R: To create on server an ACNUC list from data lines sent by...

crelistfromclientdata {seqinr} | R Documentation

## 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")`

### See Also

`choosebank`, `query`, `savelist` for the reverse operation with an ACNUC list of sequences.

### 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)

[Package seqinr version 3.4-5 Index]