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

NAME

efetch, esummary - retrieve results from an NCBI Entrez search

SYNOPSIS

efetch (edirect -fetch) [-help] [-format fmt] [-mode mode] [-db name] [-id ID] [-seq_start N] [-seq_stop N] [-strand N] [-chr_start N] [-chr_stop N] [-complexity N] [-extend N] [-extrafeat N]

esummary (edirect -summary) [-help] [-mode mode] [-db name] [-id ID] [-seq_start N] [-seq_stop N] [-strand N] [-chr_start N] [-chr_stop N] [-complexity N] [-extend N] [-extrafeat N]

DESCRIPTION

efetch and esummary retrieve results from either an edirect(1) pipeline or an immediate lookup (via -db and -id). 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 edirect -fetch or efetch.acedb(1) looks like a better fit.

OPTIONS

Format Selection

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

Direct Record Selection

Entrez database name for immediate lookups.
Unique identifier or accession for immediate lookups.

Sequence Range

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

Gene Range

First sequence position to retrieve (0-based).
Last sequence position to retrieve (1-based).

Miscellaneous

Print usage information, complete with examples of notable -db/-format/-mode combinations.
How much context to fetch:
0
default
1
Bioseq
3
Nuc-prot set
Extend sequence retrieval by N residues in both directions.
Bit flag specifying extra features.

SEE ALSO

edirect(1), efetch.acedb(1), esearch(1), xtract(1).

2017-01-24 NCBI