Scroll to navigation

EFETCH(1) NCBI Entrez Direct User's Manual EFETCH(1)


efetch, esummary - retrieve results from an NCBI Entrez search


efetch [-help] [-format fmt] [-mode mode] [-style style] [-db name] [-id ID] [-input filename] [-seq_start N] [-seq_stop N] [-strand N] [-forward] [-revcomp] [-chr_start N] [-chr_stop N] [-complexity N] [-extend N] [-extrafeat N] [-showgaps] [-start N] [-stop N] [-raw] [-express] [-immediate] [-json]

esummary [-help] [-mode mode] [-db name] [-id ID] [-input filename] [-raw]


efetch and esummary retrieve results from either an Entrez Direct pipeline or an immediate lookup (via -db and -id or -input). esummary is equivalent to efetch -format docsum.

efetch is also the name of an AceDB tool for consulting local sequence databases. To resolve this ambiguity, Debian systems with both AceDB tools and Entrez Direct installed arrange for AceDB's executable to have the name efetch.acedb(1) and for efetch to be a wrapper script that examines its usage and proceeds to run whichever of efetch.acedb(1) or efetch.ncbi looks like a better fit.


Format Selection

Format of record or report. (See -help output for examples.)
text, xml, asn.1, or json.
master or conwithfeat.

Direct Record Selection

Entrez database name for immediate lookups.
Unique identifier or accession for immediate lookups.
Read identifer(s) from file instead of standard input.

Sequence Range

First sequence position to retrieve (1-based).
Last sequence position to retrieve (1-based).
Strand of DNA to retrieve: 1 for forward (plus), 2 for reverse complement (minus).
Shortcut for -strand 1.
Shortcut for -strand 2.

Gene Range

First sequence position to retrieve (0-based).
Last sequence position to retrieve (0-based).

Sequence Flags

How much context to fetch:
Nuc-prot set
Extend sequence retrieval by N residues in both directions.
Bit flag specifying extra features.
Propagate component gaps.

Subset Retrieval

First record to fetch.
Last record to fetch.


Skip database-specific XML modifications.
Direct sequence retrieval in groups of five.
Express mode on a single record at a time.
Convert adjusted XML output to JSON.
Print usage information, complete with examples of notable -db/-format/-mode combinations (in the case of efetch) and of supplying accessions in the -id field (in the case of esummary).


combine-uid-lists(1), difference-uid-lists(1), ds2pme(1), efetch.acedb(1), esample(1), esearch(1), exclude-uid-lists(1), hgvs2spdi(1), intersect-uid-lists(1), nquire(1), pma2pme(1), rchive(1), transmute(1), xml2fsa(1), xml2tbl(1), xtract(1).

2023-02-12 NCBI