entrez_fetch: Download data from NCBI databases

Description

Pass unique identifiers to an NCBI database and receive data files in a variety of formats. A set of unique identifiers mustbe specified with either the db argument (which directly specifies the IDs as a numeric or character vector) or a web_history object as returned by entrez_link, entrez_search or entrez_post.

Usage

entrez_fetch(
  db,
  id = NULL,
  web_history = NULL,
  rettype,
  retmode = "",
  parsed = FALSE,
  config = NULL,
  ...
)

Value

character string containing the file created

XMLInternalDocument a parsed XML document if parsed=TRUE and rettype is a flavour of XML.

Arguments

db: character, name of the database to use
id: vector (numeric or character), unique ID(s) for records in database db. In the case of sequence databases these IDs can take form of an NCBI accession followed by a version number (eg AF123456.1 or AF123456.2).
web_history,: a web_history object
rettype: character, format in which to get data (eg, fasta, xml...)
retmode: character, mode in which to receive data, defaults to an empty string (corresponding to the default mode for rettype).
parsed: boolean should entrez_fetch attempt to parse the resulting file. Only works with xml records (including those with rettypes other than "xml") at present
config: vector, httr configuration options passed to httr::GET
...: character, additional terms to add to the request, see NCBI documentation linked to in references for a complete list

Details

The format for returned records is set by that arguments rettype (for a particular format) and retmode for a general format (JSON, XML text etc). See Table 1 in the linked reference for the set of formats available for each database. In particular, note that sequence databases (nuccore, protein and their relatives) use specific format names (eg "native", "ipg") for different flavours of xml.

For the most part, this function returns a character vector containing the fetched records. For XML records (including 'native', 'ipg', 'gbc' sequence records), setting parsed to TRUE will return an XMLInternalDocument,

References

https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_EFetch_

Examples

Run this code

if (FALSE) {
katipo <- "Latrodectus katipo[Organism]"
katipo_search <- entrez_search(db="nuccore", term=katipo)
kaitpo_seqs <- entrez_fetch(db="nuccore", id=katipo_search$ids, rettype="fasta")
#xml
kaitpo_seqs <- entrez_fetch(db="nuccore", id=katipo_search$ids, rettype="native")
}

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