Gff2gff Py

# 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.