[Bioperl-l] Re: [Gmod-schema] load_gff3 handles ##sequence-region

[Scott Cain]

Allen,

Thanks for doing this, but it seems I hadn't thought this all the way
through--specifying a name, a start and an end is not sufficent,
therefore, the '##sequence-region' line is not going to work in it's
current form.  The problem lies in assigning a SO type to the region. 
Is it a chromosome, contig, assembly, band, arm, etc?

So I think we will have to go back to requiring that the reference
sequence be a full GFF line that occurs in the file before any features
referring to it.

Thanks,
Scott

On Fri, 2003-11-07 at 20:51, Allen Day wrote:
> >From chado's load_gff3.pl POD:
> 
> "
> Also, in order for the load to be successful, the reference sequences (eg,
> chromosomes or contigs) must be defined in the GFF file before any
> features on them are listed. This can be done either by the
> reference-sequence meta data specification, which would be lines that look
> like this:
> 
>   ##sequence-region chr1 1 246127941  ----except that this isn't supported
>   yet--can I get Bio::Tools::GFF to give me this info?
> "
> 
> this is now fixed on bioperl-live HEAD Bio::Tools::GFF.  I've added
> parsing capability for the ##sequence region header tag, and stubbed out
> handling of other header tags from the GFF3 spec such as "##attribute 
> ontology".
> 
> segments are created as Bio::LocatableSeq objects and available via
> Bio::Tools::GFF::next_segment().
> 
> -allen
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by: ApacheCon 2003,
> 16-19 November in Las Vegas. Learn firsthand the latest
> developments in Apache, PHP, Perl, XML, Java, MySQL,
> WebDAV, and more! http://www.apachecon.com/
> _______________________________________________
> Gmod-schema mailing list
> Gmod-schema at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory