Feature request: option to colour matched patterns in seqkit grep

[bricoletc]

Hello!

(I use seqkit all the time including) When using seqkit grep, I often wish I could see the pattern I looked for (-p -r) in a FASTA of sequences I'm matching against (-s), coloured, as does Unix grep by default. Here setting this by default wouldn't make as much sense, but what about a --colour flag to seqkit grep allowing colouring the matched pattern(s) (e.g. in red as per UNIX grep)?

Otherwise I struggle to actually see where my matches are when I need to - a workaround I use is to pipe to seqkit replace to flag my matches with non nucleotide/amino acid letters

Best,
Brice

[shenwei356]

I found a great tool, sassy grep (https://github.com/RagnarGrootKoerkamp/sassy/). It supports approximate matching and shows nicely coloured output.