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 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):
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)
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)
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
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 resolve_overlapping_homologues(all_aligned_segs, lifted_feature_list,
features_to_remap, unmapped_features,
threshold, parent_dict, intermediate_dict,
children_dict, feature_db,
original_parent_order):
all_overlapping_features = {}
while len(features_to_remap) > 0:
features_to_check = {}
aligned_segs_to_remap = {}
for feature_to_remap in features_to_remap:
del lifted_feature_list[feature_to_remap]
aligned_segs_to_remap[feature_to_remap] = all_aligned_segs[
feature_to_remap]
add_overlapping_feature(features_to_remap, feature_to_remap,
all_overlapping_features)
lift_features.lift_all_features(aligned_segs_to_remap,
all_overlapping_features, threshold,
feature_db, parent_dict, children_dict,
intermediate_dict, unmapped_features,
lifted_feature_list)
clean_overlapping_features(lifted_feature_list,
all_overlapping_features, parent_dict)
for feature_to_remap in features_to_remap:
if feature_to_remap in lifted_feature_list:
features_to_check[feature_to_remap] = lifted_feature_list[
feature_to_remap]
features_to_remap = check_homologues(lifted_feature_list,
features_to_check, parent_dict,
original_parent_order)
return lifted_feature_list
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
def lift_original_annotation(gff, target_fasta, reference_fasta, ref_chroms,
target_chroms, processes, db, lifted_feature_list,
unmapped_features, infer_transcripts):
if target_chroms[0] != target_fasta:
threshold = 0.5
else:
threshold = 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)
aligned_segments = align_features.align_features_to_target(
ref_chroms, target_chroms, processes, target_fasta, parent_dict,
children_dict, "chrm_by_chrm", unmapped_features)
print("lifting features")
lift_features.lift_all_features(aligned_segments, {}, threshold,
feature_db, parent_dict, children_dict,
intermediate_dict, unmapped_features,
lifted_feature_list)
fix_overlapping_features.fix_incorrectly_overlapping_features(
lifted_feature_list, lifted_feature_list, parent_dict,
aligned_segments, unmapped_features, threshold, intermediate_dict,
children_dict, feature_db, original_parent_order)
return feature_db, parent_dict, intermediate_dict, children_dict, original_parent_order