seqinr: getliststate – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

getliststate

Asks for information about an ACNUC list of specified rank

Description

Reply gives the type of list, its name, the number of elements it contains, and, for sequence lists, says whether the list contains only parent seqs (locus=T).

Usage

getliststate(lrank, socket = autosocket())
gls(lrank, socket = autosocket())
gln(lrank, ...)

Arguments

`lrank`	the name of the ACNUC list to modify
`socket`	an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`...`	arguments passed to getliststate

Value

NA in case of problem and an warning is issued. When there is no problem a list with the following 4 components:

`type`	string. Type of ACNUC list (SQ, KW, SP)
`name`	string. ACNUC list name
`count`	numeric. Number of elements in ACNUC list
`locus`	logical. For ACNUC sequence lists TRUE means that the list contains only parent sequences. NA otherwise.

gln is a shortcut for getliststate(lrank, ...)$name

Author(s)

J.R. Lobry

References

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

citation("seqinr")

Examples

## Not run:  
  ### Need internet connection
  choosebank("emblTP")
  mylist <- query("mylist", "sp=felis catus et t=cds", virtual=TRUE)
  getliststate(glr("mylist")) # SQ, MYLIST, 603, FALSE
  gln(glr("mylist")) # MYLIST (upper case letters on server)
  closebank()
  
## 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