>I find there is usually also some file juggling, parsing, [...]

I'd say I'm 50/50 Python/R for exactly this reason: I write Python code on HPC or a server to parse many, many files, then I get some kind of MB-scale summary data I analyse locally in R.

R is not good at looping over hundreds of files in the gigabytes, Python is not good at making pretty insights from the summary. A tool for every task.