def compare_nearby_features(nearby_features, parent_list, feature, remap_features, original_parent_order, new_parent_order):
for nearby_feature in nearby_features:
if nearby_feature.attributes["copy_id"][0] != feature.attributes["copy_id"][0] and feature.strand == nearby_feature.strand:
if nearby_feature.seqid != feature.seqid or nearby_feature.start > feature.end:
break
if nearby_feature.end < feature.start:
continue
else:
original_nearby_feature, original_feature = parent_list[nearby_feature.id], parent_list[feature.id]
if original_nearby_feature.seqid != original_feature.seqid or original_nearby_feature.strand != original_feature.strand or original_nearby_feature.id == original_feature.id:
original_overlap = -1
else:
original_overlap = liftoff_utils.count_overlap(original_feature.start, original_feature.end,
original_nearby_feature.start,
original_nearby_feature.end)
lifted_overlap = liftoff_utils.count_overlap(feature.start, feature.end, nearby_feature.start,
nearby_feature.end)
if lifted_overlap >0 and original_overlap <= 0:
if feature.attributes["copy_id"][0] in remap_features:
feature_to_remap, feature_to_keep = feature, nearby_feature
elif nearby_feature.attributes["copy_id"][0] in remap_features:
feature_to_remap, feature_to_keep = nearby_feature, feature
else:
feature_to_remap, feature_to_keep = find_feature_to_remap(feature, nearby_feature,
original_parent_order, new_parent_order)
remap_features[feature_to_remap.attributes["copy_id"][0]]=[feature_to_keep.start - 1,
feature_to_keep.end - 1,
feature_to_keep.seqid,
feature_to_keep.strand]
return remap_features
def contains_child(aln, children_coords, parent):
for child_interval in children_coords:
relative_start = liftoff_utils.get_relative_child_coord(parent, child_interval[0], aln.is_reverse)
relative_end = liftoff_utils.get_relative_child_coord(parent, child_interval[1], aln.is_reverse)
child_start, child_end = min(relative_start, relative_end), max(relative_start, relative_end)
overlap = liftoff_utils.count_overlap(child_start, child_end, aln.query_block_start, aln.query_block_end)
if overlap > 0:
return True
return False
def find_overlapping_features(overlapping_features, feature_list):
for feature in feature_list:
if feature.strand == overlapping_features[
3] and feature.seqid == overlapping_features[2]:
if liftoff_utils.count_overlap(feature.start, feature.end,
overlapping_features[0],
overlapping_features[1]) > 0:
return True
return False
def spans_overlap_region(from_node, to_node, coords_to_exclude, parent):
target_chrm = from_node.reference_name
strand = get_strand(from_node, parent)
for coords in coords_to_exclude:
if strand == coords[3] and target_chrm == coords[2]:
if liftoff_utils.count_overlap(coords[0], coords[1],
from_node.reference_block_end,
to_node.reference_block_start) > 0:
return True
return False
def get_edge_weight(from_node, to_node, children_coords, parent):
unaligned_range = [
from_node.query_block_end + 1, to_node.query_block_start - 1
]
unaligned_exon_bases = 0
for child_interval in children_coords:
if from_node.reference_name == "start":
is_reverse = to_node.is_reverse
else:
is_reverse = from_node.is_reverse
relative_start = liftoff_utils.get_relative_child_coord(
parent, child_interval[0], is_reverse)
relative_end = liftoff_utils.get_relative_child_coord(
parent, child_interval[1], is_reverse)
child_start, child_end = min(relative_start, relative_end), max(
relative_start, relative_end)
overlap = liftoff_utils.count_overlap(child_start, child_end,
unaligned_range[0],
unaligned_range[1])
if overlap == 1 and unaligned_range[0] == unaligned_range[1]:
unaligned_exon_bases += to_node.reference_block_start - from_node.reference_block_end + 1
else:
unaligned_exon_bases += max(0, overlap)
return unaligned_exon_bases + 1