[Bioperl-l] Re: BioPerl LocusLink

[Hilmar Lapp]

I've just committed the locuslink parser. Note that as always this 
is bioperl, not perfect, not extremely well documented etc - but the 
code works (for us).

The format spec to SeqIO is -format => 'locuslink' (who would have 
guessed).

The POD states the format you need and the caveats: basically, you 
need the LL_tmpl, and round-tripping is not supported (in fact the 
bioperl object model doesn't support that very well for 
locuslink-sort objects). Also, the visualization stuff is ignored 
(in case you didn't know LocusLink contains all the buttons etc that 
NCBI displays in their LL browser).

Everyone who needs those additional pieces of information is more 
than welcome to enhance the module.

Suggestions and improvements always welcome.

	-hilmar

Nat, you need to update your CVS checkout to see this. I'm not sure 
what the current lag time  is for the anonymous CVS repository to 
sync, I believe we have problems there.

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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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