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I like to tell the story of when I was doing some genetics data wrangling and spent three days writing some perl code and I kept failing, then sent one of the r
by arminiusreturns 7y ago
I like to tell the story of when I was doing some genetics data wrangling and spent three days writing some perl code and I kept failing, then sent one of the researchers an email and he suggested an awk method and I turned 3 pages of perl into an awk one liner that works just fine. Now, its probably because I don't know perl very well, but as an ops type who doesnt have the classical dev/cs education, tools like it are my goto.
- bonoboTP 7y agoI find Python list/dict comprehensions, zip, range, enumerate etc. and the itertools module very good for such things. And you have immediate access to so many useful modules (csv, json, xml) and can easily extract code fragments into functions. You can also execute shell-like commands with subprocess.check_output() without ever worrying again about escaping strings or accidentally splitting them at spaces or whatever. Clever one liners are difficult to comprehend. It's better to break them up to a few variable assignments with descriptive, long names without abbreviations.
- arminiusreturns 7y agoI agree python seems to have taken over in this space since then (7+ yrs ago) and is usually a better tool in bioinformatics, I was just using the tools I knew as an ops dude.