[Biojava-l] issue with translating codons with N

[LAW Andy]

Looking at the multipliers, I would hazard a guess that the *intent* is to multiply the numbers 0,1,2,3 (ACGT) rather than the ASCII codes. Are you sure the code uses ASCII values?


On 20 Sep 2013, at 15:16, Nick England <nickengland at gmail.com> wrote:

> Everyone,
> 
> I've stepped through with a debugger, and this is a bad bug.
> 
> The code to translate from RNA->Protein does the following:
> - Take the ASCII Value for the 3 RNA bases, and multiple the first pos by
> 16, second by 4 and third by 1 and add them up.
> - Assume there won't be any collisions.
> 
> Here are the values which it then uses:
> 
> A:65
> G:71
> C:67
> U:85
> N:78
> ANA: 1417
> CAU: 1417
> ANG: 1423
> CGA: 1423
> 
> Notice any hash collisions?
> 
> I don't get why this wasn't done in a standard JavaHashMap which would
> ensure that any collisions were resolved. This is a pretty critical bug for
> a biology informatics package.
> 
> Nick
> 
> 
> On 20 September 2013 13:45, Nick England <nickengland at gmail.com> wrote:
> 
>> Hara,
>> 
>> Hmm this is rather odd. I get the same issue with that sequence with a
>> custom engine as well.
>> 
>> My code has:
>> Builder builder = new TranscriptionEngine.Builder();
>>    builder.initMet(false);
>>    builder.translateNCodons(true);
>>    builder.trimStop(false);
>>    TranscriptionEngine engine = builder.build();
>>    Sequence<AminoAcidCompound> seq=engine.translate(new
>> DNASequence("GTNTGTTAGTGT"));
>>    assertEquals("XC*C", seq.toString());
>>    Sequence<AminoAcidCompound> seq2=engine.translate(new
>> DNASequence("ANAANG"));
>>    System.out.println(seq2);
>> the first sequence translates as expected, but your sequence is
>> translating as HR, when it should be XX. This looks like a pretty bad bug!
>> 
>> Nick
>> 
>> 
>> On 19 September 2013 19:59, Hara Dilley <hdilley at sutrobio.com> wrote:
>> 
>>> Hi,
>>> 
>>> Is there an issue with the DNA Translation in biojava3.core?
>>> It appears that it wants to translate "N" in certain cases
>>> Executing:
>>> new
>>> DNASequence("ANAANG").getRNASequence().getProteinSequence().getSequenceAsString();
>>> will produce  aa HR.
>>> 
>>> thanks
>>> Hara
>>> 
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Later,

Andy
--------
Yada, yada, yada...

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