def lift_original_annotation(ref_chroms, target_chroms, lifted_features_list, args, unmapped_features, parents_to_lift):
liftover_type = "chrm_by_chrm"
if target_chroms[0] == args.t and args.exclude_partial == False:
min_cov, min_seqid = 0.0, 0.0
else:
min_cov, min_seqid = args.a, args.s
feature_hierarchy, feature_db, ref_parent_order = extract_features.extract_features_to_lift(ref_chroms,
liftover_type,
parents_to_lift, args)
align_and_lift_features(ref_chroms, target_chroms, args, feature_hierarchy, liftover_type, unmapped_features,
feature_db,
feature_hierarchy.parents, lifted_features_list, ref_parent_order, min_cov, min_seqid)
return feature_db, feature_hierarchy, ref_parent_order
def lift_original_annotation(gff, target_fasta, reference_fasta, ref_chroms,
target_chroms, processes, db, lifted_feature_list,
unmapped_features, infer_transcripts, infer_genes,
cov_threshold, seq_threshold, minimap2_path,
inter_files, max_alns, parents_to_lift):
liftover_type = "chrm_by_chrm"
if target_chroms[0] == target_fasta:
cov_threshold, seq_threshold = 0, 0
parent_dict, children_dict, intermediate_dict, feature_db, original_parent_order = extract_features.extract_features_to_lift(
gff, db, ref_chroms, reference_fasta, processes, infer_transcripts,
infer_genes, inter_files, liftover_type, parents_to_lift)
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, True, max_alns)
print("lifting features")
lift_features.lift_all_features(aligned_segments, {}, cov_threshold,
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, cov_threshold, intermediate_dict,
children_dict, feature_db, original_parent_order, seq_threshold)
return feature_db, parent_dict, intermediate_dict, children_dict, original_parent_order