NAME

       efetch, esummary - retrieve results from an NCBI Entrez search

SYNOPSIS

       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]

DESCRIPTION

       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.1, 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).

SEE ALSO

       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).

NCBI                                               2023-02-12                                          EFETCH(1)