seqinr (version 1.0-1)

GetFromSequence: Generic Functions to obtain annotation, fragment, associated keyword(s), length, location, name, sequence, or translation for a sequence

Description

All methods apply on sequences of class SeqAcnucWeb.

getAnnot, getFrag, getLength, getName, getSequence, and getTrans can also apply on sequences of classes SeqFastadna and SeqFastaAA. getFrag, getLength, getName, getSequence and getTrans can moreover apply on sequences of classes SeqFrag.

Usage

getAnnot(object, nbl = 10000)
getFrag(object, begin, end)
getKeyword(object)
getLength(object)
getLocation(object)
getName(object)
getSequence(object, as.string = FALSE)
getTrans(object, frame = 0, sens = "F", numcode = 1)

Arguments

object

an object of the class SeqAcnucWeb [ or of the classes SeqFastadna, SeqFastaAA] [ or of the class SeqFrag]

nbl

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

begin

First base

end

Last base

as.string

if TRUE sequences are returned as a string instead of a vector of chars.

frame

Frame(s) (0,1,2) to translate. By default the frame 0 is used.

sens

Sense to translate: F for forward sense and R for revers sense.

numcode

The number of the code to use. By default the standard genetic code is used.

Value

• getAnnot returns a vector of string of characters containing the annotation. getFrag returns an object of class SeqFrag, which is a vector of chars with many attributes (see SeqFrag). getKeyword returns a vector of strings containing the keyword(s) associated to a sequence. getLength returns a numeric vector giving the length of the sequence. getLocation returns a list giving the positions of the sequence on the parent sequence. If the sequence is a subsequence (e.g. coding sequence), the function will return the position of each exon on the parent sequence.

  getName returns a string of characters containing the name of the sequence. getSequence returns a vector of chars containing the sequence (default) or a string when as.string is set to TRUE. getTrans returns a vector of chars containing the sequence.

References

� citation("seqinr")

See Also

query, SeqAcnucWeb, c2s, translate

Examples

methods(getAnnot)

  methods(getFrag)

  s=choosebank.socket("embl")
  query.socket(s$socket,"fc","sp=felis catus et t=cds")
  getKeyword(fc$req[[7]])

  methods(getLength)

  methods(getLocation)

  methods(getName)

  methods(getSequence)

  methods(getTrans)