GFF-SORT(1)

🌸 NAME 🌸

gff-sort — bestie, it sorts a General Feature Format version 3 file 💖

Oh and hi, this is section 1 of the NCBI Entrez Direct User's Manual, so you know it's legit 👑

🎀 SYNOPSIS 🎀

gff-sort

That's it. That's the whole synopsis. No flags, no arguments, no drama. She just works 💅

🦋 DESCRIPTION 🦋

Okay so here's the tea, bestie 🍓 — gff-sort reads a General Feature Format version 3 (GFF3) file straight from standard input, and prints a sorted equivalent out to standard output. Nothing gets mutated, nothing gets lost, it just gets rearranged and honestly? iconic behavior ✨

The way it decides who goes first is a whole priority ranking, and it goes a little something like this 👇

• accession — this one is the highest priority, and it compares case insensitively 🫶
• feature identifier — case insensitively, and hierarchically (yes queen, hierarchy matters 💅)
• strand — with positive coming first ⭐
• start position
• length — longest first, because big main character energy 👑
• feature key — this one is the lowest priority, and she has her own whole internal ranking, so buckle up:
  • gene or pseudogene go first 🌸
  • then mRNA, primary_transcript, or a recombination site such as C_region
  • then CDS
  • then exon or intron
  • and literally anything else goes last 💀

No cap, the sort order is fully deterministic — accession first, feature key dead last. Every criterion in between is doing its lil job in that exact order 🔥

🔥 SEE ALSO 🔥

Go be nosy, bestie, these are all in the family 😌

• gff2xml(1)
• sort-table(1)
• transmute(1)
• xtract(1)

And that's the whole vibe check, bestie 🧚 This page came to you courtesy of NCBI, dated 2025-05-26, and it lives in the NCBI Entrez Direct User's Manual where it was born to slay 💖✨