CASSIOPEE(1)

💖 CASSIOPEE 💖

okay bestie, sit down, hydrate, because this is the cassiopee manual page from the User Commands section of the manual and it's lowkey iconic. she indexes and searches genomic sequences and she does NOT play. ✨

🌸 NAME 🌸

cassiopee — index and search tool in genomic sequences 🧬

🦋 SYNOPSIS 🦋

cassiopee [Options] <sequence>

✨ DESCRIPTION ✨

so the tea is: this is the Cassiopee index and search library C implementation. it's a complete rewrite of the ruby Cassiopee gem — glow up of the century, no cap. 👑

what she does: she scans an input genomic sequence (dna / rna / protein) and searches for a subsequence, either with an exact match or allowing substitutions (that's Hamming distance, iykyk) and/or insertion/deletions. the way she handles all three at once?? main character energy fr fr. 💅

🎀 OPTIONS 🎀

one bullet per flag, every single one, because we do not skip details in this house 🫶

• -l — maximum index depth / maximum pattern size 📏
• -u — save index for later use 💾
• -s — sequence to index 🧬
• -p — pattern to search 🔍
• -f — file containing pattern to search 📄
• -o — output file 📝
• -r — apply tree reduction 🌳
• -m — search mode: 0=DNA, 1=RNA, 2=Protein 🔥
• -a — allow alphabet ambiguity search 🌈
• -n — max consecutive N allowed matches in search 🅝
• -e — max substitution allowed matches in search 🔄
• -i — max indel allowed matches in search ➕➖
• -g — generates a dot file of the graph 📊
• -d — max depth of the graph 🕳️
• -t — output format: 0:tsv (default), 1:json 🗂️
• -x — minimum position in sequence ⬅️
• -y — maximum position in sequence ➡️
• -v — show version 🏷️
• -h — show this message 📢

quick reminder bestie: -t defaults to 0 which is tsv, so if you want json you gotta say so yourself 💖

and that's the whole vibe check, you're officially fluent 💜

sign-off era: this page is from Cassiopee Version 1.0, dated April 2014 — yes she's been serving since 2014 and she's still that girl. 🎀✨👑