FASTAHACK(1)

📦
version 1.0.0 · 6 versions
, in ubuntu noble, ubuntu questing

🌸 FASTAHACK(1) 🌸

okay bestie, welcome to fastahack — it's a User Command, it's in section 1 of the manual, and it's lowkey the moment. 💅

✨ NAME ✨

fastahack — indexing and extracting sequences and subsequences from FASTA files 🧬✨

🦋 DESCRIPTION 🦋

the whole vibe, in one line:

usage: fastahack [options] <fasta reference>

that's it. that's the whole thing. give it a FASTA reference and it will index, extract, entropy and dump for you. no cap. 🫶

🎀 options: 🎀

  • -i, --index — generate a fasta index at <fasta reference>.fai ✨ (yes, right next to your reference, minding its own business)
  • -r, --region REGION — print the specified region 🎯
  • -c, --stdin — read a stream of line-delimited region specifiers on stdin and print the corresponding sequence for each one on stdout 🌊 (yes, it's a whole pipeline moment)
  • -e, --entropy — print the shannon entropy of the specified region 🔥 (science!!)
  • -d, --dump — print the fasta file in the form 'seq_name <tab> sequence' 💾 (tab-separated, exactly like that)

🌈 so like, what even is a REGION? 🌈

REGION is of the form:

<seq>, <seq>:<start>[sep]<end>, <seq1>:<start>[sep]<seq2>:<end>

where start and end are 1-based, and the region includes the end position. and [sep] is "-" or ".." 💖

and the way it behaves, fr fr:

  • specifying a sequence name alone will return the entire sequence
  • specifying a range will return that range
  • and specifying a single coordinate pair, e.g. <seq>:<start>, will return just that base — one singular base, she's tiny but she's iconic 👑
ngl the 1-based + inclusive-end thing is the detail everyone gets wrong, so like, write it down bestie 📝

👑 author: 👑

Erik Garrison <erik.garrison@bc.edu> — king behaviour, we stan 💜

and that's the page!! fastahack 1.0.0+dfsg-11, dated December 2023 🌸 this has been your girl explaining FASTA hacking with main character energy. go index something. slay. 💅✨🦋

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