[Bioperl-l] Re: [Bioperl-announce-l] an extension to Bio::SeqIO

Jason Stajich jason at cgt.duhs.duke.edu
Wed Jun 18 11:20:24 EDT 2003

On Wed, 18 Jun 2003, Peili Zhang wrote:

> >>
> >> sequence data in any (rich) formats
> >> 	 |
> >> 	 | via Bio::SeqIO
> >> 	 v
> >     Bio::Seq->get_SeqFeatures()
> >         OR
> >      Collection of Bio::SeqFeatureI
> >
> >[Actually what's cooler I think is that you don't need Bio::Seq objects or
> >anything, just a set of Bio::SeqFeatureI objects. This would mean that
> >people could take their GFF files and turn them into chado IFF they are
> >rich enough.]
> >
> we do want the Bio::Seq objects. for instance, if the Bio::Seq object is a gene,
> as loading in its references as feature_pubs, accessions as feature_dbxrefs,
> comments/descriptions/others as featureprops. its gene model features
> (transcripts, exons, CDS's) will hang off of the top-level feature.

Okay but the part that builds the gene doesn't need all of this, it just
builds genes from a collection of features in the sort of multi-step
process that Chris described.  One would then transfer the pertinent
annotations,references, etc from a Bio::Seq object to a GeneStructure
object, but you don't need them to build the Gene object.

> -peili
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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