def map_unplaced_genes(unmapped_features, target_fasta, reference_fasta, ref_chroms, target_chroms, processes, lifted_feature_list, feature_db, parent_dict, intermediate_dict, children_dict, parent_order, minimap2_path, inter_files): liftoff_utils.clear_scores(lifted_feature_list, parent_dict) liftover_type = "unplaced" unplaced_dict = {} for feature_name in parent_dict: feature = parent_dict[feature_name] if feature.seqid in ref_chroms: unplaced_dict[feature.id] = feature extract_features.get_gene_sequences(unplaced_dict, ref_chroms, reference_fasta, processes, inter_files, liftover_type) aligned_segments = align_features.align_features_to_target( ref_chroms, target_chroms, processes, target_fasta, unplaced_dict, children_dict, liftover_type, unmapped_features, reference_fasta, minimap2_path, inter_files, True) print("lifting features") lift_features.lift_all_features(aligned_segments, {}, 0.0, feature_db, unplaced_dict, children_dict, intermediate_dict, unmapped_features, lifted_feature_list, 0.0) fix_overlapping_features.fix_incorrectly_overlapping_features( lifted_feature_list, lifted_feature_list, parent_dict, aligned_segments, unmapped_features, 0.0, intermediate_dict, children_dict, feature_db, parent_order, 0.0)
def map_extra_copies(target_fasta, reference_fasta, ref_chroms, target_chroms, processes, lifted_feature_list, parent_dict, children_dict, feature_db, intermediate_dict, parent_order, seq_threshold, minimap2_path, inter_files, remap): liftoff_utils.clear_scores(lifted_feature_list, parent_dict) unmapped_features = [] liftover_type = "copies" extract_features.get_gene_sequences(parent_dict, ref_chroms, reference_fasta, processes, inter_files, liftover_type) aligned_segments = align_features.align_features_to_target( ref_chroms, target_chroms, processes, target_fasta, parent_dict, children_dict, liftover_type, unmapped_features, reference_fasta, minimap2_path, inter_files, remap) print("lifting features") lift_features.lift_all_features(aligned_segments, {}, 0.0, feature_db, parent_dict, children_dict, intermediate_dict, unmapped_features, lifted_feature_list, seq_threshold) fix_overlapping_features.fix_incorrectly_overlapping_features( lifted_feature_list, lifted_feature_list, parent_dict, aligned_segments, unmapped_features, 0.0, intermediate_dict, children_dict, feature_db, parent_order, seq_threshold)
def map_unmapped_genes_agaisnt_all(unmapped_features, target_fasta, reference_fasta, ref_chroms, target_chroms, processes, lifted_feature_list, feature_db, parent_dict, intermediate_dict, children_dict, parent_order,minimap2_path,inter_files): liftoff_utils.clear_scores(lifted_feature_list, parent_dict) unmapped_dict = {} for feature in unmapped_features: unmapped_dict[feature.id]=feature extract_features.get_gene_sequences(unmapped_dict, ref_chroms, reference_fasta, processes, inter_files) unmapped_features = [] aligned_segments=align_features.align_features_to_target(ref_chroms, target_chroms, processes, target_fasta, unmapped_dict, children_dict, "missing", unmapped_features, reference_fasta, minimap2_path,inter_files, True) print("lifting features") lift_features.lift_all_features(aligned_segments, {}, 0.0, feature_db, unmapped_dict, children_dict, intermediate_dict, unmapped_features, lifted_feature_list, 0.0) fix_overlapping_features.fix_incorrectly_overlapping_features(lifted_feature_list, lifted_feature_list, parent_dict, aligned_segments, unmapped_features, 0.0, intermediate_dict, children_dict, feature_db, parent_order, 0.0, "missing") return unmapped_features