GT-UNIQ(1)

💖 GT-UNIQ(1) 💖

okay bestie, welcome to the GenomeTools Manual — this one's called gt-uniq and it's lowkey a bouncer for your GFF3 file, fr fr 🎀

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✨ NAME ✨

gt-uniq — filter out repeated feature node graphs in a sorted GFF3 file. that's it, that's the whole job 💅

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🌸 SYNOPSIS 🌸

gt uniq [option ...] [GFF3_file]

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🦋 DESCRIPTION 🦋

first things first, the options, because we love a menu 🫶

• -v [yes|no] — be verbose (default: no). like, do you want it to narrate? yes or no, no in-between.
• -o [filename] — redirect output to specified file (default: undefined). if you don't say where, it just goes... wherever it goes. nowhere specified. vibes only.
• -gzip [yes|no] — write gzip compressed output file (default: no).
• -bzip2 [yes|no] — write bzip2 compressed output file (default: no).
• -force [yes|no] — force writing to output file (default: no). it will NOT overwrite your stuff unless you say so, bestie. respect.
• -help — display help and exit. classic.
• -version — display version information and exit. also classic.

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🧚 the actual lore (traversal & similarity)

so a depth-first traversal of a feature node graph starts at the top-level feature node (or pseudo-node) and explores as far along each branch as possible before backtracking. it's giving "commit to the bit until you literally cannot, then rewind" energy. ✨

let's assume the feature nodes are stored in a list in the order of their traversal — this is called the "feature node list". iconic name, no notes.

two feature node graphs are considered to be repeated if their feature node list (from the depth-first traversal) has the same length and each feature node pair (from both lists at the same position) is "similar".

two feature nodes are "similar" if they have the same:

• sequence ID
• feature type
• range
• strand
• phase

all five, or it's not a match. the vibe check is strict. 💀

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👑 which one survives

for such a repeated feature node graph, the one with the higher score (of the top-level feature) is kept. slay. and if only one of the feature node graphs has a defined score, that one is kept. periodt.

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💜 REPORTING BUGS 💜

found a bug? don't suffer in silence, report it to https://github.com/genometools/genometools/issues. the devs wanna know 🫶

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okay that's the whole page, you ate that reading session fr fr 🌈✨ this was GenomeTools 1.6.6, dated 11/09/2025 — mwah, go filter something 💅🎀