GetFromSequence {seqinr} | R Documentation |
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
.
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)
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. |
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.
D. Charif
citation("seqinr")
query
, SeqAcnucWeb
, c2s
, translate
methods(getAnnot) methods(getFrag) ## Not run: s=choosebank.socket("embl") ## Not run: query.socket(s$socket,"fc","sp=felis catus et t=cds") ## Not run: getKeyword(fc$req[[7]]) methods(getLength) methods(getLocation) methods(getName) methods(getSequence) methods(getTrans)