[Biojava-l] Retrieving Partial gene/CDS information

[Richard Holland]

Fair enough.

Well, in that case it sounds like a potential improvement case for
BioJavaX (at the time I wrote the BioSQL mappers I'm sure there was no
way of mapping them else I would have implemented it... but I might have
been wrong).

First thing to do is to raise the appropriate bug in BugZilla. Bandaru -
could you do that? (That way you will 'own' the bug and will be notified
when people are working on it / have fixed it.)

Then, as to who fixes it... volunteers, please! I do make infrequent
trawls through BugZilla, but I rarely have the time to fix any of them. :(

cheers,
Richard


Hilmar Lapp wrote:
> 
> On Dec 18, 2008, at 12:14 PM, Richard Holland wrote:
> 
>> Whilst BioJava supports the < and > annotation, and will correctly load
>> these from the file and store them as FuzzyLocations internally, when it
>> is asked to write them to BioSQL they are lost. This is BioSQL has no
>> way of storing this information.
> 
> 
> That's actually not true. BioSQL has the location_qualifier_value table
> for storing this, and the foreign key to term to store the location type.
> 
> Bioperl-db does indeed lose this information when persisting feature
> locations to BioSQL, but that's Bioperl-db's fault, not BioSQL's.
> 
> Or am I missing something?
> 
>     -hilmar

-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/