gbf2ref

name	gbf2ref
description	Use when working with GenBank format files and need to create reference indexers for sequence data retrieval or processing within the Entrez Direct toolkit.
disable-model-invocation	true
user-invocable	true

gbf2ref

Quick Start

• Command: gbf2ref < records.gbf > ref_index.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2ref
• Full reference: See references/help.md for detailed documentation

When To Use This Tool

• Convert GenBank flatfiles into the reference-indexer form expected by EDirect's transmute -g2r path.
• Prepare GenBank-derived reference structures for downstream lookup or transformation steps.
• Keep reference-index creation inside the EDirect pipeline rather than writing a custom parser.

Common Patterns

# 1) Create a reference-index stream from GenBank input
gbf2ref < records.gbf > ref_index.xml

# 2) Inspect the generated reference-index structure on a small sample
gbf2ref < records.gbf | sed -n '1,40p'

Recommended Workflow

1. Start from a representative GenBank flatfile stream.
2. Run gbf2ref via stdin redirection or a pipe.
3. Inspect the emitted structure on a small sample before batching.
4. Pass the generated reference-index stream to the next EDirect stage once it looks right.

Guardrails

• This wrapper is only transmute -g2r, so the real behavior lives inside transmute.
• --help and --version do not produce custom docs; in the current build they fall through to the generic “Unable to create GenBank reference indexer” error.
• Prefer stdin or pipes over undocumented positional-file behavior.
• Validate output on a representative sample before depending on the exact structure in automation.