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In bioinformatics, awk is such a wonderfully useful tool - most of the data in read alignments/genomics is either in tab delimited format or is easily converted
by a_bonobo 10y ago
In bioinformatics, awk is such a wonderfully useful tool - most of the data in read alignments/genomics is either in tab delimited format or is easily converted from there (via bedtools, samtools, bamtools etc.), so that it's easy to get relevant stats via a quick chain that ends in awk.
There's even a fork of awk called bioawk which adds a few commonly needed functions (treat common bioinformatics files as tab delimited files etc.).
The recent bioinformatics book Bioinformatics Data Skills from Vince Buffalo has a whole chapter on using awk in bioinformatics. Since reading it I've gone from writing 10, 20 line python helper scripts that calculate stats for the publication to just using one line in awk. (Downside: a 20 line python helper script is still in the folder next week and is at least a little bit reproducible, simpler awk stuff disappears in the history if you're not careful)
tl;dr: in bioinformatics it's a boon.