daler/pybedtools — Issue #45: (a+b+c) is not commutative and overestimates overlap
Author: spikesd17
Created: 2011-10-27 03:19:31+00:00
State: open

I have three BED Tools, a b and c, and I expect that (a+b+c).count() should == (b+a+c).count(), since that function is intended to extract features that are common to all three BedTools. (as discussed here: http://packages.python.org/pybedtools/3-brief-examples.html#example-2-intersections-for-a-3-way-venn-diagram) However, in my tests, I find conflicting results, depending on the order of the operands. Also, the total number present in (a+b+c).count() [or any other order] seems to be an over-estimate of the actual number of overlaps, given that I find elements in (a+b+c) that are specific to only b. I can provide BED files for testing if needed.

as a consequence, "venn_mpl.py -c a.BED -a b.BED -b c.BED " gives a different result from "venn_mpl.py -a a.BED -b b.BED -c c.BED "