filter-genbank

name	filter-genbank
description	Use when filtering or processing GenBank-format sequence records retrieved via NCBI Entrez Direct tools
disable-model-invocation	true
user-invocable	true

filter-genbank

Quick Start

• Command: filter-genbank < records.gbf > filtered.gbf
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/filter-genbank
• Reference: See references/help.md for detailed usage information

When To Use This Tool

• Apply EDirect's built-in GenBank flatfile filtering/normalization step to a GenBank stream.
• Clean or reshape GenBank-format records before a downstream transmutation or extraction stage.
• Keep GenBank filtering inside the EDirect toolchain instead of writing a custom parser.

Common Patterns

# 1) Filter a saved GenBank flatfile stream
filter-genbank < records.gbf > filtered.gbf

# 2) Filter GenBank output directly from an Entrez pipeline
efetch -db nuccore -id ABC123.1 -format gbwithparts | filter-genbank

Recommended Workflow

1. Start from real GenBank flatfile content, typically from efetch.
2. Pipe it through filter-genbank rather than relying on positional filenames.
3. Inspect the first filtered records before running a large batch.
4. Pass the result to the next EDirect or archival step once the output looks right.

Guardrails

• This is a thin wrapper around transmute -gbf, so transmute must be on PATH.
• --help and --version are not implemented here; both are reported as unrecognized arguments.
• Prefer stdin or pipes over undocumented positional-file behavior.
• Because the actual filtering rules live inside transmute, validate on a representative GenBank sample before batching.