static int gff3_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtGFF3Visitor *gff3_visitor;
gt_error_check(err);
gff3_visitor = gff3_visitor_cast(nv);
gt_assert(nv && rn);
gff3_version_string(nv);
if (!gff3_visitor->outstr) {
gt_file_xprintf(gff3_visitor->outfp, "%s %s "GT_WU" "GT_WU"\n",
GT_GFF_SEQUENCE_REGION,
gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn)),
gt_genome_node_get_start((GtGenomeNode*) rn),
gt_genome_node_get_end((GtGenomeNode*) rn));
} else {
gt_str_append_cstr(gff3_visitor->outstr, GT_GFF_SEQUENCE_REGION);
gt_str_append_cstr(gff3_visitor->outstr, " ");
gt_str_append_cstr(gff3_visitor->outstr,
gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn)));
gt_str_append_char(gff3_visitor->outstr, ' ');
gt_str_append_ulong(gff3_visitor->outstr,
gt_genome_node_get_start((GtGenomeNode*) rn));
gt_str_append_char(gff3_visitor->outstr, ' ');
gt_str_append_ulong(gff3_visitor->outstr,
gt_genome_node_get_end((GtGenomeNode*) rn));
gt_str_append_char(gff3_visitor->outstr, '\n');
}
return 0;
}
static int gt_sort_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSortStream *sort_stream;
GtGenomeNode *node, *eofn;
int had_err = 0;
gt_error_check(err);
sort_stream = gt_sort_stream_cast(ns);
if (!sort_stream->sorted) {
while (!(had_err = gt_node_stream_next(sort_stream->in_stream, &node,
err)) && node) {
if ((eofn = gt_eof_node_try_cast(node)))
gt_genome_node_delete(eofn); /* get rid of EOF nodes */
else
gt_array_add(sort_stream->nodes, node);
}
if (!had_err) {
gt_genome_nodes_sort_stable(sort_stream->nodes);
sort_stream->sorted = true;
}
}
if (!had_err) {
gt_assert(sort_stream->sorted);
if (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
*gn = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
sort_stream->idx++;
/* join region nodes with the same sequence ID */
if (gt_region_node_try_cast(*gn)) {
GtRange range_a, range_b;
while (sort_stream->idx < gt_array_size(sort_stream->nodes)) {
node = *(GtGenomeNode**) gt_array_get(sort_stream->nodes,
sort_stream->idx);
if (!gt_region_node_try_cast(node) ||
gt_str_cmp(gt_genome_node_get_seqid(*gn),
gt_genome_node_get_seqid(node))) {
/* the next node is not a region node with the same ID */
break;
}
range_a = gt_genome_node_get_range(*gn);
range_b = gt_genome_node_get_range(node);
range_a = gt_range_join(&range_a, &range_b);
gt_genome_node_set_range(*gn, &range_a);
gt_genome_node_delete(node);
sort_stream->idx++;
}
}
return 0;
}
}
if (!had_err) {
gt_array_reset(sort_stream->nodes);
*gn = NULL;
}
return had_err;
}
void gt_region_node_consolidate(GtRegionNode *rn_a, GtRegionNode *rn_b)
{
GtRange range_a, range_b;
gt_assert(rn_a);
gt_assert(rn_b);
gt_assert(!gt_str_cmp(gt_genome_node_get_seqid((GtGenomeNode*) rn_a),
gt_genome_node_get_seqid((GtGenomeNode*) rn_b)));
range_a = gt_genome_node_get_range((GtGenomeNode*) rn_a);
range_b = gt_genome_node_get_range((GtGenomeNode*) rn_b);
range_a = gt_range_join(&range_a, &range_b);
gt_genome_node_set_range((GtGenomeNode*) rn_a, &range_a);
}
static int pdom_hit_attach_gff3(GtPdomModel *model, GtPdomModelHit *hit,
void *data, GT_UNUSED GtError *err)
{
unsigned long i;
GtRange rng;
GtLTRdigestStream *ls = (GtLTRdigestStream *) data;
GtStrand strand;
gt_assert(model && hit);
strand = gt_pdom_model_hit_get_best_strand(hit);
/* do not use the hits on the non-predicted strand
-- maybe identify nested elements ? */
if (strand != gt_feature_node_get_strand(ls->element.mainnode))
return 0;
for (i=0;i<gt_pdom_model_hit_best_chain_length(hit);i++)
{
GtGenomeNode *gf;
GtStr *alignmentstring,
*aastring;
GtPdomSingleHit *singlehit;
GtPhase frame;
singlehit = gt_pdom_model_hit_best_single_hit(hit, i);
alignmentstring = gt_str_new();
aastring = gt_str_new();
frame = gt_pdom_single_hit_get_phase(singlehit);
rng = gt_pdom_single_hit_get_range(singlehit);
gt_pdom_single_hit_format_alignment(singlehit, GT_ALIWIDTH,
alignmentstring);
gt_pdom_single_hit_get_aaseq(singlehit, aastring);
rng.start++; rng.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
ls->element.mainnode),
GT_PDOM_TYPE,
rng.start,
rng.end,
strand);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_alignment",
alignmentstring, (GtFree) gt_str_delete);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_aaseq",
aastring, (GtFree) gt_str_delete);
gt_feature_node_set_source((GtFeatureNode*) gf, ls->ltrdigest_tag);
gt_feature_node_set_score((GtFeatureNode*) gf,
gt_pdom_single_hit_get_evalue(singlehit));
gt_feature_node_set_phase((GtFeatureNode*) gf, frame);
if (gt_pdom_model_get_name(model)) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "name",
gt_pdom_model_get_name(model));
}
if (gt_pdom_model_get_acc(model)) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "id",
gt_pdom_model_get_acc(model));
}
gt_feature_node_add_child(ls->element.mainnode, (GtFeatureNode*) gf);
}
return 0;
}
static int md5_to_seqid(GtGenomeNode *gn, GtRegionMapping *region_mapping,
GtError *err)
{
GtStr *seqid;
int had_err = 0;
gt_error_check(err);
gt_assert(gn && region_mapping);
seqid = gt_genome_node_get_seqid(gn);
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
/* seqid is a MD5 seqid -> change id */
GtStr *desc = gt_str_new();
had_err = gt_region_mapping_get_description(region_mapping, desc, seqid,
err);
if (!had_err) {
GtStr *new_seqid = gt_str_new();
gt_regular_seqid_save(new_seqid, desc);
if (gt_feature_node_try_cast(gn)) {
M2IChangeSeqidInfo info;
info.new_seqid = new_seqid;
info.region_mapping = region_mapping;
had_err = gt_feature_node_traverse_children((GtFeatureNode*) gn, &info,
m2i_change_seqid, true,
err);
}
else
gt_genome_node_change_seqid(gn, new_seqid);
gt_str_delete(new_seqid);
}
gt_str_delete(desc);
}
return had_err;
}
static int gt_regioncov_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn,
GT_UNUSED GtError *err)
{
GtRange *old_range_ptr, old_range, new_range;
GtArray *ranges;
GtRegionCovVisitor *regioncov_visitor;
gt_error_check(err);
regioncov_visitor = gt_regioncov_visitor_cast(nv);
ranges = gt_hashmap_get(regioncov_visitor->region2rangelist,
gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
fn)));
gt_assert(ranges);
new_range = gt_genome_node_get_range((GtGenomeNode*) fn);
if (!gt_array_size(ranges))
gt_array_add(ranges, new_range);
else {
old_range_ptr = gt_array_get_last(ranges);
old_range = *old_range_ptr;
old_range.end += regioncov_visitor->max_feature_dist;
if (gt_range_overlap(&old_range, &new_range)) {
old_range_ptr->end = MAX(old_range_ptr->end, new_range.end);
}
else
gt_array_add(ranges, new_range);
}
return 0;
}
static int select_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtSelectVisitor *select_visitor;
gt_error_check(err);
select_visitor = select_visitor_cast(nv);
if (!gt_str_length(select_visitor->seqid) || /* no seqid was specified */
!gt_str_cmp(select_visitor->seqid, /* or seqids are equal */
gt_genome_node_get_seqid((GtGenomeNode*) rn))) {
if (select_visitor->contain_range.start != GT_UNDEF_ULONG) {
GtRange range = gt_genome_node_get_range((GtGenomeNode*) rn);
if (gt_range_overlap(&range, &select_visitor->contain_range)) {
/* an overlapping contain range was defined -> update range */
range.start = MAX(range.start, select_visitor->contain_range.start);
range.end = MIN(range.end, select_visitor->contain_range.end);
gt_genome_node_set_range((GtGenomeNode*) rn, &range);
gt_queue_add(select_visitor->node_buffer, rn);
}
else /* contain range does not overlap with <rn> range -> delete <rn> */
gt_genome_node_delete((GtGenomeNode*) rn);
}
else
gt_queue_add(select_visitor->node_buffer, rn);
}
else
gt_genome_node_delete((GtGenomeNode*) rn);
return 0;
}
static int feature_index_lua_add_feature_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtFeatureNode *fn;
GtStr *seqid;
GtError *err;
bool has_seqid;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
fn = gt_feature_node_cast(*gn);
luaL_argcheck(L, fn, 2, "not a feature node");
seqid = gt_genome_node_get_seqid(*gn);
luaL_argcheck(L, seqid, 2, "feature does not have a sequence id");
err = gt_error_new();
if (gt_feature_index_has_seqid(*fi, &has_seqid, gt_str_get(seqid), err))
return gt_lua_error(L, err);
gt_error_delete(err);
luaL_argcheck(L, has_seqid, 2,
"feature index does not contain corresponding sequence region");
err = gt_error_new();
if (gt_feature_index_add_feature_node(*fi, fn, err))
return gt_lua_error(L, err);
gt_error_delete(err);
return 0;
}
double agn_calc_edit_distance(GtFeatureNode *t1, GtFeatureNode *t2)
{
AgnTranscriptClique *clique1 = agn_transcript_clique_new();
agn_transcript_clique_add(clique1, t1);
AgnTranscriptClique *clique2 = agn_transcript_clique_new();
agn_transcript_clique_add(clique2, t2);
GtGenomeNode *gn1 = (GtGenomeNode *)t1;
GtRange r1 = gt_genome_node_get_range(gn1);
GtStr *seqid = gt_genome_node_get_seqid(gn1);
GtGenomeNode *gn2 = (GtGenomeNode *)t2;
GtRange r2 = gt_genome_node_get_range(gn2);
GtRange local_range = r1;
if(r2.start < r1.start)
local_range.start = r2.start;
if(r2.end > r1.end)
local_range.end = r2.end;
AgnCliquePair *pair = agn_clique_pair_new(gt_str_get(seqid), clique1, clique2,
&local_range);
agn_clique_pair_build_model_vectors(pair);
agn_clique_pair_comparative_analysis(pair);
double ed = agn_clique_pair_get_edit_distance(pair);
agn_transcript_clique_delete(clique1);
agn_transcript_clique_delete(clique2);
agn_clique_pair_delete(pair);
return ed;
}
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 int gt_ltrdigest_pdom_visitor_attach_hit(GtLTRdigestPdomVisitor *lv,
GtHMMERModelHit *modelhit,
GtHMMERSingleHit *singlehit)
{
GT_UNUSED GtUword i;
GtGenomeNode *gf;
int had_err = 0;
GtRange rrng;
gt_assert(lv && singlehit);
rrng = gt_ltrdigest_pdom_visitor_coords(lv, singlehit);
if (gt_array_size(singlehit->chains) > 0 || lv->output_all_chains) {
char buf[32];
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
lv->ltr_retrotrans),
gt_ft_protein_match,
rrng.start,
rrng.end,
singlehit->strand);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_alignment",
gt_str_ref(singlehit->alignment),
(GtFree) gt_str_delete);
gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_aaseq",
gt_str_ref(singlehit->aastring),
(GtFree) gt_str_delete);
gt_feature_node_set_source((GtFeatureNode*) gf, lv->tag);
gt_feature_node_set_score((GtFeatureNode*) gf, (float) singlehit->evalue);
(void) snprintf(buf, (size_t) 32, "%d", (int) singlehit->frame);
gt_feature_node_add_attribute((GtFeatureNode*) gf,
"reading_frame", buf);
if (modelhit->modelname != NULL) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "name",
modelhit->modelname);
}
if (gt_array_size(singlehit->chains) > 1UL && lv->output_all_chains) {
GtStr *buffer;
GtUword j;
gt_assert(singlehit->chains != NULL);
buffer = gt_str_new();
for (j = 0UL; j < gt_array_size(singlehit->chains); j++) {
gt_str_append_cstr(buffer, modelhit->modelname);
gt_str_append_char(buffer, ':');
gt_str_append_ulong(buffer,
*(GtUword*) gt_array_get(singlehit->chains, j));
if (j != gt_array_size(singlehit->chains) - 1) {
gt_str_append_char(buffer, ',');
}
}
gt_feature_node_set_attribute((GtFeatureNode*) gf, "chains",
gt_str_get(buffer));
gt_str_delete(buffer);
}
gt_feature_node_add_child(lv->ltr_retrotrans, (GtFeatureNode*) gf);
}
gt_array_delete(singlehit->chains);
singlehit->chains = NULL;
return had_err;
}
static void build_key(GtStr *key, GtFeatureNode *feature, GtStr *target_id)
{
gt_assert(key && feature && target_id);
gt_str_reset(key);
gt_str_append_str(key, gt_genome_node_get_seqid((GtGenomeNode*) feature));
gt_str_append_char(key, '\t'); /* cannot occur in seqid or target_id */
gt_str_append_str(key, target_id);
}
static int genome_node_lua_get_seqid(lua_State *L)
{
GtStr *seqid;
GtGenomeNode **gn = check_genome_node(L, 1);
if ((seqid = gt_genome_node_get_seqid(*gn)))
lua_pushstring(L, gt_str_get(seqid));
else
lua_pushnil(L);
return 1;
}
static void infer_cds_visitor_check_stop(AgnInferCDSVisitor *v)
{
if(gt_array_size(v->cds) == 0)
return;
const char *mrnaid = gt_feature_node_get_attribute(v->mrna, "ID");
unsigned int ln = gt_genome_node_get_line_number((GtGenomeNode *)v->mrna);
GtStrand strand = gt_feature_node_get_strand(v->mrna);
GtRange stoprange;
GtUword threeprimeindex = gt_array_size(v->cds) - 1;
GtGenomeNode **threeprimesegment = gt_array_get(v->cds, threeprimeindex);
stoprange = gt_genome_node_get_range(*threeprimesegment);
stoprange.start = stoprange.end - 2;
if(strand == GT_STRAND_REVERSE)
{
threeprimesegment = gt_array_get(v->cds, 0);
stoprange = gt_genome_node_get_range(*threeprimesegment);
stoprange.end = stoprange.start + 2;
}
if(gt_array_size(v->stops) > 1)
{
gt_logger_log(v->logger, "mRNA '%s' (line %u) has %lu stop codons", mrnaid,
ln, gt_array_size(v->starts));
}
else if(gt_array_size(v->stops) == 1)
{
GtGenomeNode **codon = gt_array_get(v->stops, 0);
GtRange testrange = gt_genome_node_get_range(*codon);
if(gt_range_compare(&stoprange, &testrange) != 0)
{
gt_logger_log(v->logger, "stop codon inferred from CDS [%lu, %lu] does "
"not match explicitly provided stop codon [%lu, %lu] for "
"mRNA '%s'", stoprange.start, stoprange.end,
testrange.start, testrange.end, mrnaid);
}
}
else // agn_assert(gt_array_size(v->stops) == 0)
{
GtStr *seqid = gt_genome_node_get_seqid((GtGenomeNode *)v->mrna);
GtGenomeNode *codonfeature = gt_feature_node_new(seqid, "stop_codon",
stoprange.start,
stoprange.end,
strand);
if(v->source)
gt_feature_node_set_source((GtFeatureNode *)codonfeature, v->source);
GtFeatureNode *cf = (GtFeatureNode *)codonfeature;
gt_feature_node_add_child(v->mrna, cf);
gt_array_add(v->stops, cf);
}
}
static void infer_cds_visitor_infer_cds(AgnInferCDSVisitor *v)
{
GtFeatureNode **start_codon = NULL, **stop_codon = NULL;
bool exonsexplicit = gt_array_size(v->exons) > 0;
bool startcodon_check = gt_array_size(v->starts) == 1 &&
(start_codon = gt_array_get(v->starts, 0)) != NULL;
bool stopcodon_check = gt_array_size(v->stops) == 1 &&
(stop_codon = gt_array_get(v->stops, 0)) != NULL;
if(gt_array_size(v->cds) > 0)
{
return;
}
else if(!exonsexplicit || !startcodon_check || !stopcodon_check)
{
return;
}
GtRange left_codon_range, right_codon_range;
left_codon_range = gt_genome_node_get_range(*(GtGenomeNode **)start_codon);
right_codon_range = gt_genome_node_get_range(*(GtGenomeNode **)stop_codon);
if(gt_feature_node_get_strand(v->mrna) == GT_STRAND_REVERSE)
{
left_codon_range = gt_genome_node_get_range(*(GtGenomeNode **)stop_codon);
right_codon_range = gt_genome_node_get_range(*(GtGenomeNode **)start_codon);
}
GtUword i;
for(i = 0; i < gt_array_size(v->exons); i++)
{
GtFeatureNode *exon = *(GtFeatureNode **)gt_array_get(v->exons, i);
GtGenomeNode *exon_gn = (GtGenomeNode *)exon;
GtRange exon_range = gt_genome_node_get_range(exon_gn);
GtStrand exon_strand = gt_feature_node_get_strand(exon);
GtRange cdsrange;
bool exon_includes_cds = infer_cds_visitor_infer_range(&exon_range,
&left_codon_range,
&right_codon_range,
&cdsrange);
if(exon_includes_cds)
{
GtGenomeNode *cdsfeat;
cdsfeat = gt_feature_node_new(gt_genome_node_get_seqid(exon_gn), "CDS",
cdsrange.start, cdsrange.end, exon_strand);
if(v->source)
gt_feature_node_set_source((GtFeatureNode *)cdsfeat, v->source);
gt_feature_node_add_child(v->mrna, (GtFeatureNode *)cdsfeat);
gt_array_add(v->cds, cdsfeat);
}
}
}
static int create_block_features(GtBEDParser *bed_parser, GtFeatureNode *fn,
GtUword block_count,
GtSplitter *size_splitter,
GtSplitter *start_splitter, GtIO *bed_file,
GtError *err)
{
GtUword i;
int had_err = 0;
gt_assert(fn && block_count && size_splitter && start_splitter);
gt_assert(gt_splitter_size(size_splitter) == block_count);
gt_assert(gt_splitter_size(start_splitter) == block_count);
for (i = 0; !had_err && i < block_count; i++) {
GtUword block_size, block_start, start, end;
GtGenomeNode *block;
const char *name;
if (gt_parse_uword(&block_size, gt_splitter_get_token(size_splitter, i))) {
gt_error_set(err,
"file \"%s\": line "GT_WU": could not parse blockSize '%s'",
gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file),
gt_splitter_get_token(size_splitter, i));
had_err = -1;
}
if (!had_err && gt_parse_uword(&block_start,
gt_splitter_get_token(start_splitter, i))) {
gt_error_set(err, "file \"%s\": line "GT_WU": could not parse blockStart "
"'%s'", gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file),
gt_splitter_get_token(start_splitter, i));
had_err = -1;
}
if (!had_err) {
start = gt_genome_node_get_start((GtGenomeNode*) fn) + block_start;
end = start + block_size - 1;
block = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*) fn),
bed_parser->block_type
? bed_parser->block_type
: BED_BLOCK_TYPE,
start, end, gt_feature_node_get_strand(fn));
if ((name = gt_feature_node_get_attribute(fn, GT_GFF_NAME))) {
gt_feature_node_add_attribute((GtFeatureNode*) block, GT_GFF_NAME,
name);
}
gt_feature_node_set_score((GtFeatureNode*) block,
gt_feature_node_get_score(fn));
gt_feature_node_set_strand((GtFeatureNode*) block,
gt_feature_node_get_strand(fn));
gt_feature_node_add_child(fn, (GtFeatureNode*) block);
}
}
return had_err;
}
static void pbs_attach_results_to_gff3(GtPBSResults *results,
GtLTRElement *element,
GtStrand *canonical_strand,
GtStr *tag)
{
GtRange pbs_range;
GtGenomeNode *gf;
unsigned long i = 0;
char buffer[BUFSIZ];
GtPBSHit* hit = gt_pbs_results_get_ranked_hit(results, i++);
if (*canonical_strand == GT_STRAND_UNKNOWN)
*canonical_strand = gt_pbs_hit_get_strand(hit);
else
{
/* do we have to satisfy a strand constraint?
* then find best-scoring PBS on the given canonical strand */
while (gt_pbs_hit_get_strand(hit) != *canonical_strand
&& i < gt_pbs_results_get_number_of_hits(results))
{
gt_log_log("dropping PBS because of nonconsistent strand: %s\n",
gt_feature_node_get_attribute(element->mainnode, "ID"));
hit = gt_pbs_results_get_ranked_hit(results, i++);
}
/* if there is none, do not report a PBS */
if (gt_pbs_hit_get_strand(hit) != *canonical_strand)
return;
}
pbs_range = gt_pbs_hit_get_coords(hit);
pbs_range.start++; pbs_range.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
element->mainnode),
GT_PBS_TYPE,
pbs_range.start,
pbs_range.end,
gt_pbs_hit_get_strand(hit));
gt_feature_node_set_source((GtFeatureNode*) gf, tag);
gt_feature_node_set_score((GtFeatureNode*) gf,
(float) gt_pbs_hit_get_score(hit));
if (gt_pbs_hit_get_trna(hit) != NULL) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trna",
gt_pbs_hit_get_trna(hit));
}
gt_feature_node_set_strand(element->mainnode, gt_pbs_hit_get_strand(hit));
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_tstart(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trnaoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_offset(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "pbsoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_edist(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "edist", buffer);
gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
}
static int gt_regioncov_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtRegionCovVisitor *regioncov_visitor;
GtArray *rangelist;
gt_error_check(err);
regioncov_visitor = gt_regioncov_visitor_cast(nv);
rangelist = gt_array_new(sizeof (GtRange));
gt_hashmap_add(regioncov_visitor->region2rangelist,
gt_cstr_dup(gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
rn))),
rangelist);
return 0;
}
static int select_visitor_sequence_node(GtNodeVisitor *nv, GtSequenceNode *sn,
GT_UNUSED GtError *err)
{
GtSelectVisitor *select_visitor;
gt_error_check(err);
select_visitor = select_visitor_cast(nv);
if (!gt_str_length(select_visitor->seqid) || /* no seqid was specified */
!gt_str_cmp(select_visitor->seqid, /* or seqids are equal */
gt_genome_node_get_seqid((GtGenomeNode*) sn))) {
gt_queue_add(select_visitor->node_buffer, sn);
}
else
gt_genome_node_delete((GtGenomeNode*) sn);
return 0;
}
static int gff3_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtGFF3Visitor *gff3_visitor;
gt_error_check(err);
gff3_visitor = gff3_visitor_cast(nv);
gt_assert(nv && rn);
gff3_version_string(nv);
gt_file_xprintf(gff3_visitor->outfp, "%s %s %lu %lu\n",
GT_GFF_SEQUENCE_REGION,
gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn)),
gt_genome_node_get_start((GtGenomeNode*) rn),
gt_genome_node_get_end((GtGenomeNode*) rn));
return 0;
}
static int feature_index_lua_add_feature_node(lua_State *L)
{
GtFeatureIndex **fi;
GtGenomeNode **gn;
GtFeatureNode *gf;
GtStr *seqid;
gt_assert(L);
fi = check_feature_index(L, 1);
gn = check_genome_node(L, 2);
gf = gt_genome_node_cast(gt_feature_node_class(), *gn);
luaL_argcheck(L, gf, 2, "not a feature node");
seqid = gt_genome_node_get_seqid(*gn);
luaL_argcheck(L, seqid, 2, "feature does not have a sequence id");
luaL_argcheck(L, gt_feature_index_has_seqid(*fi, gt_str_get(seqid)), 2,
"feature index does not contain corresponding sequence region");
gt_feature_index_add_feature_node(*fi, gf);
return 0;
}
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 void construct_thick_feature(GtBEDParser *bed_parser, GtFeatureNode *fn,
GtRange range)
{
GtGenomeNode *thick_feature;
const char *name;
gt_assert(fn);
thick_feature = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
fn),
bed_parser->thick_feature_type
? bed_parser->thick_feature_type
: BED_THICK_FEATURE_TYPE,
range.start, range.end,
gt_feature_node_get_strand(fn));
if ((name = gt_feature_node_get_attribute(fn, "Name")))
gt_feature_node_add_attribute((GtFeatureNode*) thick_feature, "Name", name);
gt_feature_node_set_score((GtFeatureNode*) thick_feature,
gt_feature_node_get_score(fn));
gt_feature_node_set_strand((GtFeatureNode*) thick_feature,
gt_feature_node_get_strand(fn));
gt_feature_node_add_child(fn, (GtFeatureNode*) thick_feature);
}
static void orf_attach_results_to_gff3(GtFeatureNode *gf,
GtRange orf_rng, unsigned int orf_frame,
GtStrand strand, GT_UNUSED GtError *err)
{
GtGenomeNode *child;
GtStr *tag;
tag = gt_str_new_cstr(GT_ORF_FINDER_TAG);
orf_rng.start++; orf_rng.end++;
GtFeatureNodeIterator *gfi;
GtFeatureNode *curnode = NULL, *parent_node = NULL;
GtRange gfi_range;
char frame_buf[3];
sprintf(frame_buf, "%d", orf_frame);
gfi = gt_feature_node_iterator_new(gf);
while ((curnode = gt_feature_node_iterator_next(gfi))) {
if (strcmp(gt_feature_node_get_type(curnode),
(const char*) GT_ORF_TYPE) != 0) {
gfi_range = gt_genome_node_get_range((GtGenomeNode*) curnode);
if (gt_range_contains(&gfi_range, &orf_rng)) {
parent_node = curnode;
}
}
}
if (parent_node) {
child = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*) gf),
GT_ORF_TYPE,
orf_rng.start,
orf_rng.end,
strand);
gt_feature_node_set_source((GtFeatureNode*) child, tag);
gt_feature_node_set_attribute((GtFeatureNode*) child, "frame", frame_buf);
gt_feature_node_add_child(parent_node,(GtFeatureNode*) child);
}
gt_str_delete(tag);
gt_feature_node_iterator_delete(gfi);
}
static double gaeval_visitor_calculate_coverage(AgnGaevalVisitor *v,
GtFeatureNode *genemodel,
GtError *error)
{
agn_assert(v && genemodel);
GtStr *seqid = gt_genome_node_get_seqid((GtGenomeNode *)genemodel);
GtRange mrna_range = gt_genome_node_get_range((GtGenomeNode *)genemodel);
GtArray *overlapping = gt_array_new( sizeof(GtFeatureNode *) );
bool hasseqid;
gt_feature_index_has_seqid(v->alignments, &hasseqid, gt_str_get(seqid),error);
if(hasseqid)
{
gt_feature_index_get_features_for_range(v->alignments, overlapping,
gt_str_get(seqid), &mrna_range,
error);
}
GtArray *exon_coverage = gt_array_new( sizeof(GtRange) );
GtUword i;
for(i = 0; i < gt_array_size(overlapping); i++)
{
GtFeatureNode *alignment = *(GtFeatureNode **)gt_array_get(overlapping, i);
GtArray *covered_parts = gaeval_visitor_intersect((GtGenomeNode*)genemodel,
(GtGenomeNode*)alignment);
if(covered_parts != NULL)
{
GtArray *temp = gaeval_visitor_union(exon_coverage, covered_parts);
gt_array_delete(covered_parts);
gt_array_delete(exon_coverage);
exon_coverage = temp;
}
}
double coverage = gaeval_visitor_coverage_resolve(genemodel, exon_coverage);
gt_array_delete(exon_coverage);
gt_array_delete(overlapping);
return coverage;
}
static void ppt_attach_results_to_gff3(GtPPTResults *results,
GtLTRElement *element,
GtStrand *canonical_strand,
GtStr *tag)
{
GtRange ppt_range;
unsigned long i = 0;
GtGenomeNode *gf;
GtPPTHit* hit = gt_ppt_results_get_ranked_hit(results, i++);
if (*canonical_strand == GT_STRAND_UNKNOWN)
*canonical_strand = gt_ppt_hit_get_strand(hit);
else
{
/* find best-scoring PPT on the given canonical strand */
while (gt_ppt_hit_get_strand(hit) != *canonical_strand
&& i < gt_ppt_results_get_number_of_hits(results))
{
gt_log_log("dropping PPT because of nonconsistent strand: %s\n",
gt_feature_node_get_attribute(element->mainnode, "ID"));
hit = gt_ppt_results_get_ranked_hit(results, i++);
}
/* if there is none, do not report a PPT */
if (gt_ppt_hit_get_strand(hit) != *canonical_strand)
return;
}
ppt_range = gt_ppt_hit_get_coords(hit);
ppt_range.start++; ppt_range.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
element->mainnode),
GT_PPT_TYPE,
ppt_range.start,
ppt_range.end,
gt_ppt_hit_get_strand(hit));
gt_feature_node_set_source((GtFeatureNode*) gf, tag);
gt_feature_node_set_strand(element->mainnode, gt_ppt_hit_get_strand(hit));
gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
}
static int extract_join_feature(GtGenomeNode *gn, const char *type,
GtRegionMapping *region_mapping,
GtStr *sequence, bool *reverse_strand,
bool *first_child_of_type_seen, GtPhase *phase,
GtError *err)
{
char *outsequence;
GtFeatureNode *fn;
GtRange range;
int had_err = 0;
gt_error_check(err);
fn = gt_feature_node_cast(gn);
gt_assert(fn);
if (gt_feature_node_has_type(fn, type)) {
if (gt_feature_node_get_strand(fn) == GT_STRAND_REVERSE) {
*reverse_strand = true;
*phase = gt_feature_node_get_phase(fn);
} else {
if (!(*first_child_of_type_seen)) {
*first_child_of_type_seen = true;
*phase = gt_feature_node_get_phase(fn);
} else *phase = GT_PHASE_UNDEFINED;
}
range = gt_genome_node_get_range(gn);
had_err = gt_region_mapping_get_sequence(region_mapping, &outsequence,
gt_genome_node_get_seqid(gn),
range.start, range.end, err);
if (!had_err) {
gt_str_append_cstr_nt(sequence, outsequence, gt_range_length(&range));
gt_free(outsequence);
}
}
return had_err;
}
static int add_ids_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn,
GT_UNUSED GtError *err)
{
GtAddIDsVisitor *aiv;
const char *seqid;
int had_err = 0;
gt_error_check(err);
aiv = add_ids_visitor_cast(nv);
seqid = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn));
if (gt_hashmap_get(aiv->undefined_sequence_regions, seqid)) {
gt_error_set(err, "genome feature with id \"%s\" has been defined before "
"the corresponding \"%s\" definition on line %u in file "
"\"%s\"", seqid, GT_GFF_SEQUENCE_REGION,
gt_genome_node_get_line_number((GtGenomeNode*) rn),
gt_genome_node_get_filename((GtGenomeNode*) rn));
had_err = -1;
}
if (!had_err) {
if (!gt_cstr_table_get(aiv->defined_seqids, seqid))
gt_cstr_table_add(aiv->defined_seqids, seqid);
gt_queue_add(aiv->node_buffer, rn);
}
return had_err;
}
static int inter_feature_in_children(GtFeatureNode *current_feature, void *data,
GT_UNUSED GtError *err)
{
GtInterFeatureVisitor *aiv = (GtInterFeatureVisitor*) data;
GtFeatureNode *inter_node;
GtRange previous_range, current_range, inter_range;
GtStrand previous_strand, /*current_strand, */inter_strand;
GtStr *parent_seqid;
gt_error_check(err);
gt_assert(current_feature);
if (gt_feature_node_has_type(current_feature, aiv->outside_type)) {
if (aiv->previous_feature) {
/* determine inter range */
previous_range = gt_genome_node_get_range((GtGenomeNode*)
aiv->previous_feature);
current_range = gt_genome_node_get_range((GtGenomeNode*) current_feature);
if (previous_range.end >= current_range.start) {
gt_warning("overlapping boundary features " GT_WU "-" GT_WU " and "
GT_WU "-" GT_WU ", " "not placing '%s' inter-feature",
previous_range.start,
previous_range.end,
current_range.start,
current_range.end,
aiv->inter_type);
return 0;
}
if (current_range.start - previous_range.end < 2) {
gt_warning("no space for inter-feature '%s' between " GT_WU " and "
GT_WU,
aiv->inter_type,
previous_range.end,
current_range.start);
return 0;
}
inter_range.start = previous_range.end + 1;
inter_range.end = current_range.start - 1;
/* determine inter strand */
previous_strand = gt_feature_node_get_strand(aiv->previous_feature);
/*current_strand = gt_feature_node_get_strand(current_feature);*/
gt_assert(previous_strand == gt_feature_node_get_strand(current_feature));
inter_strand = previous_strand;
/* determine sequence id */
parent_seqid =
gt_genome_node_get_seqid((GtGenomeNode*) aiv->parent_feature);
gt_assert(!gt_str_cmp(parent_seqid,
gt_genome_node_get_seqid((GtGenomeNode*)
aiv->previous_feature)));
gt_assert(!gt_str_cmp(parent_seqid,
gt_genome_node_get_seqid((GtGenomeNode*)
current_feature)));
/* create inter feature */
inter_node = (GtFeatureNode*)
gt_feature_node_new(parent_seqid, aiv->inter_type,
inter_range.start, inter_range.end,
inter_strand);
gt_feature_node_add_child(aiv->parent_feature, inter_node);
}
aiv->previous_feature = current_feature;
}
return 0;
}
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;
}
