def remove_repeats_from_pacbp_list(pacbplist, overlap_ratio=0.85):
"""
"""
if not pacbplist: return pacbplist
# order pacbplist by `bits` attribute, highest first
ordered = pacb.ordering.order_list_by_attribute(pacbplist,
order_by='bits',
reversed=True)
# make upper cross of element indexes in ordered list of pacbps
pairs = recombination.pairwise(range(0, len(ordered)))
# loop over all pacbp combis, calculate overlap and store the
# index to `toberemoved` when higher than `overlap_ratio`
toberemoved = []
for (posA, posB) in pairs:
if posA in toberemoved: continue
if posB in toberemoved: continue
pacbpA = ordered[posA]
pacbpB = ordered[posB]
if ordering.overlap(pacbpA, pacbpB) >= overlap_ratio:
toberemoved.append(posB)
# order `toberemoved` and pop the (pacbp) elements from the ordered input list
toberemoved.sort()
toberemoved.reverse()
for pos in toberemoved:
ordered.pop(pos)
# return the remainder of the odered input list
return ordered
def remove_repeats_from_pacbp_list(pacbplist, overlap_ratio=0.85):
"""
"""
if not pacbplist:
return pacbplist
# order pacbplist by `bits` attribute, highest first
ordered = pacb.ordering.order_list_by_attribute(pacbplist, order_by="bits", reversed=True)
# make upper cross of element indexes in ordered list of pacbps
pairs = recombination.pairwise(range(0, len(ordered)))
# loop over all pacbp combis, calculate overlap and store the
# index to `toberemoved` when higher than `overlap_ratio`
toberemoved = []
for (posA, posB) in pairs:
if posA in toberemoved:
continue
if posB in toberemoved:
continue
pacbpA = ordered[posA]
pacbpB = ordered[posB]
if ordering.overlap(pacbpA, pacbpB) >= overlap_ratio:
toberemoved.append(posB)
# order `toberemoved` and pop the (pacbp) elements from the ordered input list
toberemoved.sort()
toberemoved.reverse()
for pos in toberemoved:
ordered.pop(pos)
# return the remainder of the odered input list
return ordered
def overlap(self,pacbp):
"""
Give the overlap between this and another pacbp
@attention: see pacb.ordering.overlap for documentation
@rtype: positive float
@return: highest overlap ratio of query and sbjct of these 2 pacbps
"""
return ordering.overlap(self,pacbp)
def overlap(self, pacbp):
"""
Give the overlap between this and another pacbp
@attention: see pacb.ordering.overlap for documentation
@rtype: positive float
@return: highest overlap ratio of query and sbjct of these 2 pacbps
"""
return ordering.overlap(self, pacbp)