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I’ll do you the immense favor of taking the bait. What’s so bad about it?
by Fraterkes 1y ago
I’ll do you the immense favor of taking the bait. What’s so bad about it?
- jszymborski 1y agoIt's a fine format for what it is. A parser to stream FASTA can be written in like 30 lines [0], much easier than say CSV where the edge cases can get hairy. If you need something like fast random reads, use the FAIDX format [1], or even better just store it in an LMDB or SQLite embedded db. People forget FASTA was from 1985, and it sticks around because (1) it's easy to parse and write (2) we have mountains of sequences in that format going back 4 decades. [O] https://gist.github.com/jszym/9860a2671dabb45424f2673a49e4b582 https://gist.github.com/jszym/9860a2671dabb45424f2673a49e4b5... [1] https://seqan.readthedocs.io/en/main/Tutorial/InputOutput/IndexedFastaIO.html https://seqan.readthedocs.io/en/main/Tutorial/InputOutput/In...