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;
}
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;
}
GtRegionNode* gt_region_node_try_cast(GtGenomeNode *gn)
{
return gt_genome_node_try_cast(gt_region_node_class(), gn);
}
