Hi, I'm trying to filter a maf file with the scripts provided. What I'd like to do is filter a maf such that only blocks that only contain sequence from a listed set of species are returned. The maf_limit_to_species.py script looks promising, but when I run:
maf_limit_to_species.py species1,species2,species3 < maf > newmaf
I get blocks that contain only species1 and species 2, but not species 3, for example. Is there another script or a modification to this script that I can use to only return blocks that only contain sequence from all listed species?
thanks for your help,