Gbf2info

gbf2info

Quick Start

• Command: gbf2info
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2info
• Reference: See references/help.md for detailed documentation

When To Use This Tool

• Convert GenBank flatfiles into structured GenBankInfo XML.
• Expose accession, locus, organism, feature, qualifier, sequence, transcription, and translation content in a machine-friendly XML layout.
• Provide a richer intermediate representation for downstream xtract-based extraction than raw GenBank text.

Common Patterns

# 1) Convert a GenBank flatfile into structured GenBankInfo XML
gbf2info < records.gbf > records.info.xml

# 2) Convert and inspect feature-level content immediately
gbf2info < records.gbf | xtract -pattern feature -element feature_key gene product protein_id

Recommended Workflow

1. Start from real GenBank flatfile content, typically from efetch.
2. Pipe it into gbf2info and inspect a small sample first.
3. Confirm that the emitted GenBankInfo structure contains the features and qualifiers you expect.
4. Feed that XML into downstream xtract, CDS extraction, or reporting steps.

Guardrails

• The wrapper is an xtract-heavy pipeline over GenBank XML, so the broader EDirect toolchain must be on PATH.
• --help / --version do not provide custom documentation; with no input the wrapper falls through to xtract-style “no data supplied” errors.
• Feature names that would collide with qualifier names or invalid XML tags are remapped internally (for example 3'UTR becomes 3_UTR), so do not assume raw GenBank feature names survive unchanged.