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"""
Merge criteria used by FeatureDB merge() and merge_all()
"""
from gffutils.feature import Feature
def seqid(acc, cur, components):
return cur.seqid == acc.seqid
def strand(acc, cur, components):
return acc.strand == cur.strand
def feature_type(acc, cur, components):
return acc.featuretype == cur.featuretype
def exact_coordinates_only(acc, cur, components):
return cur.start == acc.start and cur.stop == acc.end
def overlap_end_inclusive(acc, cur, components):
return acc.start <= cur.start <= acc.end + 1
def overlap_start_inclusive(acc, cur, components):
return acc.start <= cur.end + 1 <= acc.end + 1
def overlap_any_inclusive(acc, cur, components):
return (
acc.start <= cur.start <= acc.end + 1 or acc.start <= cur.end + 1 <= acc.end + 1
)
def overlap_end_threshold(threshold):
def partial(acc, cur, components):
return acc.start <= cur.start <= acc.end + threshold
return partial
def overlap_start_threshold(threshold):
def partial(acc, cur, components):
return acc.start - threshold <= cur.end + 1 <= acc.end + 1
return partial
def overlap_any_threshold(threshold):
def partial(acc, cur, components):
return (
acc.start - threshold <= cur.end + 1 <= acc.end + 1
or acc.start <= cur.start <= acc.end + threshold
)
return partial
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