efetch1
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
-helpoutput for examples.)
-
-mode mode -
text,xml,asn,binary, orjson.
-
-style style -
masterorconwithfeat.
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:
1for forward (plus),2for 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/-modecombinations (in the case ofefetch) and of supplying accessions in the-idfield (in the case ofesummary).
Releases
7 releases since Debian 7 (Wheezy); the text changed 5 times.
-chr_start since Debian 9 (Stretch);
-chr_stop since Debian 9 (Stretch);
-complexity since Debian 9 (Stretch);
-db since Debian 9 (Stretch);
-express since Debian 12 (Bookworm);
-extend since Debian 9 (Stretch);
-extrafeat since Debian 9 (Stretch);
-format since Debian 9 (Stretch);
-forward since Debian 12 (Bookworm);
-help since Debian 9 (Stretch);
-id since Debian 9 (Stretch);
-immediate since Debian 12 (Bookworm);
-input since Debian 12 (Bookworm);
-json since Debian 10 (Buster);
-mode since Debian 9 (Stretch);
-raw since Debian 10 (Buster);
-revcomp since Debian 11 (Bullseye);
-seq_start since Debian 9 (Stretch);
-seq_stop since Debian 9 (Stretch);
-showgaps since Debian 12 (Bookworm);
-start since Debian 11 (Bullseye);
-stop since Debian 11 (Bullseye);
-strand since Debian 9 (Stretch);
-style since Debian 10 (Buster).
-examples until Debian 11 (Bullseye).