getSequence: Generic function to get sequence data

Description

getSequence returns the sequence either as vector of single chararacters or as a single string of multiple characters.

Usage

getSequence(object, as.string = FALSE, ...)
# S3 method for SeqAcnucWeb
getSequence(object, as.string = FALSE, ..., socket = autosocket())

Value

For a single sequence an object of class character containing the characters of the sequence, either of length 1 when as.string is TRUE, or of the length of the sequence when as.string is FALSE. For many sequences, a list of these.

Arguments

object: an object of the class SeqAcnucWeb or SeqFastadna, or SeqFastaAA or SeqFrag or a list of these objects, or an object of class qaw created by query
as.string: if TRUE sequences are returned as strings of multiple characters instead of a vector of single characters
socket: an object of class sockconn connecting to a remote ACNUC database (default is a socket to the last opened database).
...: further arguments passed to or from other methods

Author

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

References

citation("seqinr")

Examples

Run this code

#
# List all available methods for getSequence generic function:
#
   methods(getSequence)
#
# SeqAcnucWeb class example:
#
  if (FALSE) # Need internet connection
  choosebank("emblTP")
  fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
  getSequence(fc$req[[1]])
  getSequence(fc$req[[1]], as.string = TRUE)
  closebank()
  
#
# SeqFastaAA class example:
#
  aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
  sfaa <- read.fasta(aafile, seqtype = "AA")
  getSequence(sfaa[[1]])
  getSequence(sfaa[[1]], as.string = TRUE)
#
# SeqFastadna class example:
#
  dnafile <- system.file("sequences/someORF.fsa", package = "seqinr")
  sfdna <- read.fasta(file = dnafile)
  getSequence(sfdna[[1]])
  getSequence(sfdna[[1]], as.string = TRUE)
#
# SeqFrag class example:
#
  sfrag <- getFrag(object = sfdna[[1]], begin = 1, end = 10)
  getSequence(sfrag)
  getSequence(sfrag, as.string = TRUE)

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