Re: [Gusdev-gusdev] GUS & bioperl

[<pi...@pc...>]

Hi Ed,

Having some difficult scheduling problems today but I (& Steve) will dedicate
time to this tomorrow or later today.

                                                       -Debbie

Quoting Ed Robinson <ed_...@be...>:

> The first step in writing such an adapter needs to be a document, though,
> which shows what fields, in what formats go where in GUS.  One of the main
> problems with the parsers is that they have been developed without a common
> document saying what kind of information goes where.
>
> To this end, I have a simple analysis of where our TCruzi and Crypto data are
> being loaded by the different parsers.  I am attaching copies of these two
> brief documents in MS Word format.Presently this analysis is in Open Office
> format.  I would like to use these to start developing a data-destination
> document that we can use as a standard for all further parser development.
>
> Also, I am not sure that this solution is really necessary for GFF Format.
> Writing a GFF adapter involves two steps 1. Querying the data and 2. Passing
> it correctly to BioPerl.  The solution we have so far is simply to put the
> formating information in the SQL query (it's one step).  Of course this is a
> solution that is ignorant of the GUS object model. It would be nice to embedd
> this process in an object which maps from GUS objects to BioPERL for a number
> of reasons.  But I also think it might be something to put off until later
> since the formatted SQL query is a quick-and-dirty time saver.
>
> -Ed
>
>
>
>
> >
> > From: Steve Fischer <sfi...@pc...>
> > Date: 2004/11/05 Fri AM 11:25:32 EST
> > To: gusdev-gusdev <gus...@li...>,
> >         "Aaron J. Mackey" <am...@pc...>
> > Subject: [Gusdev-gusdev] GUS & bioperl
> >
> > folks-
> >
> > We should immediately explore a GUS <--> bioperl adaptor.
> >
> > we would use it for:
> >    - Genbank and TIGR XML -> GUS
> >    - GUS -> GBrowse
> >    - possibly GUS -> Chado
> >
> > Here is what Aaron has to say about parsing Genbank, etc:
> >
> > Bio::SeqIO::GenBank is the BioPerl parser for GenBank; it parses and
> > represents all of it (split between Bio::Seq [sequence, id, accession,
> > etc], Bio::SeqFeature [everything found in the feature table] and
> > Bio::Annotation [comments, references, etc] objects).  Similar parsers
> > exist for practically all common sequence formats (including TIGR-XML
> > and other genome annotation-relevant formats).
> >
> > Here is what Aaron has to say about GBrowse:
> >
> > IMO, the "best" way to generate (valid) GFF is to use BioPerl's tools
> > for GFF manipulation: Bio::Tools::GFF in older BioPerl's, and
> > Bio::Feature::IO in the latest development release (due out any day
> > now, as soon as I stop reading my email; for now, you can get it from
> > CVS).
> >
> > To use these tools, you build Bio::SeqFeature objects that represent
> > the items you wish to dump as GFF; thus you can build complicated
> > hierarchies of gene models, exons, CDS, UTR, etc, adding deeply
> > structured attributes/annotations to each, and let the BioPerl GFF code
> > figure out how to represent it (in GFF2 or GFF3) so that other tools
> > (including Gbrowse) can read it.
> >
> >
> >
> >
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>
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
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