gff2gff-py

name	gff2gff-py
description	Use when converting GenBank-derived GFF into bcftools/csq-friendly Ensembl-like GFF3 with the legacy `gff2gff.py` helper.
disable-model-invocation	true
user-invocable	true

gff2gff-py

Quick Start

• Command: /home/vimalinx/miniforge3/envs/bio/bin/gff2gff.py input.gff scratch.db > output.gff3
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gff2gff.py
• Full reference: See references/help.md for complete options and usage

When To Use This Tool

• Salvage certain GenBank-style GFF inputs for downstream bcftools csq use.
• Build a temporary gffutils database and emit a simplified gene / transcript / CDS hierarchy to stdout.
• Use only when the input flavor matches the script's assumptions about gene, mRNA, CDS, ncRNA, Name, and locus_tag attributes.

Common Patterns

# 1) Convert a GenBank-derived GFF and keep the intermediate gffutils DB
/home/vimalinx/miniforge3/envs/bio/bin/gff2gff.py \
  input.gff \
  scratch.db \
  > output.gff3

# 2) Write the scratch DB to a temporary location
tmp_db=$(mktemp /tmp/gffutils.XXXXXX.db)
/home/vimalinx/miniforge3/envs/bio/bin/gff2gff.py input.gff "$tmp_db" > output.gff3

Recommended Workflow

1. Confirm that the Python environment actually provides gffutils; this script imports it before any argument parsing.
2. Use a disposable path for the second argument, because the script creates a gffutils database there with force=True.
3. Redirect stdout to your desired output GFF3 file.
4. Inspect the result for expected ### separators plus gene, transcript, and CDS records before trusting it in annotation workflows.

Guardrails

• In this environment gff2gff.py --help and --version both fail immediately with ModuleNotFoundError: No module named 'gffutils'.
• The second positional argument is a database path, not the converted GFF output path; converted records are printed to stdout.
• Source inspection shows it skips ncRNA feature groups and prints only gene, transcript, and CDS records.
• The script assumes attributes such as Name and locus_tag; mismatched GFF flavors can crash or assert instead of degrading gracefully.