EFETCH

NAME

efetch, esummary - retrieve results from an NCBI Entrez search

SYNOPSIS

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]

DESCRIPTION

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.

OPTIONS

Format Selection

-format fmt

Format of record or report. (See -help output for examples.)

-mode mode

text, xml, asn.1, or json.

-style style

master or conwithfeat.

Direct Record Selection

-db name

Entrez database name for immediate lookups.

-id ID

Unique identifier or accession for immediate lookups.

-input filename

Read identifer(s) from file instead of standard input.

Sequence Range

-seq_start N

First sequence position to retrieve (1-based).

-seq_stop N

Last sequence position to retrieve (1-based).

-strand N

Strand of DNA to retrieve: 1 for forward (plus), 2 for reverse complement (minus).

-forward

Shortcut for -strand 1.

-revcomp

Shortcut for -strand 2.

Gene Range

-chr_start N

First sequence position to retrieve (0-based).

-chr_stop N

Last sequence position to retrieve (0-based).

Sequence Flags

-complexity N

How much context to fetch:

	0		default
	1		Bioseq
	3		Nuc-prot set

-extend N

Extend sequence retrieval by N residues in both directions.

-extrafeat N

Bit flag specifying extra features.

-showgaps

Propagate component gaps.

Subset Retrieval

-start N

First record to fetch.

-stop N

Last record to fetch.

Miscellaneous

-raw

Skip database-specific XML modifications.

-express

Direct sequence retrieval in groups of five.

-immediate

Express mode on a single record at a time.

	-json		Convert adjusted XML output to JSON.
	-help		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).

SEE ALSO

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).