[Bioc-devel] AAString validity

[Hervé Pagès]

Hi Laurent,

Sorry for the late reply. You're right that the letters in an AAString
objects are not encoded. And actually I don't think they need to be.
I think all we need is enforcing that the letters in the objects belong
to AA_ALPHABET, which is not the case right now. I'll add that.

Thanks!
H.


On 02/10/2012 05:05 PM, Laurent Gatto wrote:
> Dear all,
>
> AAString instances can contain invalid amino acids characters,
> although the corresponding documentation says it should not.
>
>> DNAString("AA123") ## positive control
> Error in .Call2("new_XString_from_CHARACTER", classname, x,
> start(solved_SEW),  :
>    key 49 not in lookup table
>
>> AAString("AA123")
>    5-letter "AAString" instance
> seq: AA123
>> alphabet(AAString("AA123"))
>   [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" "W" "Y"
> [20] "V" "*" "-" "+"
>
> I suspect that the table in xsbasetype.R explains why it does not work.
>
> Would it be possible to encode the AA_ALPHABET for AAStrings?
>
> Thank you very much in advance.
>
> Laurent
>
>> sessionInfo()
> R Under development (unstable) (2012-01-29 r58227)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] Biostrings_2.23.6  IRanges_1.13.22    BiocGenerics_0.1.4
>
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-- 
Hervé Pagès

Program in Computational Biology
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