[Bioperl-l] mzef parser

[Ewan Birney]

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On Mon, 31 Jul 2000, Jason Stajich wrote:

> I need a MZEF parser/annotator as well as some other prediction software.

So - I have attached the Ensembl genscan parser. For reasons
waaaaaaaaaaaaay too complicated to say here, this parser needs the DNA
sequence to parse the file completely. (It is to do with the phase problem
on reverse strands. If anyone can figure this out for us - boy that would
be a help). 

The business with the phase here is pretty nasty. Otherwise it is
reasonably clean. I believe. 

> 
> I have thinking about Analysis objects in the big sense.  A Bioperl object
> that could generically add annotations parsed from various analysis
> procedures would be the idea.  I am thinking about this model being used
> for both Biocorba objects (to make distributing analysis easy) and the
> ensembl-lite analysis pipeline.
> 

Hmmm. I see where you are coming from. From an Ensembl perspective I think
this is something like a

	SeqFeatureProducerI

which is-a RunnableDB object. What do you think? (PS biojava seems to have
solved this one relatively well. We might do better stealing some design
from over there)



Don't use the word the "Analysis" in the object name --- we already have
too many of these about. 


Something for BOSC...


> So I'd be happy to work with you to design something and put it into play.
> 
> -Jason
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office) 
> (919)684-2275 (fax) 
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/ 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------

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