seqinr: crelistfromclientdata – R documentation

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crelistfromclientdata

To create on server an ACNUC list from data lines sent by client

Description

This function is usefull if you have a local file with sequence names (sequence ID), or sequence accession numbers, or species names, or keywords. This allows you to create on the server a list with the corresponding items.

Usage

crelistfromclientdata(listname, file, type,
 socket = autosocket(), invisible = TRUE,
 verbose = FALSE, virtual = FALSE)
clfcd(listname, file, type, socket = autosocket(),
 invisible = TRUE, verbose = FALSE, virtual = FALSE)

Arguments

`listname`	The name of the list as a quoted string of chars
`file`	The local file name
`type`	Could be one of "SQ", "AC", "SP", "KW", see examples
`socket`	an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`invisible`	if `FALSE`, the result is returned visibly.
`verbose`	if `TRUE`, verbose mode is on
`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`.

Details

clfcd is a shortcut for crelistfromclientdata.

Value

The result is directly assigned to the object listname 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

citation("seqinr")

Examples

## Not run:  # Need internet connection
 choosebank("emblTP")
 #
 # Example with a file that contains sequence names:
 #
 fileSQ <- system.file("sequences/bb.mne", package = "seqinr")
 listSQ <- crelistfromclientdata("listSQ", file = fileSQ, type = "SQ")
 sapply(listSQ$req, getName)
 #
 # Example with a file that contains sequence accession numbers:
 #
 fileAC <- system.file("sequences/bb.acc", package = "seqinr")
 listAC <- crelistfromclientdata("listAC", file = fileAC, type = "AC")
 sapply(listAC$req, getName) 
 #
 # Example with a file that contains species names:
 #
 fileSP <- system.file("sequences/bb.sp", package = "seqinr")
 listSP <- crelistfromclientdata("listSP", file = fileSP, type = "SP")
 sapply(listSP$req, getName) 
 #
 # Example with a file that contains keywords:
 #
 fileKW <- system.file("sequences/bb.kwd", package = "seqinr")
 listKW <- crelistfromclientdata("listKW", file = fileKW, type = "KW")
 sapply(listKW$req, getName)
 #
 # Summary of ACNUC lists:
 #
 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