Gbf2fsa

gbf2fsa

Quick Start

• Command: gbf2fsa [input.gbf] > output.fsa
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gbf2fsa
• Reference: See references/help.md for full documentation

When To Use This Tool

• Convert GenBank flatfiles into plain FASTA sequences.
• Flatten annotation-rich GenBank records down to sequence headers plus raw sequence for downstream sequence tools.
• Reuse the existing gbf2xml | xml2fsa pipeline without rebuilding it by hand.

Common Patterns

# 1) Convert a GenBank flatfile into FASTA
gbf2fsa < records.gbf > records.fsa

# 2) Stream GenBank output straight from efetch into FASTA
efetch -db nuccore -id TEST0001 -format gb | gbf2fsa > TEST0001.fsa

Recommended Workflow

1. Verify input file is valid GenBank format (.gbf)
2. Run gbf2fsa through stdin redirection or a pipe.
3. Inspect the FASTA header and sequence on a small sample first.
4. Proceed with downstream FASTA-based analysis

Guardrails

• Input must be valid GenBank format
• This wrapper is just gbf2xml | xml2fsa, so transmute, xtract, and the companion wrappers must all be on PATH.
• The wrapper does not provide meaningful --help / --version output.
• Output FASTA headers follow the xml2fsa accession-plus-definition pattern, so confirm they match downstream expectations.