Gbf2tbl

gbf2tbl

Quick Start

• Command: gbf2tbl
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2tbl
• Full reference: See references/help.md for detailed usage and options

When To Use This Tool

• Convert GenBank flatfiles into a feature-table view.
• Flatten GenBank annotations into the >Feature / interval / qualifier layout used by table-oriented downstream tools.
• Reuse the existing gbf2xml | xml2tbl pipeline without reconstructing it by hand.

Common Patterns

# 1) Convert a GenBank flatfile into a feature table
gbf2tbl < records.gbf > records.tbl

# 2) Stream GenBank output directly into a feature-table dump
efetch -db nuccore -id TEST0001 -format gb | gbf2tbl

Recommended Workflow

1. Prepare your GenBank format input file
2. Run gbf2tbl through stdin redirection or a pipe.
3. Inspect the first >Feature block and qualifier rows on a small sample.
4. Integrate results into downstream analysis or reporting

Guardrails

• Verify input files are valid GenBank format before processing
• This wrapper is just gbf2xml | xml2tbl, so transmute, xtract, and the companion wrappers must be on PATH.
• The wrapper does not provide meaningful --help / --version output.
• Output follows the xml2tbl feature-table layout, beginning with >Feature <accession> and then interval/qualifier rows.