seqinr: isenum – R documentation

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isenum

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")

Examples

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

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19