[Bioperl-guts-l] [Bug 3163] AssemblyIO takes too long (especially 454)

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http://bugzilla.open-bio.org/show_bug.cgi?id=3163





------- Comment #14 from florent.angly at gmail.com  2011-03-05 00:23 EST -------
Created an attachment (id=1571)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1571&action=view)
Computation time after migration to and optimization of
Bio::DB::SeqFeature::Store::memory

Ok. So, I finally manage to migrate all the Bio::Assembly modules so that their
features and seqfeatures are saved in a Bio::DB::SeqFeature::Store::memory. The
code in the Git development repository.

This migration in itself accelerated the code significantly, but did not remove
the exponential behavior. After fixing the way that some
Bio::DB::SeqFeature::Store::memory methods work, I then got a nice linear
behavior. The attached graphs speak for themselves.

Thank you Lee for reporting the bug and providing test data!


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