R: Get the ACNUC number of a sequence from its name or accession...

isenum {seqinr} | R Documentation

## Get the ACNUC number of a sequence from its name or accession number

### Description

Gives the ACNUC number of a sequence in the `number` element of the returned list. More informations are returned for subsequences corresponding to coding sequences.

### Usage

    isenum(what, idby = c("name", "access"), socket = autosocket())
    isn(what, ...)
    getNumber.socket(socket, name)
    getAttributsocket(socket, name)

### Arguments

`what` | a sequence name or a sequence accession number
`idby` | is the sequence identified by name or by accession number? Default to name
`socket` | an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`...` | arguments passed to `isenum`.
`name` | a sequence name.

### Value

A list whith the following 6 components:

`number` | numeric. The ACNUC number of the sequence.
`length` | numeric. The length of the sequence.
`frame` | numeric. The reading frame (0, 1, or 2) of the sequence for CDS.
`gencode` | numeric. ACNUC's genetic code (0 means universal) of the sequence for CDS.
`ncbigc` | numeric. NCBI's genetic code (0 means universal) of the sequence for CDS.
`otheraccessmatches` | logical. If TRUE it means that several sequences are attached to the given accession nunmber, and that only the ACNUC number of the first attached sequence is returned in the `number` component of the list.

`isn(what, ...)` is a shortcut for `isenum(what, ...)$number`.

As from seqinR 1.1-3 `getNumber.socket` and `getAttributsocket` are deprecated (a warning is issued).

### Author(s)

J.R. Lobry

### References

http://doua.prabi.fr/databases/acnuc.html

`citation("seqinr")`

### See Also

`choosebank`, `query`

### Examples

    ## Not run:
      ### Need internet connection
      choosebank("emblTP")
      isenum("LMFLCHR36")
      isn("LMFLCHR36")
      stopifnot(isn("LMFLCHR36") == 13682678)
      # Example with CDS:
      isenum("AB004237")

    ## End(Not run)

[Package seqinr version 3.4-5 Index]