NAME¶

edirect - access NCBI Entrez from the command line (DEPRECATED)

SYNOPSIS¶

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

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.)

COMMON 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.

-http[s] get

Force the use of GET rather than POST HTTPS requests.

-alias filename

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.

-base URL

Specify a particular server for quality assurance testing.

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.

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).