[Biojava-dev] Code Update

[Andreas Prlic]

Looks good, Andy!

Andreas

On Sat, Feb 6, 2010 at 7:12 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> Finally it's in. I've managed to get enough time to finish the
> transcription code off. The main features of this check-in are:
>
> * DNA -> RNA -> Codon -> Peptide translation
> * Support for all IUPAC tables
> * New views for reversing sequences & complementing them
> * Windowed sequence views giving portions of a sequence as requested
> * TranscriptionEngine & TranscriptionEngine.Builder deal with the business
> of assembling the classes together as required
> * Singletons provided from the classes they are in (e.g. IUPACParser has
> one) *but* no class requires a singleton!
> * Utilities for working with IO streams & classpath resources (useful for
> testing)
> * Test case shows 1000 translations of BRCA2 (from DNA) in 0.7seconds (on
> my MacBook Pro; YMMV); test case will break if it takes longer than a second
> ** This is a vast improvement over my first attempt that had a rate of 1
> per second hence why that was not checked in
>
> Limitations are:
>
> * Not much checking WRT lengths of sequence given to the code; need a
> strict & lenient mode
> * Stop codon trimming controlled by a boolean
> * No init-met translation (very important as some programs get a bit
> annoyed if they're given a V as an initiator AA)
> * Not sure if there is a way to ask if a codon is a start codon easily; I'm
> sure it can be done just not as easily as we may want
> * No way of modifying a badly translated peptide which we expect to badly
> translate
>
> However it's workable & means if you have a DNASequence technically you can
> get a peptide by saying:
>
> DNASequence s = getSeq();
> ProteinSequence p = s.getRNASequence().getProteinSequence();
>
> Now how's that for easy :)
>
> Share & enjoy!
>
> Andy
>
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