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; }