static GtArray*
gaeval_visitor_intersect(GtGenomeNode *genemodel, GtGenomeNode *alignment)
{
agn_assert(genemodel && alignment);
GtFeatureNode *genefn = gt_feature_node_cast(genemodel);
GtFeatureNode *algnfn = gt_feature_node_cast(alignment);
agn_assert(gt_feature_node_has_type(genefn, "mRNA"));
GtStrand genestrand = gt_feature_node_get_strand(genefn);
GtStrand algnstrand = gt_feature_node_get_strand(algnfn);
if(genestrand != algnstrand)
return NULL;
GtArray *covered_parts = gt_array_new( sizeof(GtRange) );
GtArray *exons = agn_typecheck_select(genefn, agn_typecheck_exon);
GtWord i;
for(i = 0; i < gt_array_size(exons); i++)
{
GtGenomeNode *exon = *(GtGenomeNode **)gt_array_get(exons, i);
GtRange exonrange = gt_genome_node_get_range(exon);
GtFeatureNodeIterator *aniter = gt_feature_node_iterator_new(algnfn);
GtFeatureNode *tempaln;
GtRange nullrange = {0, 0};
for(tempaln = gt_feature_node_iterator_next(aniter);
tempaln != NULL;
tempaln = gt_feature_node_iterator_next(aniter))
{
if(gt_feature_node_has_type(tempaln, "match_gap"))
continue;
GtRange alnrange = gt_genome_node_get_range((GtGenomeNode *) tempaln);
GtRange intr = gaeval_visitor_range_intersect(&exonrange, &alnrange);
if(gt_range_compare(&intr, &nullrange) != 0)
gt_array_add(covered_parts, intr);
}
gt_feature_node_iterator_delete(aniter);
}
gt_array_delete(exons);
for(i = 0; i < gt_array_size(covered_parts); i++)
{
GtRange *r1 = gt_array_get(covered_parts, i);
GtUword j;
for(j = i+1; j < gt_array_size(covered_parts); j++)
{
GtRange *r2 = gt_array_get(covered_parts, j);
agn_assert(gt_range_overlap(r1, r2) == false);
}
}
return covered_parts;
}
static int save_exon_node(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err)
{
GtGTFVisitor *gtf_visitor;
gt_error_check(err);
gt_assert(fn && data);
gtf_visitor = (GtGTFVisitor*) data;
if (gt_feature_node_has_type(fn, gt_ft_exon))
gt_array_add(gtf_visitor->exon_features, fn);
else if (gt_feature_node_has_type(fn, gt_ft_CDS))
gt_array_add(gtf_visitor->CDS_features, fn);
return 0;
}
static int add_exon_or_cds_number(GtFeatureNode *fn, void *data,
GT_UNUSED GtError *err)
{
GtStatVisitor *sv = (GtStatVisitor*) data;
gt_error_check(err);
gt_assert(sv && fn);
if (gt_feature_node_has_type(fn, gt_ft_exon))
sv->exon_number_for_distri++;
else if (gt_feature_node_has_type(fn, gt_ft_CDS)) {
GtRange range = gt_genome_node_get_range((GtGenomeNode*) fn);
sv->cds_length_for_distri += gt_range_length(&range);
}
return 0;
}
static int
visit_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn, GtError *error)
{
AgnLocusMapVisitor *v = locus_map_visitor_cast(nv);
gt_error_check(error);
agn_assert(gt_feature_node_has_type(fn, "locus"));
const char *locuslabel = agn_feature_node_get_label(fn);
GtFeatureNodeIterator *iter = gt_feature_node_iterator_new(fn);
GtFeatureNode *current;
for(current = gt_feature_node_iterator_next(iter);
current != NULL;
current = gt_feature_node_iterator_next(iter))
{
if(agn_typecheck_gene(current) && v->genefh != NULL)
{
const char *genelabel = agn_feature_node_get_label(current);
fprintf(v->genefh, "%s\t%s\n", genelabel, locuslabel);
}
if(agn_typecheck_mrna(current) && v->mrnafh != NULL)
{
const char *mrnalabel = agn_feature_node_get_label(current);
fprintf(v->mrnafh, "%s\t%s\n", mrnalabel, locuslabel);
}
}
gt_feature_node_iterator_delete(iter);
return 0;
}
static int gtf_show_feature_node(GtFeatureNode *fn, void *data, GtError *err)
{
GtGTFVisitor *gtf_visitor = (GtGTFVisitor*) data;
int had_err = 0;
if (gt_feature_node_has_type(fn, gt_ft_gene)) {
gtf_visitor->gene_id++;
gtf_visitor->transcript_id = 0;
had_err = gtf_show_transcript(fn, gtf_visitor, err);
}
else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) {
had_err = gtf_show_transcript(fn, gtf_visitor, err);
}
else if (!(gt_feature_node_has_type(fn, gt_ft_CDS) ||
gt_feature_node_has_type(fn, gt_ft_exon))) {
gt_warning("skipping GFF3 feature of type \"%s\" (from line %u in file "
"\"%s\")",
gt_feature_node_get_type(fn),
gt_genome_node_get_line_number((GtGenomeNode*) fn),
gt_genome_node_get_filename((GtGenomeNode*) fn));
}
return had_err;
}
static void infer_cds_visitor_set_utrs(AgnInferCDSVisitor *v)
{
GtGenomeNode **start;
GtUword i, cds_start;
if(!v->starts || gt_array_size(v->starts) != 1)
return;
start = gt_array_get(v->starts, 0);
cds_start = gt_genome_node_get_start(*start);
for(i = 0; i < gt_array_size(v->utrs); i++)
{
GtFeatureNode *utr = *(GtFeatureNode **)gt_array_get(v->utrs, i);
GtStrand strand = gt_feature_node_get_strand(utr);
GtUword utr_start = gt_genome_node_get_start((GtGenomeNode *)utr);
if(!gt_feature_node_has_type(utr, "five_prime_UTR") &&
!gt_feature_node_has_type(utr, "three_prime_UTR"))
{
if(strand == GT_STRAND_FORWARD)
{
if(utr_start < cds_start)
gt_feature_node_set_type(utr, "five_prime_UTR");
else
gt_feature_node_set_type(utr, "three_prime_UTR");
}
else
{
if(utr_start < cds_start)
gt_feature_node_set_type(utr, "three_prime_UTR");
else
gt_feature_node_set_type(utr, "five_prime_UTR");
}
}
}
}
static int check_cds_phases_if_necessary(GtFeatureNode *fn,
GtCDSCheckVisitor *v,
bool second_pass, GtError *err)
{
GtFeatureNodeIterator *fni;
GtFeatureNode *node;
GtArray *cds_features = NULL;
GtHashmap *multi_features = NULL;
int had_err = 0;
gt_error_check(err);
gt_assert(fn);
fni = gt_feature_node_iterator_new_direct(fn);
while ((node = gt_feature_node_iterator_next(fni))) {
if (gt_feature_node_has_type(node, gt_ft_CDS)) {
if (gt_feature_node_is_multi(node)) {
GtArray *features;
if (!multi_features)
multi_features = gt_hashmap_new(GT_HASH_DIRECT, NULL,
(GtFree) gt_array_delete);
if ((features =
gt_hashmap_get(multi_features,
gt_feature_node_get_multi_representative(node)))) {
gt_array_add(features, node);
}
else {
GtFeatureNode *representative;
features = gt_array_new(sizeof (GtFeatureNode*));
representative = gt_feature_node_get_multi_representative(node);
gt_array_add(features, representative);
gt_hashmap_add(multi_features, representative, features);
}
}
else {
if (!cds_features)
cds_features = gt_array_new(sizeof (GtFeatureNode*));
gt_array_add(cds_features, node);
}
}
}
if (cds_features)
had_err = check_cds_phases(cds_features, v, false, second_pass, err);
if (!had_err && multi_features)
had_err = gt_hashmap_foreach(multi_features, check_cds_phases_hm, v, err);
gt_array_delete(cds_features);
gt_hashmap_delete(multi_features);
gt_feature_node_iterator_delete(fni);
return had_err;
}
static double gaeval_visitor_coverage_resolve(GtFeatureNode *genemodel,
GtArray *exon_coverage)
{
agn_assert(genemodel && exon_coverage);
agn_assert(gt_feature_node_has_type(genemodel, "mRNA"));
GtUword cum_exon_length =
agn_typecheck_feature_combined_length(genemodel, agn_typecheck_exon);
GtUword i, covered = 0;
for(i = 0; i < gt_array_size(exon_coverage); i++)
{
GtRange *range = gt_array_get(exon_coverage, i);
covered += gt_range_length(range);
}
agn_assert(covered <= cum_exon_length);
return (double)covered / (double)cum_exon_length;
}
static void compute_type_statistics(GtFeatureNode *fn, GtStatVisitor *sv)
{
GtRange range;
gt_assert(fn && sv);
if (gt_feature_node_has_type(fn, gt_ft_gene)) {
sv->number_of_genes++;
if (gt_feature_node_has_CDS(fn))
sv->number_of_protein_coding_genes++;
if (sv->gene_length_distribution) {
range = gt_genome_node_get_range((GtGenomeNode*) fn);
gt_disc_distri_add(sv->gene_length_distribution, gt_range_length(&range));
}
if (sv->gene_score_distribution) {
gt_disc_distri_add(sv->gene_score_distribution,
gt_feature_node_get_score(fn) * 100.0);
}
}
else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) {
sv->number_of_mRNAs++;
if (gt_feature_node_has_CDS(fn))
sv->number_of_protein_coding_mRNAs++;
}
else if (gt_feature_node_has_type(fn, gt_ft_exon)) {
sv->number_of_exons++;
if (sv->exon_length_distribution) {
range = gt_genome_node_get_range((GtGenomeNode*) fn);
gt_disc_distri_add(sv->exon_length_distribution,
gt_range_length(&range));
}
}
else if (gt_feature_node_has_type(fn, gt_ft_CDS)) {
sv->number_of_CDSs++;
}
else if (gt_feature_node_has_type(fn, gt_ft_intron)) {
if (sv->intron_length_distribution) {
range = gt_genome_node_get_range((GtGenomeNode*) fn);
gt_disc_distri_add(sv->intron_length_distribution,
gt_range_length(&range));
}
}
else if (gt_feature_node_has_type(fn, gt_ft_LTR_retrotransposon)) {
sv->number_of_LTR_retrotransposons++;
}
}
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 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;
}
static bool gaeval_visitor_typecheck_gap(GtFeatureNode *fn)
{
return gt_feature_node_has_type(fn, "match_gap");
}
static int CpGIOverlap_stream_next(GtNodeStream * ns,
GtGenomeNode ** gn,
GtError * err)
{
GtGenomeNode * cur_node, * next_node;
GtFeatureNodeIterator * iter;
int err_num = 0;
*gn = NULL;
CpGIOverlap_stream * context;
const char * gene_name = NULL;
const char * overlap_name = NULL;
char chr_str[255];
int chr_num;
unsigned int TSS;
float CpGIOverlap;
context = CpGIOverlap_stream_cast(ns);
// find the genes, determine expression level
if(!gt_node_stream_next(context->in_stream,
&cur_node,
err
) && cur_node != NULL
)
{
*gn = cur_node;
// try casting as a feature node so we can test type
if(!gt_genome_node_try_cast(gt_feature_node_class(), cur_node))
{
return 0;
}
else // we found a feature node
{
// first check if it is a pseudo node, if so find the gene in it if available
if (gt_feature_node_is_pseudo(cur_node))
{
iter = gt_feature_node_iterator_new(cur_node);
if (iter == NULL)
return;
while ((next_node = gt_feature_node_iterator_next(iter)) && !gt_feature_node_has_type(next_node, feature_type_gene));
gt_feature_node_iterator_delete(iter);
if (NULL == (cur_node = next_node))
return 0;
}
if(!gt_feature_node_has_type(cur_node, feature_type_gene))
return 0;
// find name of gene
gene_name = gt_feature_node_get_attribute(cur_node, "Name");
if (gene_name == NULL)
return;
if ( 1 != sscanf(gt_str_get(gt_genome_node_get_seqid(cur_node)), "Chr%d", &chr_num))
return 0;
TSS = (gt_feature_node_get_strand(cur_node) == GT_STRAND_FORWARD) ? gt_genome_node_get_start(cur_node) : gt_genome_node_get_end(cur_node);
// now figure out the overlapping gene
if (! (overlap_name = CpGIOverlap_stream_find_gene_overlap( context, TSS, chr_num)))
return 0;
// save the score into the node
gt_feature_node_set_attribute(cur_node, "cpgi_at_tss", overlap_name);
return 0;
}
}
return err_num;
}
static int CpGI_score_stream_next(GtNodeStream * ns,
GtGenomeNode ** gn,
GtError * err)
{
GtGenomeNode * cur_node;
int err_num = 0;
*gn = NULL;
CpGI_score_stream * score_stream;
unsigned long island_start;
unsigned long island_end;
float island_score;
int chromosome_num;
GtStr * seqID_gtstr;
char * seqID_str;
char * num_cg_str;
unsigned long num_cg = 0;
score_stream = CpGI_score_stream_cast(ns);
// find the CpGI's, process methylome score
if(!gt_node_stream_next(score_stream->in_stream,
&cur_node,
err
) && cur_node != NULL
)
{
*gn = cur_node;
// try casting as a feature node so we can test type
if(!gt_genome_node_try_cast(gt_feature_node_class(), cur_node))
{
return 0;
}
else // we found a feature node
{
if(!gt_feature_node_has_type(cur_node, feature_type_CpGI))
return 0;
#if DEBUG_SCORE
printf("found CpGI\n");
#endif
island_start = gt_genome_node_get_start(cur_node);
island_end = gt_genome_node_get_end(cur_node);
seqID_gtstr = gt_genome_node_get_seqid(cur_node);
seqID_str = gt_str_get(seqID_gtstr);
sscanf(seqID_str, "Chr%d", &chromosome_num);
num_cg_str = gt_feature_node_get_attribute(cur_node, "sumcg");
if (!num_cg_str)
return 0;
sscanf(num_cg_str, "%d", &num_cg);
// now figure out the score
island_score = CpGI_score_stream_score_island(score_stream ,
chromosome_num,
num_cg,
island_start,
island_end);
// gt_str_delete(seqID_gtstr);
// save the score into the node
gt_feature_node_set_score(cur_node, island_score);
return 0;
}
}
return err_num;
}
