getLocation {seqinr}

Generic function to get the location of subsequences on the parent sequence

Description

This function works only with subsequences from an ACNUC server.

Usage

getLocation(object, ...)
## S3 method for class 'SeqAcnucWeb'
getLocation(object, ..., socket = autosocket())

Arguments

object

an object of the class SeqAcnucWeb, or a list of them, or an object created by query

socket

an object of class sockconn connecting to a remote ACNUC database (default is a socket to the last opened database by choosebank).

...

further arguments passed to or from other methods

Value

A list giving the positions of the sequence on the parent sequence. If the sequence is a subsequence (e.g. coding sequence), the function returns the position of each exon on the parent sequence. NA is returned for parent sequences and a warning is isued.

Author(s)

D. Charif, J.R. Lobry, L. Palmeira

References

citation("seqinr")

See Also

SeqAcnucWeb

Examples

#
# List all available methods for getLocation generic function:
#
   methods(getLocation)
#
# Example with a subsequence from an ACNUC server:
#
  ## Not run: 
  # Need internet connection
  choosebank("emblTP")
  fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
  getLocation(fc$req[[5]])
  closebank()  

## End(Not run)