[ensembl-dev] VariationAdaptor::fetch_all_by_Individual not completely deprecated

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Fri Oct 22 19:26:49 BST 2010


I have noticed that CompressedGenotypeAdaptor::fetch_all_by_Individual
has been deprecated as of August 2007
.html), yet the method VariationAdaptor::fetch_all_by_Individual, which
directly calls CompressedGenotypeAdaptor::fetch_all_by_Individual, still
exists to this day. There is no reason to keep a non-functional method
in Ensembl-Variation, and should be removed.

On the other hand, I have noticed that, probably due to the said
database restructuring, accessing IndividualGenotypes through the
Ensembl API is very slow-- are there any way that I can improve the

Any help is appreciated!


John MC Ma
Graduate Assistant
Kwitek Lab
Department of Internal Medicine
3125E MERF
375 Newton Road
Iowa City IA 52242

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