NAME

       efetch, esummary - retrieve results from an NCBI Entrez search

SYNOPSIS

       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]

DESCRIPTION

       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.

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  (shell  implementation  only),  withparts  (Perl  implementation  only), or
              conwithfeat.

   Direct Record Selection
       -db name
              Entrez database name for immediate lookups.

       -id ID Unique identifier or accession for immediate lookups.

       -input filename (shell implementation only)
              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 (shell implementation only)
              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 (shell implementation only)
              Propagate component gaps.

   Subset Retrieval
       -start N
              First record to fetch.

       -stop N
              Last record to fetch.

   Miscellaneous
       -raw   Skip database-specific XML modifications.

       -json  Convert adjusted XML output to JSON.

       -help  Print usage  information,  complete  with  examples  of  notable  -db/-format/-mode
              combinations.

   Accession Mapping
       -examples
              Print esummary examples with accessions in the -id field.

ENVIRONMENT

       USE_NEW_EDIRECT
              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).

SEE ALSO

       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).