static int gt_seqids_runner(GT_UNUSED int argc, const char **argv,
int parsed_args,
GT_UNUSED void *tool_arguments, GtError *err)
{
GtNodeStream *in_stream, *v_stream;
GtCstrTable *cst;
int had_err = 0;
gt_error_check(err);
cst = gt_cstr_table_new();
in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
v_stream = gt_visitor_stream_new(in_stream, gt_collect_ids_visitor_new(cst));
had_err = gt_node_stream_pull(v_stream, err);
if (!had_err) {
GtStrArray *seqids;
GtUword i;
seqids = gt_cstr_table_get_all(cst);
for (i = 0; i < gt_str_array_size(seqids); i++) {
printf("%s\n", gt_str_array_get(seqids, i));
}
gt_str_array_delete(seqids);
}
gt_node_stream_delete(v_stream);
gt_node_stream_delete(in_stream);
gt_cstr_table_delete(cst);
return had_err;
}
static int sequence_node_add_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSequenceNodeAddStream *s;
int had_err;
gt_error_check(err);
s = gt_sequence_node_add_stream_cast(ns);
/* stream nodes as long as we have some, record seen seqids */
if (!(had_err = gt_node_stream_next(s->in_stream, gn, err)) && *gn) {
had_err = gt_genome_node_accept(*gn, s->collect_vis, err);
}
/* if there are no more */
if (!had_err && !*gn) {
if (!s->seqids) {
s->seqids = gt_cstr_table_get_all(s->seqid_table);
}
gt_assert(s->seqids);
if (s->cur_seqid >= gt_str_array_size(s->seqids)) {
*gn = NULL;
return 0;
} else {
GtGenomeNode *new_sn;
GtUword len;
char *seq = NULL;
GtStr *seqid = gt_str_new(),
*seqstr = gt_str_new();
gt_str_append_cstr(seqid, gt_str_array_get(s->seqids, s->cur_seqid));
had_err = gt_region_mapping_get_sequence_length(s->rm, &len, seqid, err);
if (!had_err) {
had_err = gt_region_mapping_get_sequence(s->rm, &seq, seqid, 1, len,
err);
}
if (!had_err) {
gt_str_append_cstr_nt(seqstr, seq, len);
new_sn = gt_sequence_node_new(gt_str_get(seqid), seqstr);
*gn = new_sn;
}
s->cur_seqid++;
gt_free(seq);
gt_str_delete(seqid);
gt_str_delete(seqstr);
}
}
return had_err;
}
void gt_stat_visitor_show_stats(GtNodeVisitor *nv, GtFile *outfp)
{
GtStatVisitor *sv = stat_visitor_cast(nv);
if (sv->number_of_sequence_regions) {
gt_file_xprintf(outfp, "sequence regions: %lu (total length: %llu)\n",
sv->number_of_sequence_regions,
sv->total_length_of_sequence_regions);
}
if (sv->number_of_multi_features) {
gt_file_xprintf(outfp, "multi-features: %lu\n",
sv->number_of_multi_features);
}
if (sv->number_of_genes)
gt_file_xprintf(outfp, "genes: %lu\n", sv->number_of_genes);
if (sv->number_of_protein_coding_genes) {
gt_file_xprintf(outfp, "protein-coding genes: %lu\n",
sv->number_of_protein_coding_genes);
}
if (sv->number_of_mRNAs)
gt_file_xprintf(outfp, "mRNAs: %lu\n", sv->number_of_mRNAs);
if (sv->number_of_protein_coding_mRNAs) {
gt_file_xprintf(outfp, "protein-coding mRNAs: %lu\n",
sv->number_of_protein_coding_mRNAs);
}
if (sv->number_of_exons)
gt_file_xprintf(outfp, "exons: %lu\n", sv->number_of_exons);
if (sv->number_of_CDSs)
gt_file_xprintf(outfp, "CDSs: %lu\n", sv->number_of_CDSs);
if (sv->number_of_LTR_retrotransposons) {
gt_file_xprintf(outfp, "LTR_retrotransposons: %lu\n",
sv->number_of_LTR_retrotransposons);
}
if (sv->gene_length_distribution) {
gt_file_xprintf(outfp, "gene length distribution:\n");
gt_disc_distri_show(sv->gene_length_distribution, outfp);
}
if (sv->gene_score_distribution) {
gt_file_xprintf(outfp, "gene score distribution:\n");
gt_disc_distri_show(sv->gene_score_distribution, outfp);
}
if (sv->exon_length_distribution) {
gt_file_xprintf(outfp, "exon length distribution:\n");
gt_disc_distri_show(sv->exon_length_distribution, outfp);
}
if (sv->exon_number_distribution) {
gt_file_xprintf(outfp, "exon number distribution:\n");
gt_disc_distri_show(sv->exon_number_distribution, outfp);
}
if (sv->intron_length_distribution) {
gt_file_xprintf(outfp, "intron length distribution:\n");
gt_disc_distri_show(sv->intron_length_distribution, outfp);
}
if (sv->cds_length_distribution) {
gt_file_xprintf(outfp, "CDS length distribution:\n");
gt_disc_distri_show(sv->cds_length_distribution, outfp);
}
if (sv->used_sources) {
GtStrArray *sources;
unsigned long i;
gt_file_xprintf(outfp, "used source tags:\n");
sources = gt_cstr_table_get_all(sv->used_sources);
for (i = 0; i < gt_str_array_size(sources); i++)
gt_file_xprintf(outfp, "%s\n", gt_str_array_get(sources, i));
gt_str_array_delete(sources);
}
}
GtStrArray* gt_gff3_in_stream_plain_get_used_types(GtNodeStream *ns)
{
GtGFF3InStreamPlain *is = gff3_in_stream_plain_cast(ns);
gt_assert(is);
return gt_cstr_table_get_all(is->used_types);
}
