|EFETCH(1)||NCBI Entrez Direct User's Manual||EFETCH(1)|
efetch, esummary - retrieve results from an NCBI Entrez search
efetch (edirect -fetch) [-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] [-json] [-examples]
esummary (edirect -summary) [-help] [-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] [-json] [-examples]
efetch and esummary retrieve results from either an edirect(1) pipeline or an immediate lookup (via -db and -id or -input). esummary is equivalent to efetch -format docsum.
Both have two implementations: a shell implementation on top of nquire(1) and a historical Perl implementation that amounts to running edirect -fetch or edirect -summary, enabled by setting the environment variable USE_NEW_EDIRECT to a false value as described in the ENVIRONMENT section. Some options are implementation-specific, as detailed below.
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.
Direct Record Selection¶
- -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 (shell implementation only)
- Shortcut for -strand 1.
- Shortcut for -strand 2.
- -complexity N
- How much context to fetch:
- Nuc-prot set
- Print esummary examples with accessions in the -id field.
- Whether to use the current shell implementation or revert to the historical Perl implementation. Canonical true values are 1, on (case-insensitive), true (case-insensitive), and yes (case-insensitive); canonical false values are 0, off (case-insensitive), false (case-insensitive), and no (case-insensitive).