[Bioperl-l] How good is Bio::Assembly::IO::ace ?

[Robson Francisco de Souza]

	Hi,

On Fri, 13 Dec 2002, Lu, Hong wrote:
> I found today that bioperl-live has phrap ace parser Bio::Assembly::IO::ace,
> is it already working?

	Yes, its working. I use it here at my lab to analyse assemblies of
bacterial genomes. It has some problems: its is a bit slow and takes up a
lot of memory (what about lazy parsing here, people? I don know how it
should be implemented... has anyone used lazy parsing on any IO module?),
but it works.

> When will it be incorporated into formal release?

	Only if I (or someone else) have the time to write some tests for
its methods, I believe. There are only a couple of tests implemented for
Bio::Assembly modules right now, written by Heikki. I guess more tests are
necessary before including it in a stable release.

					Robson

> Thanks
> 
> Hong (Henry) Lu
> Bioinformatics Scientist
> 454 Corporation
> Branford, CT 06405
> 
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