efilter

name	efilter
description	Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines.
disable-model-invocation	true
user-invocable	true

efilter

Quick Start

• Command: efilter
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/efilter
• Full reference: See references/help.md

When To Use This Tool

• Narrow an existing Entrez result set by date, organism, publication type, sequence feature, SNP class, or assembly status.
• Add database-specific shortcuts after esearch or elink without rewriting the whole query string.
• Prototype filters interactively before folding them back into a single esearch command.

Common Patterns

# 1) Keep only recent PubMed hits from a pipeline
esearch -db pubmed -query "opsin gene conversion" \
  | efilter -mindate 2015 \
  | efetch -format docsum

# 2) Restrict sequence results to mammalian RefSeq entries
esearch -db protein -query hemoglobin \
  | efilter -organism mammals -source refseq

# 3) Keep only latest assemblies
esearch -db assembly -query "Escherichia coli" \
  | efilter -status latest

Recommended Workflow

1. Start with an esearch or elink pipeline that already identifies the right Entrez database.
2. Apply only the shortcut family that matches that database category, such as -pub for PubMed or -organism for sequence databases.
3. Inspect counts or summaries if the filter logic is non-obvious.
4. Fetch full records only after the filter stage is stable.

Guardrails

• The local executable is just a wrapper around esearch -filter, so it depends on valid Entrez pipeline state and is not an offline post-processor.
• Shortcut families are database-specific; mixing incompatible groups produces confusing or empty results.
• Many efilter shortcuts can also be expressed directly in esearch, which is often cleaner once you know the final query.
• In this local install, help output can still emit network-version-check noise from EDirect before printing the real usage text.