GETCDS(1)

🌸 NAME 🌸

okay so bestie, meet getcds.pl (a Perl situation, obviously) — it does CDS extraction from various annotation formats 💅 like it just. goes and gets your coding sequences out of whatever annotation chaos you handed it. iconic behavior, honestly.

---

✨ SYNOPSIS ✨

the vibe check, literally:

getcds.pl [options] input file [output file] [input file [outputfile] ...]

so yeah, it takes options, then an input file, then optionally an output file, and then it can just. keep going. pairs of files, over and over, as many as you want 🫶

---

💅 OPTIONS 💅

the options, as promised, include:

• redirect => turns on a redirect at runtime. and yes, it's explained below, keep reading babe, don't scroll past me 😭
• force => lets you write empty .cds files. that's it, that's the whole thing. sometimes empty is a valid lifestyle ✨

🎀 tiny but important: if you don't specify an [output file], it just uses [input file].cds. so it AutoPicks for you. no cap.

🦋 the redirect lore 🦋

there's a lot of dark magic you can do with .redirect files 👀. redirects exist to modify the ordinary behavior of the program, and you can apply them:

• globally — a .redirect file sitting in the same directory as [input file] 🏠
• per-input — a [input file].redirect file, just for that one file 🌟

and the order matters: they get read in that order, so per-input effects get applied on top of the global effects. global is the base, per-input is the glitter on top 💖

also, a cute little convenience: if you left the filename exactly as-is from an Ensembl download, the right Ensembl DB source gets guessed automatically for you. no extra work. we love a self-sufficient file 🌈

---

🧚 possible redirects 🧚

here's the whole menu, bestie, every single one:

• CDS — changes what tag type gets searched for when running on bioperl files. (the default is CDS, in case you were wondering.)
• offset — adds some value to all coordinates. shift the whole thing, why not ✨
• +bioperl — on top of any other redirect-based data, this also extracts annotation via bioperl (using a direct disables bioperl's parser by default). yes, the + is doing something. it's giving additive 🔥
• ensembl_build — grab data from the ensembl (in the specified schema).
• ucsc_build — grab data from ucsc (in the specified schema).
• murasaki_synth — synthesize annotation data for each anchor from an alignment. and if this is a directory, then each input file (eg input.lav) is checked for a corresponding .anchors file (eg. input.anchors). very "we'll find it ourselves" of it 👑
• primary — what type of tags to create from data gathered from outside data (eg: ensembl, ucsc, or murasaki). the default is the same as the CDS redirect. so like, it inherits the vibe 💜
• chromosome — forces a specific chromosome rather than deriving it from the filename. assertive. we stan 🎀
• gtf — extract annotation from a .gtf file. that's the whole redirect, lowkey perfect 🦋

💀 warning-ish energy, but in a nice way: the redirect files are genuinely dark magic territory. you can stack them, and per-input beats global, so if your output looks cursed, check your .redirect files first bestie. not me speaking from experience 🙈

---

and that's the whole page, fr fr 🫶

sign-off moment, because you deserve it: this lovely thing is documented as part of the User Contributed Perl Documentation ✨, running under perl v5.40.1 💖, and this version of the page is dated 2026-08-12. go extract some CDS, you absolute main character 👑🌸