efetch

Quick Start

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

When To Use This Tool

• Retrieve full records or sequence data after esearch or epost.
• Fetch records by ID or accession from PubMed, Nucleotide, Protein, Gene, SRA, Assembly, and related databases.
• Export in FASTA, abstract, docsum, XML, JSON, or native record formats.
• Pull sequence subranges when you only need a locus, not the entire accession.

Common Patterns

# 1) Fetch PubMed abstracts from a search result
esearch -db pubmed -query 'ebola virus[Title/Abstract]' | efetch -format abstract

# 2) Fetch a nucleotide record in FASTA
efetch -db nucleotide -id NM_000546.6 -format fasta

# 3) Fetch only a sequence subrange
efetch \
  -db nucleotide \
  -id NC_000001.11 \
  -format fasta \
  -seq_start 100000 \
  -seq_stop 101000

# 4) Fetch summaries in JSON-compatible mode
efetch -db assembly -id GCF_000001405.40 -format docsum -mode json

Recommended Workflow

1. Get stable IDs first with esearch or epost.
2. Choose -format deliberately, because downstream parsing depends on it.
3. Save raw outputs for reproducibility when the fetched record is part of an analysis result.
4. Pipe XML-style outputs into xtract only after verifying the record shape.

Guardrails

• Always specify -db and usually specify -format; implicit defaults are easy to misread.
• Large fetches should be chunked with -start and -stop, or handled through batched EDirect pipelines.
• -seq_start, -seq_stop, and strand options only apply to sequence-style retrieval.
• Invalid or mismatched IDs often yield empty output, so validate the upstream search first.