[Bioperl-l] Hierarchical location parsing

[Mark Hoebeke]

Sorry I messed up the example I gave, but an "in-nature" hierarchical
location can be found in the complete genome of Streptococcus pyogenes
strain MGAS315 (Genbank access number AE014074) :


source  join(1..749107,join(788646..977266,join(1018339..1137553,
                     join(1171973..1230114,join(1271911..1313193,
                     join(1351400..1410541,1450556..1900521))))))

In this case, it seems likely that the joins could be flattened out.
However, when massively feeding Genbank entries into a database it could
be unpractical to re-parse location strings  to determine if 1/ they
contain nested joins and 2/ they can or cannot be flattened out.


I don't know to what extent the FTLocationFactory is tested when running
'make test' on a bioper-live tree, but it yields the same results on
both patched and unpatched trees.

Mark

Le jeudi 24 mars 2005 à 17:55 -0800, Jason Stajich a écrit :
> Is there a real example where these types of locations exist - why  
> can't it be flattened without the nested joins?  At any rate - I don't  
> really care to parse these if they never exist "in-nature".  If your  
> bugfix soln works and doesn't slow things down we can use it I guess,  
> although I prefer a regexp.  I don't really have time to patch or test  
> in the near future so it will have to wait for someone to volunteer to  
> get to it.
> 
> -jason
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/

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