EDIRECT_PUBMED_MASTER
Local archive directory to use in the absence of -path. Expected to hold an absolute path; mandatory when not supplying a path on the command line.
fetch-pubmed1
Fetch records from a local ncbi pubmed archive by uid
Usage
fetch-pubmed [{-strict | -mixed}]
[[-path]
dir]
[-all]
[-fresh]
[{-asn | -xml | -pme}]
[-turbo]
Overview
fetch-pubmed reads a list of record IDs from standard input and prints to standard output the corresponding portions of a local NCBI PubMed archive produced by archive-pubmed(1), typically for further processing by xtract(1) or the like.
Options
|
Run rchive(1) with -flag strict or -flag mixed, respectively. |
|---|---|
[-path] dir
|
Use the local archive in dir. |
-
-all -
Dump the entire archive.
-
-fresh -
Dump the entire archive into filenames of the form
pubmed001.xml.gz, using any existing such files as a starting point.
-
-asn -
Retrieve ASN.1.
-
-xml -
Retrieve XML (default).
-
-pme -
Produce ASN.1 on the fly, via pma2pme.
-
-turbo -
Add NEXT_RECORD_SIZE nodes to speed navigation.
Environment
Releases
3 releases since Debian 10 (Buster); the text changed 2 times.
-all since Debian 11 (Bullseye);
-asn since Debian 12 (Bookworm);
-fresh since Debian 11 (Bullseye);
-pme since Debian 12 (Bookworm);
-turbo since Debian 12 (Bookworm);
-xml since Debian 12 (Bookworm).