XFETCH(1)

✨ XFETCH(1) ✨

okay so bestie, welcome to xfetch — it's from the NCBI Entrez Direct User's Manual and it's genuinely one of the good ones. 💖

🌸 NAME 🌸

xfetch — grab records out of a local NCBI Entrez Direct archive by UID. that's it, that's the whole vibe. 👑

🎀 SYNOPSIS 🎀

xfetch [-db database] [-id str...|-input file] [-stream]

🦋 DESCRIPTION 🦋

xfetch prints the requested portions of a local NCBI Entrez Direct archive to standard output — you know, the kind of archive that archive-pubmed(1) or something like it made. and like… usually you're doing that so xtract(1) or one of its little friends can chew on it next. it's giving pipeline energy. 💅

by default, xfetch looks at standard input and expects either:

• a raw list of UIDs, or
• an ENTREZ_DIRECT XML object, which is the fancy version because it also carries a database name with it. ✨

💖 OPTIONS 💖

• -db database — fetch from the database you name here. default is pubmed, for now at least. heads up bestie: eventually it's gonna be mandatory to say which database you want, whether you do it on the command line or through the ENTREZ_DIRECT XML. so don't get too comfy relying on the default. 😭
• -id str ... — the UID(s) you wanna fetch! and plot twist: they can be internally delimited by whitespace and literally any punctuation other than . or _. so like, go off with the separators, just not those two. 🍓
• -input file — read the UIDs out of the file you point at instead. 🎀
• -stream — leaves records compressed. that's the whole thing. it just… doesn't decompress them. iconic. 🔥

🌈 ENVIRONMENT 🌈

• EDIRECT_LOCAL_ARCHIVE — the local archive directory. it's expected to hold an absolute path, and it is mandatory when you're not supplying a path on the command line. no path + no env var = we can't help you, bestie. 💀

👑 SEE ALSO 👑

archive-nihocc(1), archive-nlmnlp(1), archive-nmcds(1), archive-pids(1), archive-pmc(1), archive-pubmed(1), archive-taxonomy(1), cit2pmid(1), combine-uid-lists(1), difference-uid-lists(1), download-ncbi-data(1), download-pmc(1), download-pubmed(1), ds2pme(1), ds2pme(1), ecollect(1), edict(1), efetch(1), elink(1), esample(1), esearch(1), exclude-uid-lists(1), intersect-uid-lists(1), pm-refresh(1), pma2apa(1), pma2apa(1), pma2pme(1), pma2pme(1), pmc2bioc(1), pmc2info(1), rchive(1), transmute(1), xfilter(1), xinfo(1), xlink(1), xsearch(1), xtract(1).

and that's the whole page, bestie!! 🫶 this one came from NCBI, dated 2025-05-26, and it's page XFETCH(1) of the NCBI Entrez Direct User's Manual. go fetch something cute. 💜🧚