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

[Peili Zhang]

>> >>
>> >> 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.
>
you're right that we don't need the annotation stuff to build the Gene object. 
but we don't want to lose any data during the data load. and I was hoping the 
GeneStructure object will keep the annotations since it inherits 
Bio::SeqFeature::Generic which in turn inherits Bio::Annotation::Collection etc.
is this right?

-peili