gbf2facds

name	gbf2facds
description	Use when converting GenBank format files to FASTA coding sequences (CDS) for downstream sequence analysis.
disable-model-invocation	true
user-invocable	true

gbf2facds

Quick Start

• Command: gbf2facds -na < records.gbf > cds.fna
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2facds
• Reference: See references/help.md for detailed usage

When To Use This Tool

• Extract CDS sequences from GenBank flatfiles in FASTA form.
• Choose nucleotide CDS output (-na) or translated protein output (-aa) from the same GenBank input.
• Flatten GenBank CDS annotations into FASTA records for downstream alignment, clustering, or annotation QC.

Common Patterns

# 1) Extract nucleotide CDS sequences
gbf2facds -na < records.gbf > cds.fna

# 2) Extract translated CDS protein sequences
gbf2facds -aa < records.gbf > cds.faa

Recommended Workflow

1. Prepare GenBank format input files
2. Pick -na for nucleotide CDS or -aa for protein translation output.
3. Run gbf2facds on a representative sample and inspect the FASTA headers.
4. Use extracted CDS for downstream bioinformatics analyses

Guardrails

• --help and --version are rejected as unrecognized arguments; the only real switches are the nucleotide/protein selectors.
• The wrapper depends on gbf2info and xtract, so the broader EDirect toolchain must be on PATH.
• FASTA headers include accession, protein_id, gene, product, location, and gbkey, so downstream parsers should expect metadata-rich headers rather than bare accessions.