Get NCBI taxonomy UID from GenBankID
Get NCBI taxonomy UID from GenBankID
genbank2uid(id, batch_size = 100, key = NULL, ...)
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 |
See https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html for help on why there are two identifiers, and the difference between them.
one or more NCBI taxonomic IDs
See taxize-authentication for help on authentication. We recommend getting an API key.
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')
In case you run into errors due to your rate limit being exceeded, see
taxize_options(), where you can set ncbi_sleep.
## Not run:
# 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)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.