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

[Peili Zhang]

>Date: Wed, 18 Jun 2003 09:15:44 -0700 (PDT)
>From: Chris Mungall <cjm at fruitfly.org>
>
>
>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,
>> we'll want to create a top-level feature of type 'gene' for it in chado, as 
well
>> 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.
>
>Hi Peili
>
>Can you give an example of where a Bio::Seq object is created for a gene?

the ARGS.