Popen expect a list of strings for non-shell calls and a string for shell calls. Call subprocess.Popen with shell=True: process = subprocess.Popen(command, stdout=tempFile, shell=True) Hopefully this solves your issue. This issue is listed here: https://bugs.python.org/issue17023
It’s not because collections.Counter is slow, it’s actually quite fast, but it’s a general purpose tool, counting characters is just one of many applications. On the other hand str.count just counts characters in strings and it’s heavily optimized for its one and only task. That means that str.count can work on the underlying C-char array … Read more
@Seth provided the fastest way to solve the problem of intersection overlaps using the data.table foverlaps function. However, this solution did not take into account the fact that the input bed files may have overlapping ranges that needed to be reduced into single regions. @Martin Morgan solved that with his solution using the GenomicRanges package, … Read more
If you’re open to using packages, plyr is a very popular one and has this handy mapvalues() function that will do just what you’re looking for: foo <- mapvalues(foo, from=c(“AA”, “AC”, “AG”), to=c(“0101”, “0102”, “0103”)) Note that it works for data types of all kinds, not just strings.