|EFETCH(1)||NCBI Entrez Direct User's Manual||EFETCH(1)|
efetch, esummary - retrieve results from an NCBI Entrez search
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]
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.
Direct Record Selection¶
- -complexity N
- How much context to fetch:
- Nuc-prot set
- Skip database-specific XML modifications.
- Direct sequence retrieval in groups of five.
- Express mode on a single record at a time.
- Convert adjusted XML output to JSON.
- 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).
combine-uid-lists(1), difference-uid-lists(1), ds2pme(1), efetch.acedb(1), esample(1), esearch(1), exclude-uid-lists(1), hgvs2spdi(1), intersect-uid-lists(1), nquire(1), pma2pme(1), rchive(1), transmute(1), xml2fsa(1), xml2tbl(1), xtract(1).