edirect - access NCBI Entrez from the command line (DEPRECATED)
Contents
Common Options
Most subcommands accept the following options, in addition to command-specific options.
-help Print usage information.
-emailaddress
Send the given e-mail address to have someone to notify in case a runaway script causes problems
with an NCBI Entrez server.
-toolname
Send the given client name.
-http[s] get
Force the use of GET rather than POST HTTPS requests.
-aliasfilename
Specify a file of shortcut keywords and query strings or URL sections.
-silent
Suppress connection failure retry messages.
-verbose
Display the ENTREZ_DIRECT XML 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.
Description
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.)
Environment
EDIRECT_DO_AUTO_ABBREV
Accept (currently) unambiguous truncated option names, as in -verbo for -verbose.
NCBI_API_KEY
NCBI E-Utilities API key, allowing for a higher request rate at the cost of some anonymity.
Name
edirect - access NCBI Entrez from the command line (DEPRECATED)
See Also
eaddress(1), eblast(1), ecitmatch(1), econtact(1), efetch(1), efilter(1), einfo(1), elink(1), enotify(1), entrez-phrase-search(1), epost(1), eproxy(1), esearch(1), espell(1), esummary(1), ftp-cp(1), ftp-ls(1), nquire(1), transmute(1), xtract(1). NCBI 2021-03-07 EDIRECT(1)
Synopsis
edirect-versionesearch (edirect-search) optionselink (edirect-link) optionsefilter (edirect-filter) optionsesummary (edirect-summary) optionsefetch (edirect-fetch) optionseinfo (edirect-info) optionsepost (edirect-post) optionsespell (edirect-spell) optionsecitmatch (edirect-citmatch) optionseproxy (edirect-proxy) optionsecontact (edirect-contact) optionsenotify (edirect-notify) optionseaddress (edirect-address) optionseblast (edirect-blast) optionsftp-ls (edirect-ftpls) optionsftp-cp (edirect-ftpcp) optionstransmute (edirect-tmute) optionsedirect-nquiroptions
