[Bioperl-pipeline] Genewise matters

[Elia Stupka]

> Like the contig_id (currently hardcoded for testing purposes.....we
> have to pass the contig information somehow right??) in the exon table

Ah ehm... contig_id is definiteyl not fine tuning :) if you don't have the
contig how can you store it? not sure how you managed to store results
without contig id for the exons???? Anway, it shuold be easy to just keep
always the contig_id as teh seqname of teh features across the process,
right?

> translation_id in the transcript table and the type(currently im
> putting the module name eg genewise)  in the gene table. But I will
> commit it so that you can take a look also.

You need to generate a translation object, not just "put a fake
id"... make sure you look athte the ensembl genewise runnable...

Elia

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