EFETCH(1)

💖 EFETCH(1) 💖

okay bestie, welcome to the NCBI Entrez Direct User's Manual — no cap, this is the page for efetch and esummary, and it's gonna be a whole vibe. 🧚

---

✨ NAME ✨

efetch, esummary — retrieve results from an NCBI Entrez search 🫶

---

🌸 SYNOPSIS 🌸

efetch [-help] [-format fmt] [-mode mode] [-style style] [-db name]
[-id ID] [-input filename] [-seq_start N] [-seq_stop N] [-strand N]
[-forward] [-revcomp] [-chr_start N] [-chr_stop N] [-complexity N]
[-extend N] [-extrafeat N] [-showgaps] [-start N] [-stop N] [-raw]
[-express] [-immediate] [-json]

esummary [-help] [-mode mode] [-db name] [-id ID] [-input filename]
[-raw]

---

🦋 DESCRIPTION 🦋

so like, efetch and esummary are your girls for pulling results out of an Entrez Direct pipeline, or from an immediate lookup — that's the -db plus -id or -input situation. lowkey iconic.

and the tea: esummary is literally just efetch -format docsum. same girl, different font. 💅

⚠️ okay but here's the plot twist — efetch is also the name of an AceDB tool for consulting local sequence databases. two completely different queens, one name. not me having to clarify this 😭

to resolve this ambiguity, Debian systems with both AceDB tools and Entrez Direct installed arrange for AceDB's executable to have the name efetch.acedb(1), and for efetch to be a wrapper script that examines its usage and proceeds to run whichever of efetch.acedb(1) or efetch.ncbi looks like a better fit. she's a diplomat, she's a matchmaker, she's everything. 👑

---

💅 OPTIONS 💅

🎀 Format Selection

• -format fmt — the format of the record or report. (peep the -help output for examples, bestie ✨)
• -mode mode — pick your girl: text, xml, asn, binary, or json.
• -style style — master or conwithfeat.

🍓 Direct Record Selection

• -db name — Entrez database name for immediate lookups.
• -id ID — unique identifier or accession for immediate lookups.
• -input filename — read identifer(s) from file instead of standard input. (yes, that's how it's spelled in the original, we keep it fr fr 🫶)

🌈 Sequence Range

• -seq_start N — first sequence position to retrieve (1-based).
• -seq_stop N — last sequence position to retrieve (1-based).
• -strand N — strand of DNA to retrieve: 1 for forward (plus), 2 for reverse complement (minus).
• -forward — shortcut for -strand 1. ⭐
• -revcomp — shortcut for -strand 2. 🔄

🧚 Gene Range

• -chr_start N — first sequence position to retrieve (0-based).
• -chr_stop N — last sequence position to retrieve (0-based).

👀 heads up: this one's 0-based, the sequence range up there was 1-based. they are NOT the same girl.

💜 Sequence Flags

• -complexity N — how much context to fetch, like how nosy are we feeling today:
  • 0 — default
  • 1 — Bioseq
  • 3 — Nuc-prot set
• -extend N — extend sequence retrieval by N residues in both directions.
• -extrafeat N — bit flag specifying extra features.
• -showgaps — propagate component gaps.

🌸 Subset Retrieval

• -start N — first record to fetch.
• -stop N — last record to fetch.

✨ Miscellaneous

• -raw — skip database-specific XML modifications.
• -express — direct sequence retrieval in groups of five. 🖐️
• -immediate — Express mode on a single record at a time.
• -json — convert adjusted XML output to JSON.
• -help — print usage information, complete with examples of notable -db/-format/-mode combinations (in the case of efetch) and of supplying accessions in the -id field (in the case of esummary). she's helpful AND gorgeous 💖

---

🔥 SEE ALSO 🔥

bsmp2info(1), combine-uid-lists(1), difference-uid-lists(1), ds2pme(1), ecollect(1), efetch.acedb(1), elink(1), esample(1), esearch(1), exclude-uid-lists(1), gbf2facds(1), gbf2fsa(1), gbf2info(1), gbf2tbl(1), hgvs2spdi(1), intersect-uid-lists(1), nquire(1), pm-refresh(1), pma2apa(1), pma2pme(1), pmc2bioc(1), pmc2info(1), run-ncbi-converter(1), snp2hgvs(1), snp2tbl(1), spdi2tbl(1), transmute(1), xfetch(1), xinfo(1), xlink(1), xml2fsa(1), xml2tbl(1), xsearch(1), xtract(1).

the whole friend group came out for this one, periodt. 💀🌈

---

that's the whole page bestie — brought to you by NCBI, dated 2025-05-26, and it's giving main character energy. go fetch something iconic 🎀✨