[Biojava-dev] GenbankFormat and BASE COUNT

[mark.schreiber at novartis.com]

OK, go ahead with the change.

Are you OK to watch for format changes?

Thanks,

- Mark





"george waldon" <gwaldon at geneinfinity.org>
Sent by: biojava-dev-bounces at lists.open-bio.org
08/26/2006 01:46 AM
Please respond to george waldon

 
        To:     biojava-dev at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        Re: [Biojava-dev] GenbankFormat and BASE COUNT


-----Original Message-----
>From: mark.schreiber at novartis.com 
>Will this be removed from the GenebankFormat in 
>org.biojavax ? 

- Yes


>Also, what will happen if I have a legacy Sequence annotate
> with that keyword and I try to write it out with the new 
>format?

It will be lost, as an output but not as information which can be easily 
recovered from the sequence data. Nothing will happen then; I don't think 
this line is parsed anyway, not in biojavax for sure. Note that until 
yesterday the output was incorrect; the COUNT keyword was missing and only 
BASE was written out. This is now corrected in the trunk. I think removing 
it completely is a logical move and is very safe. If you look in genbank 
last release notes (genbank release 154.0- june 15 2006), you'll see that 
more things are going to change and we need to keep our output updated.

- George



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