GtFeatureIndex *agn_import_simple(int numfiles, const char **filenames,
char *type, AgnLogger *logger)
{
GtFeatureIndex *features = gt_feature_index_memory_new();
GtNodeStream *gff3 = gt_gff3_in_stream_new_unsorted(numfiles, filenames);
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)gff3);
gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)gff3);
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, type, type);
GtNodeStream *filterstream = agn_filter_stream_new(gff3, typestokeep);
GtNodeStream *featstream = gt_feature_out_stream_new(filterstream, features);
GtError *error = gt_error_new();
int result = gt_node_stream_pull(featstream, error);
if(result == -1)
{
agn_logger_log_error(logger, "error processing node stream: %s",
gt_error_get(error));
}
gt_error_delete(error);
if(agn_logger_has_error(logger))
{
gt_feature_index_delete(features);
features = NULL;
}
gt_node_stream_delete(gff3);
gt_node_stream_delete(filterstream);
gt_node_stream_delete(featstream);
return features;
}
static void gv_test_calc_integrity(AgnUnitTest *test)
{
const char *filename = "data/gff3/gaeval-stream-unit-test-2.gff3";
GtNodeStream *align_in = gt_gff3_in_stream_new_unsorted(1, &filename);
AgnGaevalParams params = { 0.6, 0.3, 0.05, 0.05, 400, 200, 100 };
GtNodeVisitor *nv = agn_gaeval_visitor_new(align_in, params);
AgnGaevalVisitor *gv = gaeval_visitor_cast(nv);
gt_node_stream_delete(align_in);
GtNodeStream *gff3in = gt_gff3_in_stream_new_unsorted(1, &filename);
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, "mRNA", "mRNA");
GtNodeStream *filtstream = agn_filter_stream_new(gff3in, typestokeep);
GtLogger *logger = gt_logger_new(true, "", stderr);
GtNodeStream *ics = agn_infer_cds_stream_new(filtstream, NULL, logger);
GtNodeStream *ies = agn_infer_exons_stream_new(ics, NULL, logger);
GtError *error = gt_error_new();
GtArray *feats = gt_array_new( sizeof(GtFeatureNode *) );
GtNodeStream *featstream = gt_array_out_stream_new(ies, feats, error);
int result = gt_node_stream_pull(featstream, error);
if(result == -1)
{
fprintf(stderr, "[AgnGaevalVisitor::gv_test_calc_integrity] error "
"processing GFF3: %s\n", gt_error_get(error));
return;
}
gt_node_stream_delete(gff3in);
gt_node_stream_delete(filtstream);
gt_node_stream_delete(featstream);
gt_node_stream_delete(ics);
gt_node_stream_delete(ies);
gt_logger_delete(logger);
gt_hashmap_delete(typestokeep);
agn_assert(gt_array_size(feats) == 2);
GtFeatureNode *g1 = *(GtFeatureNode **)gt_array_get(feats, 0);
GtFeatureNode *g2 = *(GtFeatureNode **)gt_array_get(feats, 1);
double cov1 = gaeval_visitor_calculate_coverage(gv, g1, error);
double cov2 = gaeval_visitor_calculate_coverage(gv, g2, error);
double int1 = gaeval_visitor_calculate_integrity(gv, g1, cov1, NULL, error);
double int2 = gaeval_visitor_calculate_integrity(gv, g2, cov2, NULL, error);
bool test1 = fabs(cov1 - 1.000) < 0.001 &&
fabs(cov2 - 0.997) < 0.001 &&
fabs(int1 - 0.850) < 0.001 &&
fabs(int2 - 0.863) < 0.001;
agn_unit_test_result(test, "calculate integrity", test1);
gt_error_delete(error);
gt_array_delete(feats);
gt_genome_node_delete((GtGenomeNode *)g1);
gt_genome_node_delete((GtGenomeNode *)g2);
gt_node_visitor_delete(nv);
}
GtNodeVisitor*
agn_gaeval_visitor_new(GtNodeStream *astream, AgnGaevalParams gparams)
{
agn_assert(astream);
// Create the node visitor
GtNodeVisitor *nv = gt_node_visitor_create(gaeval_visitor_class());
AgnGaevalVisitor *v = gaeval_visitor_cast(nv);
v->alignments = gt_feature_index_memory_new();
v->tsvout = NULL;
v->params = gparams;
// Check that sum of weights is 1.0
double weights_total = gparams.alpha + gparams.beta +
gparams.gamma + gparams.epsilon;
if(fabs(weights_total - 1.0) > 0.0001)
{
fprintf(stderr, "[AgnGaevalVisitor::agn_gaeval_visitor_new] warning: "
"sum of weights is not 1.0 %.3lf; integrity calculations will be "
"incorrect\n", weights_total);
}
// Set up node stream to load alignment features into memory
GtQueue *streams = gt_queue_new();
GtNodeStream *stream, *last_stream;
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, "cDNA_match", "cDNA_match");
gt_hashmap_add(typestokeep, "EST_match", "EST_match");
gt_hashmap_add(typestokeep, "nucleotide_match", "nucleotide_match");
stream = agn_filter_stream_new(astream, typestokeep);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_feature_out_stream_new(last_stream, v->alignments);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "cDNA_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "EST_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "nucleotide_match",
"match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
// Process the node stream
GtError *error = gt_error_new();
int result = gt_node_stream_pull(last_stream, error);
if(result == -1)
{
fprintf(stderr, "[AEGeAn::AgnGaevalStream] error parsing alignments: %s\n",
gt_error_get(error));
gt_node_visitor_delete(nv);
return NULL;
}
gt_error_delete(error);
gt_hashmap_delete(typestokeep);
while(gt_queue_size(streams) > 0)
{
stream = gt_queue_get(streams);
gt_node_stream_delete(stream);
}
gt_queue_delete(streams);
return nv;
}
