entrez_fetch: Entrez fetch

In restez: Create and Query a Local Copy of 'GenBank' in R

Entrez fetch

Description

Wrapper for rentrez::entrez_fetch.

Usage

entrez_fetch(db, id = NULL, rettype, retmode = "", ...)

Arguments

db	character, name of the database
id	vector, unique ID(s) for record(s)
rettype	character, data format
retmode	character, data mode
...	Arguments to be passed on to rentrez

Details

Attempts to first search local database with user-specified parameters, if the record is missing in the database, the function then calls rentrez::entrez_fetch to search GenBank remotely.

rettype='fasta' and rettype='gb' are respectively equivalent to gb_fasta_get() and gb_record_get().

Value

character string containing the file created

Supported return types and modes

XML retmode is not supported. Rettypes 'seqid', 'ft', 'acc' and 'uilist' are also not supported.

Note

It is advisable to call restez and rentrez functions with '::' notation rather than library() calls to avoid namespace issues. e.g. restez::entrez_fetch().

See Also

rentrez::entrez_fetch()

Examples

library(restez)
restez_path_set(tempdir())
demo_db_create(n = 5)
# return fasta record
fasta_res <- entrez_fetch(db = 'nucleotide',
                          id = c('demo_1', 'demo_2'),
                          rettype = 'fasta')
cat(fasta_res)
# return whole GB record in text format
gb_res <- entrez_fetch(db = 'nucleotide',
                       id = c('demo_1', 'demo_2'),
                       rettype = 'gb')
cat(gb_res)
# NOT RUN
# whereas these request would go through rentrez
# fasta_res <- entrez_fetch(db = 'nucleotide',
#                           id = c('S71333', 'S71334'),
#                           rettype = 'fasta')
# gb_res <- entrez_fetch(db = 'nucleotide',
#                        id = c('S71333', 'S71334'),
#                        rettype = 'gb')

# delete demo after example
db_delete(everything = TRUE)

restez documentation built on Oct. 25, 2023, 5:06 p.m.