getFrag {seqinr}

Generic function to extract sequence fragments

Description

getFrag is used to extract the sequence fragment starting at the begin position and ending at the end position.

Usage

getFrag(object, begin, end, ...)
## S3 method for class 'SeqAcnucWeb'
getFrag(object, begin, end, ..., socket = autosocket(), name = getName(object))
## S3 method for class 'SeqFastadna'
getFrag(object, begin, end, ..., name = getName(object))
## S3 method for class 'SeqFastaAA'
getFrag(object, begin, end, ..., name = getName(object))
## S3 method for class 'SeqFrag'
getFrag(object, begin, end, ..., name = getName(object))

Arguments

object

an object of the class SeqAcnucWeb or SeqFastadna, or SeqFastaAA or SeqFrag or a list of these objects

begin

First position of the fragment to extract. This position is included. Numerotation starts at 1.

end

Last position of the fragment to extract. This position is included.

socket

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

name

the sequence name

...

further arguments passed to or from other methods

Value

getFrag returns an object of class SeqFrag.

Author(s)

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

References

citation("seqinr")

See Also

SeqAcnucWeb, SeqFastadna, SeqFastaAA, SeqFrag

Examples

#
# List all available methods for getFrag generic function:
#
   methods(getFrag)
#
# Example with a DNA sequence from a FASTA file:
#
  dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
  sfdna <- read.fasta(file = dnafile)
  myfrag <- getFrag(sfdna[[1]], begin = 1, end = 10)
  stopifnot(getSequence(myfrag, as.string = TRUE) == "atgaaaatga")