def get_edge_weight(from_node, to_node, children_coords, parent, args):
node_overlap = get_node_overlap(from_node, to_node)
unaligned_range = [
from_node.query_block_end + 1,
to_node.query_block_start + node_overlap - 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, min(unaligned_range[0],
unaligned_range[1]),
max(unaligned_range[0], unaligned_range[1]))
if overlap == 1 and unaligned_range[0] == unaligned_range[1] + 1 and from_node.reference_name == \
to_node.reference_name:
unaligned_exon_bases += ((to_node.reference_block_start + node_overlap) - from_node.reference_block_end \
- 1) * args.gap_extend
else:
unaligned_exon_bases += max(0, overlap) * args.gap_extend
if unaligned_exon_bases > 0:
unaligned_exon_bases += (args.gap_open - args.gap_extend
) # gap open penalty
return unaligned_exon_bases
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 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.strand and target_chrm == coords.seqid:
if liftoff_utils.count_overlap(coords.start-1, coords.end-1, from_node.reference_block_end,
to_node.reference_block_start) > 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 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 overlaps_in_ref_annotation(ref_feature1, ref_feature2):
if ref_feature1.seqid != ref_feature2.seqid:
return False
if ref_feature1.strand != ref_feature2.strand:
return False
if ref_feature1.id == ref_feature2.id:
return False
else:
return liftoff_utils.count_overlap(
ref_feature1.start, ref_feature1.end, ref_feature2.start,
ref_feature2.end) > 0
def find_overlapping_children(aln, children_coords, parent):
overlapping_children = []
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:
overlapping_children.append(child_start)
overlapping_children.append(child_end)
return overlapping_children
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