focal (1) efetch.1.gz

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]
       [-seq_start N]  [-seq_stop N]  [-strand N]  [-chr_start N]  [-chr_stop N]   [-complexity N]   [-extend N]
       [-extrafeat N] [-raw] [-json]

       esummary  (edirect -summary)  [-help]  [-mode mode]  [-style style]  [-db name]  [-id ID]  [-seq_start N]
       [-seq_stop N] [-strand N] [-chr_start N] [-chr_stop N] [-complexity N] [-extend N] [-extrafeat N]  [-raw]
       [-json]

DESCRIPTION

       efetch  and  esummary retrieve results from either an edirect(1) pipeline or an immediate lookup (via -db
       and -id).  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 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
              withparts or conwithfeat.

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

       -id ID Unique identifier or accession for immediate lookups.

   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 plus, 2 for minus.

   Gene Range
       -chr_start N
              First sequence position to retrieve (0-based).

       -chr_stop N
              Last sequence position to retrieve (1-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.

   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.

SEE ALSO

       eblast(1),     edirect(1),     efetch.acedb(1),     esample(1),     esearch(1),     exclude-uid-lists(1),
       intersect-uid-lists(1), rchive(1), transmute(1), xml2tbl(1), xtract(1).