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.
eblast(1), edirect(1), efetch.acedb(1), esample(1), esearch(1), exclude-uid-lists(1), intersect-uid-lists(1), nquire(1), rchive(1), transmute(1), xml2tbl(1), xtract(1).
2021-01-24 | NCBI |