Excerpts from Amit Indap's message of Tue Dec 07 04:10:09 +0000 2010:
But I'm trying to see if there is a way I can get the complement, bases in the second file that don't overlap the first. The desired answer would be: chr22 147 267 chr22 572 627
bed_complement.py is the key here. There are multiple ways to get the desired result, but here is one: bed_complement.py 1.bed <(echo "chr22 1000") | bed_intersect_basewise.py /dev/stdin 2.bed bed_complement.py needs a LEN file, here I just make a fake one on the fly, you will probably want to use a real one, although for this particular case, it doesn't matter as long as the lengths are larger than any end position in the second file. (In Galaxy, this is 'complement' followed by 'intersect' with overlapping pieces, LEN files are handled automagically). -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University