You must download the following to use MPRA-RAT:
phastcons and phyloP 100 way bigwig files from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/
twoBitToFa from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Questions: how to use both python 3, 2, and R?