seqinr (version 4.2-36)

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")

See Also

SeqAcnucWeb, SeqFastadna, SeqFastaAA, SeqFrag

Examples

#
# 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)