R: Extract sequence identified by name or by number from an...

gfrag {seqinr} | R Documentation

## Extract sequence identified by name or by number from an ACNUC server

### Description

Get `length` characters from sequence identified by name or by number starting from position `start` (counted from 1).

### Usage

    gfrag(what, start, length, idby = c("name", "number"), socket = autosocket())

### Arguments

`what` | A sequence name or number
`start` | Start position from 1
`length` | Number of requested characters (answer may be shorter)
`idby` | Is the sequence identified by name or number? Default to name
`socket` | an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).

### Value

A string of characters with at most `length` characters (may be shorter than asked for). NA is returned and a warning is issued in case of problem (non existent sequence for instance).

### Author(s)

J.R. Lobry

### References

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

`citation("seqinr")`

### See Also

`choosebank`, `query`

### Examples

    ## Not run: # Need internet connection
      choosebank("emblTP")
      gfrag("LMFLCHR36", start = 1, length = 3529852) -> myseq
      stopifnot(nchar(myseq) == 3529852)
      closebank()

    ## End(Not run)

[Package seqinr version 3.4-5 Index]