How do I install the Gff Sort skill?

Run npx skillmds add vimalinx/gff-sort in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Gff Sort safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Gff Sort?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Gff Sort free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Gff Sort?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Gff Sort by vimalinx — Agent Skill

Name: Gff Sort
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

gff-sort

Quick Start

Command: PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/gff-sort < input.gff3 > sorted.gff3
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gff-sort
Full reference: See references/help.md for complete usage details

When To Use This Tool

Sort unsorted GFF3 feature streams while keeping gene / pseudogene before transcripts, then CDS, then exon / intron.
Clean up record order after concatenating annotations or generating GFF programmatically.
Use inside EDirect pipelines when you already have companion helpers such as tbl2xml, xtract, transmute, and sort-table.

Common Patterns

# 1) Sort an unsorted GFF3 body in EDirect's expected feature order
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gff-sort \
  < unsorted.gff3 \
  > sorted.gff3

# 2) Re-sort merged annotation fragments before downstream use
cat part1.gff3 part2.gff3 part3.gff3 | \
  PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/gff-sort \
  > merged.sorted.gff3

Recommended Workflow

Put the EDirect bin directory on PATH; this wrapper depends on sibling tools and cannot run standalone by absolute path alone.
Feed it a valid tab-delimited GFF3 stream on stdin.
Spot-check that parent-child ordering is now gene -> transcript/RNA -> CDS -> exon / intron.
Reattach header or directive lines separately if downstream tools require them.

Guardrails

This script has no real built-in help or version mode; with missing companion tools it can still exit after printing command not found errors.
It strips comment and directive lines such as ##gff-version 3, so preserve headers separately if you need them later.
Feature precedence is hard-coded: gene / pseudogene first, RNA-like features second, CDS third, exon / intron fourth, everything else last.
Sorting relies on sibling EDirect tools (tbl2xml, xtract, transmute, sort-table) being discoverable on PATH.

---name: gff-sortdescription: Use when you need to reorder GFF3 records so parent features stay ahead of children in EDirect-style annotation pipelines.--- # gff-sort ## Quick Start - **Command:** `PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH /home/vimalinx/miniforge3/envs/bio/bin/gff-sort < input.gff3 > sorted.gff3` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/gff-sort` - **Full reference:** See [references/help.md](references/help.md) for complete usage details ## When To Use This Tool - Sort unsorted GFF3 feature streams while keeping `gene` / `pseudogene` before transcripts, then `CDS`, then `exon` / `intron`. - Clean up record order after concatenating annotations or generating GFF programmatically. - Use inside EDirect pipelines when you already have companion helpers such as `tbl2xml`, `xtract`, `transmute`, and `sort-table`. ## Common Patterns ```bash # 1) Sort an unsorted GFF3 body in EDirect's expected feature order PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \ /home/vimalinx/miniforge3/envs/bio/bin/gff-sort \ < unsorted.gff3 \ > sorted.gff3 ``` ```bash # 2) Re-sort merged annotation fragments before downstream use cat part1.gff3 part2.gff3 part3.gff3 | \ PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \ /home/vimalinx/miniforge3/envs/bio/bin/gff-sort \ > merged.sorted.gff3 ``` ## Recommended Workflow 1. Put the EDirect bin directory on `PATH`; this wrapper depends on sibling tools and cannot run standalone by absolute path alone. 2. Feed it a valid tab-delimited GFF3 stream on stdin. 3. Spot-check that parent-child ordering is now `gene` -> transcript/RNA -> `CDS` -> `exon` / `intron`. 4. Reattach header or directive lines separately if downstream tools require them. ## Guardrails - This script has no real built-in help or version mode; with missing companion tools it can still exit after printing `command not found` errors. - It strips comment and directive lines such as `##gff-version 3`, so preserve headers separately if you need them later. - Feature precedence is hard-coded: `gene` / `pseudogene` first, RNA-like features second, `CDS` third, `exon` / `intron` fourth, everything else last. - Sorting relies on sibling EDirect tools (`tbl2xml`, `xtract`, `transmute`, `sort-table`) being discoverable on `PATH`.

Frequently asked questions