[Biojava-l] issue with translating codons with N

[LAW Andy]

I would expect a HashMap to perform every bit as well as a hand-rolled array.


On 20 Sep 2013, at 15:57, Nick England <nickengland at gmail.com> wrote:

> 
> Andy and Andy,
> 
> Does the array really result in that much performance improvement from a hashmap? Rather than a huge empty array you could just use a char[][][] for the three codons if you want to do it that way. I think the problem is that the code for translating "N" as X isn't called if the array lookup returns a match. And the array lookup doesn't seem calibrated to cope with Ns (or indeed any ambiguous bases.)
> 
> And Andy Law yes, its using the int values (but used to use the numbers 1,2,3,4 from the looks of it.)
> 
>        public int compoundToInt(NucleotideCompound c) {
>             char b = c.getUpperedBase().charAt(0);
>             return (int)b;
> //            int v = -1;
> //            if('A' == b) {
> //                v = 1;
> //            }
> //            else if('C' == b) {
> //                v = 2;
> //            }
> //            else if('G' == b) {
> //                v = 3;
> //            }
> //            else if('T' == b || 'U' == b) {
> //                v = 4;
> //            }
> //            return v;
> }
> 
> 
> On 20 September 2013 15:51, LAW Andy <andy.law at roslin.ed.ac.uk> wrote:
> 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
> --------
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Later,

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

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-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.