t');
if (gt_feature_node_score_is_defined(fn)) {
char buf[BUFSIZ];
(void) snprintf(buf, BUFSIZ, "%.3g", gt_feature_node_get_score(fn));
gt_str_append_cstr(outstr, buf);
} else
gt_str_append_char(outstr, '.');
gt_str_append_char(outstr, '\t');
gt_str_append_char(outstr, GT_STRAND_CHARS[gt_feature_node_get_strand(fn)]);
gt_str_append_char(outstr, '\t');
gt_str_append_char(outstr, GT_PHASE_CHARS[gt_feature_node_get_phase(fn)]);
gt_str_append_char(outstr, '\t');
}
static void compute_source_statistics(GtFeatureNode *fn,
GtCstrTable *used_sources)
{
const char *source;
gt_assert(fn && used_sources);
source = gt_feature_node_get_source(fn);
if (!gt_cstr_table_get(used_sources, source))
gt_cstr_table_add(used_sources, source);
}
static int feature_node_lua_get_source(lua_State *L)
{
GtGenomeNode **gn = check_genome_node(L, 1);
GtFeatureNode *fn;
/* make sure we get a feature node */
fn = gt_feature_node_try_cast(*gn);
luaL_argcheck(L, fn, 1, "not a feature node");
lua_pushstring(L, gt_feature_node_get_source(fn));
return 1;
}
void gt_gff3_output_leading(GtFeatureNode *fn, GtFile *outfp)
{
GtGenomeNode *gn;
gt_assert(fn);
gn = (GtGenomeNode*) fn;
gt_file_xprintf(outfp, "%s\t%s\t%s\t"GT_WU"\t"GT_WU"\t",
gt_str_get(gt_genome_node_get_seqid(gn)),
gt_feature_node_get_source(fn),
gt_feature_node_get_type(fn),
gt_genome_node_get_start(gn),
gt_genome_node_get_end(gn));
if (gt_feature_node_score_is_defined(fn))
gt_file_xprintf(outfp, "%.3g", gt_feature_node_get_score(fn));
else
gt_file_xfputc('.', outfp);
gt_file_xprintf(outfp, "\t%c\t%c\t",
GT_STRAND_CHARS[gt_feature_node_get_strand(fn)],
GT_PHASE_CHARS[gt_feature_node_get_phase(fn)]);
}
static int select_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn,
GT_UNUSED GtError *err)
{
GtSelectVisitor *fv;
bool filter_node = false;
gt_error_check(err);
fv = select_visitor_cast(nv);
fv->current_feature++;
if ((!gt_str_length(fv->seqid) || /* no seqid was specified or seqids are
equal */
!gt_str_cmp(fv->seqid, gt_genome_node_get_seqid((GtGenomeNode*) fn))) &&
(!gt_str_length(fv->source) || /* no source was specified or sources are
equal */
!strcmp(gt_str_get(fv->source), gt_feature_node_get_source(fn)))) {
GtRange range = gt_genome_node_get_range((GtGenomeNode*) fn);
/* enforce maximum gene length */
/* XXX: we (spuriously) assume that genes are always root nodes */
if (fn && gt_feature_node_has_type(fn, gt_ft_gene)) {
if (fv->max_gene_length != GT_UNDEF_ULONG &&
gt_range_length(&range) > fv->max_gene_length) {
filter_node = true;
}
else if (fv->max_gene_num != GT_UNDEF_ULONG &&
fv->gene_num >= fv->max_gene_num) {
filter_node = true;
}
else if (fv->min_gene_score != GT_UNDEF_DOUBLE &&
gt_feature_node_get_score(fn) < fv->min_gene_score) {
filter_node = true;
}
else if (fv->max_gene_score != GT_UNDEF_DOUBLE &&
gt_feature_node_get_score(fn) > fv->max_gene_score) {
filter_node = true;
}
else if (fv->feature_num != GT_UNDEF_ULONG &&
fv->feature_num != fv->current_feature) {
filter_node = true;
}
if (!filter_node)
fv->gene_num++; /* gene passed filter */
}
}
else
filter_node = true;
if (!filter_node)
filter_node = filter_contain_range(fn, fv->contain_range);
if (!filter_node)
filter_node = filter_overlap_range(fn, fv->overlap_range);
if (!filter_node)
filter_node = filter_strand(fn, fv->strand);
if (!filter_node)
filter_node = filter_targetstrand(fn, fv->targetstrand);
if (!filter_node)
filter_node = filter_has_CDS(fn, fv->has_CDS);
if (!filter_node)
filter_node = filter_min_average_ssp(fn, fv->min_average_splice_site_prob);
if (filter_node)
gt_genome_node_delete((GtGenomeNode*) fn);
else
gt_queue_add(fv->node_buffer, fn);
return 0;
}
