getAnnot {seqinr}

Generic Function to get sequence annotations

Description

Annotations are taken from the Annot attribute for sequences imported from a FASTA file and retrieved from an ACNUC server for objects of the SeqAcnucWeb class.

Usage

getAnnot(object, ...)
## S3 method for class 'SeqAcnucWeb'
getAnnot(object, ..., nbl = 100, socket = autosocket())

Arguments

object

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

nbl

the maximum number of line of annotation to read. Reading of lines stops when nbl lines have been transmitted or at the last annotation line of the sequence (SQ or ORIGIN line).

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

Value

getAnnot returns a vector of string of characters containing the annotations for the sequences.

Author(s)

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

References

citation("seqinr")

See Also

query, SeqAcnucWeb, c2s, translate and prepgetannots to select the annotation lines.

Examples

#
# List all available methods for getAnnot generic function:
#
   methods(getAnnot)
#
# SeqAcnucWeb class example:
#
  ## Not run: 
  # Need internet connection
  choosebank("emblTP")
  fc<-query("fc", "sp=felis catus et t=cds et O=mitochondrion et Y>2001 et no k=partial")
  # get the first 5 lines annotating the first sequence:
  annots <- getAnnot(fc$req[[1]], nbl = 5)
  cat(annots, sep = "\n")
  # or use the list method to get them all at once:
  annots <- getAnnot(fc$req, nbl = 5)
  cat(annots, sep = "\n")
  closebank()
  
## End(Not run)
#
# SeqFastaAA class example:
#
   aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
   sfaa <- read.fasta(aafile, seqtype = "AA")
   getAnnot(sfaa[[1]])
#
# SeqFastadna class example:
#
   dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
   sfdna <- read.fasta(file = dnafile)
   getAnnot(sfdna[[1]])
#
# Example with a FASTA file with multiple entries:
#
  ff <- system.file("sequences/someORF.fsa", package = "seqinr")
  fs <- read.fasta(ff)
  getAnnot(fs) # the list method is used here to get them all at once
#
# Default getAnnot method example. An error is produced because 
# there are no annotations by default:
#
   result <- try(getAnnot(letters))
   stopifnot(!inherits("result", "try-error"))