FETCH-PMC(1)

📦 version 19.2.20230331, in debian bookworm, ubuntu noble

✨ fetch-pmc — the manual, but make it make sense ✨

okay bestie, this is the FETCH-PMC(1) page from the NCBI Entrez Direct User's Manual, and I'm gonna walk you through it like we're texting at 2am 💖

🌸 NAME 🌸

fetch-pmc — grab records out of a local NCBI PubMed Central archive by UID. that's the whole vibe 🦋

🎀 SYNOPSIS 🎀

fetch-pmc [-strict|-mixed] [[-path] dir]

like. that's it. that's the whole thing. iconic. 💅

✨ DESCRIPTION ✨

so here's what's happening, bestie 👑

fetch-pmc reads a list of record IDs from standard input and prints to standard output the corresponding portions of a local NCBI PubMed archive — specifically one that was produced by archive-pmc(1).

and why do we care?? because you're typically gonna hand that output off to xtract(1) or something like it for further processing. it's giving pipeline main character energy 🌈

💖 OPTIONS 💖

  • -strict|-mixed — runs rchive(1) with -flag strict or -flag mixed, respectively. pick your fighter, both are valid 💪
  • [-path] dir — use the local archive sitting in dir. yes the -path is optional-optional, that's the brackets talking 🎀

🌈 ENVIRONMENT 🌈

  • EDIRECT_PMC_MASTER — the local archive directory to use when -path isn't there. it's expected to hold an absolute path, and it is mandatory when you're not supplying a path on the command line. so like. don't skip it. fr fr 😭
⚠️ no cap: if you don't pass a path and you don't have EDIRECT_PMC_MASTER set, you've got nothing to fetch from. that's not a vibe check you want to fail.

🦋 SEE ALSO 🦋

archive-pmc(1), rchive(1), xtract(1) — go read those too, they're part of the squad 🫶

that's the whole page, bestie!! 💖 this one came from NCBI, dated 2023-02-25, and honestly? it ate. now go fetch those records ✨👑🌸

📦 where this page comes from