[Bioc-devel] AAString validity

[Laurent Gatto]

Hi Hervé,

2012/2/22 Hervé Pagès <hpages at fhcrc.org>:
> 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.

Yes, that was indeed my initial motivation.
Thank you very much for taking care of this.

Best wishes,

Laurent
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
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