Gbf2xml

gbf2xml

Quick Start

• Command: gbf2xml < records.gbf > records.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2xml
• Full reference: See references/help.md for complete usage details

When To Use This Tool

• Convert GenBank flatfiles into XML so they can be queried with XML tools.
• Bridge annotated sequence records from flatfile form into EDirect pipelines that expect XML.
• Normalize GenBank content before further extraction, transformation, or archiving.

Common Patterns

# 1) Convert a GenBank flatfile into XML
gbf2xml < records.gbf > records.xml

# 2) Convert and inspect the resulting XML structure quickly
gbf2xml < records.gbf | sed -n '1,40p'

Recommended Workflow

1. Start from a representative GenBank flatfile sample.
2. Run gbf2xml through stdin redirection or a pipe.
3. Check that non-empty XML is produced before processing a large dataset.
4. Feed the XML into xtract or other downstream tools only after that smoke test passes.

Guardrails

• This wrapper simply runs transmute -g2x, so the companion transmute binary must be on PATH.
• The installed wrapper does not provide a real --help / --version interface.
• Prefer stdin/pipes over relying on undocumented positional-file behavior.
• Malformed flatfiles can yield empty output, so inspect a small sample before batching.