efetch.ncbi1

Retrieve results from an ncbi entrez search

Usage

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]

Overview

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, binary, 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).

Releases

3 releases since Debian 11 (Bullseye); the text changed 2 times.

-express since Debian 12 (Bookworm); -forward since Debian 12 (Bookworm); -immediate since Debian 12 (Bookworm); -input since Debian 12 (Bookworm); -showgaps since Debian 12 (Bookworm).

-examples until Debian 11 (Bullseye).