R: Generic Function to get sequence annotations

getAnnot {seqinr} | R Documentation

## 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"))

[Package seqinr version 3.4-5 Index]