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

Peili Zhang peili at morgan.harvard.edu
Wed Jun 18 11:27:48 EDT 2003

>> >>
>> >> 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 
>> 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?


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