BIOAWK(1)

📦
version 1.0 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ NAME ✨

bioawk — bestie, it's literally awk but for biological sequence analysis 💖

🦋 DESCRIPTION 🦋

okay so listen. bioawk is here to make your bioinformatics life SO much easier, and the way it does that is by knowing your file formats by heart. Like, it already knows which column is which, so you don't have to count fields on your fingers every single time. iconic behaviour honestly 👑

here's the vibe check on every format it understands, and what field number maps to what:

🛏️ bed:

1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart
8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts

🧬 sam:

1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext
9:tlen 10:seq 11:qual

🍓 vcf:

1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info

🌸 gff:

1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter
8:strand 9:group 10:attribute

🧚 fastx:

1:name 2:seq 3:qual 4:comment

👑 AUTHOR 👑

this manpage was written by Nilesh Patra for the Debian distribution, and can be used for any other usage of the program. slay 💅

k that's the whole page bestie, no cap 🫶 this was bioawk 1.0 from February 2021 — BIOAWK(1) fr fr, go parse some sequences ✨🧬💖

📦 where this page comes from