EDIRECT_DO_AUTO_ABBREV
Accept (currently) unambiguous truncated option names, as in -verbo for -verbose.
edirect1
Access ncbi entrez from the command line (deprecated)
Usage
edirect -version
esearch (edirect
-search)
options
elink (edirect
-link)
options
efilter (edirect
-filter)
options
esummary (edirect
-summary)
options
efetch (edirect
-fetch)
options
einfo (edirect
-info)
options
epost (edirect
-post)
options
espell (edirect
-spell)
options
ecitmatch (edirect
-citmatch)
options
eproxy (edirect
-proxy)
options
econtact (edirect
-contact)
options
enotify (edirect
-notify)
options
eaddress (edirect
-address)
options
eblast (edirect
-blast)
options
ftp-ls (edirect
-ftpls)
options
ftp-cp (edirect
-ftpcp)
options
transmute (edirect
-tmute)
options
edirect -nquir
options
Overview
Note: edirect might not appear in future releases of NCBI Entrez Direct. However, several individual commands (esearch through epost) live on as nquire-based shell scripts.
edirect (Entrez Direct) is a command-line utility for consulting NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) in a variety of fashions, most of which are documented individually in dedicated man pages. (The one exception is edirect -nquir, which roughly corresponds to nquire but is fully independent.)
Options
Most subcommands accept the following options, in addition to command-specific options.
-
-help -
Print usage information.
-
-email address -
Send the given e-mail address to have someone to notify in case a runaway script causes problems with an NCBI Entrez server.
-
-tool name -
Send the given client name.
|
Force the use of GET rather than POST HTTPS requests. |
|---|---|
|
Specify a file of shortcut keywords and query strings or URL sections. |
-
-silent -
Suppress connection failure retry messages.
-
-verbose -
Display the
ENTREZ_DIRECTXML field values at each step.
-
-debug -
Print the internal URL query and XML results of each step.
-baseURL-
Specify a particular server for quality assurance testing.
Environment
-
NCBI_API_KEY -
NCBI E-Utilities API key, allowing for a higher request rate at the cost of some anonymity.
Releases
3 releases since Debian 9 (Stretch); the text changed 2 times.