is there a built in function to compute the overlap between two discrete intervals, e.g. the overlap between [10, 15] and [20, 38]? In that case the overlap is 0. If it\'s
You can use max and min:
>>> def getOverlap(a, b):
... return max(0, min(a[1], b[1]) - max(a[0], b[0]))
>>> getOverlap([10, 25], [20, 38])
5
>>> getOverlap([10, 15], [20, 38])
0
Here is a good function from Aaron Quinlan's chrom_sweep, modified for your interval representation. It returns the number of bp of overlap if they do overlap, otherwise it returns the distance as a negative int.
def overlaps(a, b):
"""
Return the amount of overlap, in bp
between a and b.
If >0, the number of bp of overlap
If 0, they are book-ended.
If <0, the distance in bp between them
"""
return min(a[1], b[1]) - max(a[0], b[0])
Check out pyinterval http://code.google.com/p/pyinterval/
import interval
x=interval.interval[10, 15]
y=interval.interval[20, 38]
z=interval.interval[12,18]
print(x & y)
# interval()
print(x & z)
# interval([12.0, 15.0])
Just wrote this:
def overlap(interval1, interval2):
"""
Given [0, 4] and [1, 10] returns [1, 4]
"""
if interval2[0] <= interval1[0] <= interval2[1]:
start = interval1[0]
elif interval1[0] <= interval2[0] <= interval1[1]:
start = interval2[0]
else:
raise Exception("Intervals are not overlapping")
if interval2[0] <= interval1[1] <= interval2[1]:
end = interval1[1]
elif interval1[0] <= interval2[1] <= interval1[1]:
end = interval2[1]
else:
raise Exception("Intervals are not overlapping")
return (start, end)
def percentage_overlap(interval1, interval2):
"""
Given [0, 4] and [1, 10] returns 0.75
"""
try:
overlap = _overlap(interval1, interval2)
except Exception:
return 0.0
return (overlap[1] - overlap[0]) / (interval1[1] - interval1[0])