gff-sort

name	gff-sort
description	Use when you need to reorder GFF3 records so parent features stay ahead of children in EDirect-style annotation pipelines.
disable-model-invocation	true
user-invocable	true

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

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.