R: Get NCBI taxonomy UID from GenBankID

genbank2uid {taxize} | R Documentation

## Get NCBI taxonomy UID from GenBankID

### Description

Get NCBI taxonomy UID from GenBankID

### Usage

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

### Arguments

`id` | A GenBank accession alphanumeric string, or a gi numeric string.
`batch_size` | The number of queries to submit at a time.
`...` | Curl args passed on to `GET`

### Details

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

Note that if you pass in > 1 item, if one or more of your items is not found, the entire batch will return `NA`'s. To get around this, set `batch_size = 1` - so each is sent separtaely to NCBI. However, this of course is much slower than the default, which is to send up to 100 at a time.

### Value

one or more NCBI taxonomic IDs

### Examples

    ## 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
    library('httr')
    genbank2uid(id = 156446673, config=verbose())

    ## End(Not run)

[Package taxize version 0.9.0 Index]