GFFUTILS-CLI(1)

💖 GFFUTILS-CLI 💖

okay bestie, welcome to the gffutils-cli(1) page — user commands, but make it a vibe. this is the command line interface for python-gffutils, and it's genuinely so useful. let's get into it 🫶

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🌸 NAME 🌸

gffutils-cli — Command line interface for python-gffutils.

like, literally the front door to python-gffutils from your terminal. no python required, just vibes and flags ✨

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🎀 SYNOPSIS 🎀

gffutils-cli [-h]
             {fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}
             ...

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🦋 DESCRIPTION 🦋

so you run it, and it hands you a whole menu of subcommands. no cap. here's the layout, and yes we're going through every single one because they all eat 💅

✨ positional arguments ✨

these are your main character subcommands, pick one:

• {fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}
• fetch — Fetch IDs.
• children — Fetch children from the database according to ID.
• parents — Fetch parents from the database according to ID.
• region — Returns features within provided genomic coordinates.
• create — Create a database.
• common — Identify child features in common (e.g., common exons across multiple isoforms)
• clean — Perform various QC operations to clean a GFF or GTF file.
• search — Search the attributes.
• sanitize — Sanitize a GFF file. Might get merged with clean feature later. Cleans and adds useful annotations to a GFF file: - Ensures that start > end in all entries - Adds an entry id (eid) to each entry to make files grep-able Outputs result to stdout unless asked to sanitize in place.
• rmdups — Remove duplicates from a GFF file.

ngl, sanitize is out here doing the most — fixing up your entries and adding an eid so your files are grep-able. it writes to stdout unless you tell it to sanitize in place. iconic behavior honestly. 💅

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🌈 options 🌈

short list, but every one counts:

• -h, --help — show this help message and exit

that's it. that's the whole options list. she's minimalist, she's efficient, she's the moment 😌

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👑 SEE ALSO 👑

there's no SEE ALSO section in this page bestie, we're keeping it exactly as it is — no invented cross-references, periodt. the facts stay the facts 💖

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quick reminder before you go: the vibe is silly, but the facts are sacred. every flag, every subcommand, every path and number above is exactly what's in the real page. no extras, no guesses, no drama. 🧚

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and that's the whole page, bestie!! go forth and process those GFF files, you've got this 💜🌸🦋

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if you ever forget where this came from: gffutils-cli 0.14, dropped August 2026, living happily inside the GFFUTILS-CLI(1) manual. slay 💅✨