modifylist: Modification of an ACNUC list

In seqinr: Biological Sequences Retrieval and Analysis

Modification of an ACNUC list

Description

This function modifies a previously existing ACNUC list by selecting sequences either by length, either by date, either for the presence of a given string in annotations.

Usage

modifylist(listname, modlistname = listname, operation,
 type = c("length", "date", "scan"), socket = autosocket(),
 virtual = FALSE, verbose = FALSE)

Arguments

listname	the name of the ACNUC list to modify
modlistname	the name of the modified ACNUC list. Default is to use the same list name so that previous list is lost.
operation	a string of character describing the operation to be done, see details.
type	the type of operation, could be one of "length", "date", "scan". Default is "length"
socket	an object of class sockconn connecting to a remote ACNUC database (default is a socket to the last opened database).
virtual	if TRUE, no attempt is made to retrieve the information about all the elements of the list. In this case, the req component of the list is set to NA.
verbose	logical, if TRUE mode verbose is on

Details

Example of possible values for the argument operation:

length

as in "> 10000" or "< 500"

date

as in "> 1/jul/2001" or "< 30/AUG/98"

scan

specify the string to be searched for

Character < is to be understood as <= and > likewise.

Value

The result is directly assigned to the object modlistname in the user workspace. This is an objet of class qaw, a list with the following 6 components:

call	the original call
name	the ACNUC list name
nelem	the number of elements (for instance sequences) in the ACNUC list
typelist	the type of the elements of the list. Could be SQ for a list of sequence names, KW for a list of keywords, SP for a list of species names.
req	a list of sequence names that fit the required criteria or NA when called with parameter virtual is TRUE
socket	the socket connection that was used

Author(s)

J.R. Lobry

References

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

citation("seqinr")

See Also

choosebank, query and prepgetannots to select the annotation lines for scan.

Examples

## Not run:  # Need internet connection
  choosebank("emblTP")
  mylist <- query("mylist", "sp=felis catus et t=cds", virtual=TRUE)
  mylist$nelem # 603 sequences
  stopifnot(mylist$nelem == 603)

  # select sequences with at least 1000 bp:
  mylist <- modifylist("mylist", operation = ">1000", virtual = TRUE)
  mylist$nelem # now, only 132 sequences
  stopifnot(mylist$nelem == 132)

  # scan for "felis" in annotations:
  mylist <- modifylist("mylist", op = "felis", type = "scan", virtual = TRUE)
  mylist$nelem # now, only 33 sequences
  stopifnot(mylist$nelem == 33)

  # modify by date:
  mylist <-  modifylist("mylist", op = "> 1/jul/2001", type = "date", virtual = TRUE)
  mylist$nelem # now, only 15 sequences
  stopifnot(mylist$nelem == 15)

  # Summary of current ACNUC lists, one list called MYLIST on sever:
  sapply(alr()$rank, getliststate)
  closebank()
  
## End(Not run)

seqinr documentation built on May 29, 2024, 6:36 a.m.