[Bioperl-pipeline] Re: New sub routine

[Elia Stupka]

> Elia I was thinking about  what you asked me to do.......but I found some
> obstacles on the way.

Bala please remember to include others on the mail, we all need to discuss
these issues...

> Since  to have the runnable run(since it takes 2 seqs)... I need to have
done
> the fetching part(of the protein seq and the genomic subseq) right?In
which
> module should I do this??This is the converter part right??

No. The inputs will already be stored with their name (e.g. protein id) and
iohandler (e.g. bioperl-db->get_Seq_by_id).... and the same for contigs,
which will come with its get_Contig_start_end method, so you don't need to
worry about it, all Genewise needs to do is take the two sequences, run and
give results...

>           There seems to be no method to get the protein sequence by
> display_id in  Bio::DB::SQL
>           There appears to be a method which does that in
> Bio::DB::BioSeqDatabase, but it requires
>           an adaptor to do that(which adaptor is that??).

That is the adaptor for the BioDatabase in bioperl-db, the first one is
fine.

> Getting the genomic sequence is pretty staright forward right  given the
> contig,start,stop and strand?

Yes in practice you just need to test that it works...

Elia