def getOverlappingRegionDict(bd1, bd2, debug=True):
''' Return a dictionary of overlapping regions within two dictionaries of Bed regions '''
retval = {}
for chrom, bedList1 in bd1.items():
bedList2 = bd2.get(chrom, [])
if bedList2 == []:
continue
if debug:
if not isNonContiguous(bedList1):
errAbort(
"Calculating overlapping regions must have non-contiguous input elements."
)
if not isNonContiguous(bedList2):
errAbort(
"Calculating overlapping regions must have non-contiguous input elements."
)
b1Len = len(bedList1)
b1Idx = 0
b2Len = len(bedList2)
b2Idx = 0
while (b1Idx < b1Len) and (b2Idx < b2Len):
b1Curr = bedList1[b1Idx]
b2Curr = bedList2[b2Idx]
assert b1Curr.chrom == b2Curr.chrom
maxStart = max(b1Curr.chromStart, b2Curr.chromStart)
minEnd = min(b1Curr.chromEnd, b2Curr.chromEnd)
if maxStart < minEnd:
retval[b1Curr.chrom] = retval.get(b1Curr.chrom, []) + [
Bed.Bed("%s\t%d\t%d" % (b1Curr.chrom, maxStart, minEnd))
]
if b1Curr.chromEnd < b2Curr.chromEnd:
b1Idx += 1
elif b1Curr.chromEnd > b2Curr.chromEnd:
b2Idx += 1
else:
b1Idx += 1
b2Idx += 1
return retval
def bedReadFromFile(fn, chromSizes=None):
''' Read a file of Bed regions into a list of Beds and return it '''
f = open(fn)
retval = [Bed.Bed(line, chromSizes=chromSizes) for line in f.readlines()]
f.close()
return retval
