seqinr: modifylist – R documentation

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modifylist

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

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)
  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

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