taxize (version 0.9.100.1)

genbank2uid: Get NCBI taxonomy UID from GenBankID

Description

Get NCBI taxonomy UID from GenBankID

Usage

genbank2uid(id, batch_size = 100, key = NULL, ...)

Value

one or more NCBI taxonomic IDs

Arguments

id

A GenBank accession alphanumeric string, or a gi numeric string.

batch_size

The number of queries to submit at a time.

key

(character) NCBI Entrez API key. optional. See Details.

...

Curl args passed on to crul::HttpClient

Authentication

See taxize-authentication for help on authentication. We recommend getting an API key.

HTTP version

We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Details

See https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html for help on why there are two identifiers, and the difference between them.

Examples

if (FALSE) {
# with accession numbers
genbank2uid(id = 'AJ748748')
genbank2uid(id = 'Y13155')
genbank2uid(id = 'X78312')
genbank2uid(id = 'KM495596')

# with gi numbers
genbank2uid(id = 62689767)
genbank2uid(id = 22775511)
genbank2uid(id = 156446673)

# pass in many accession or gi numbers
genbank2uid(c(62689767,156446673))
genbank2uid(c('X78312','KM495596'))
genbank2uid(list('X78312',156446673))

# curl options
res <- genbank2uid(id = 156446673, verbose = TRUE)
}