[Bioperl-l] extract feature seq when split between 2 GenBank accessions

[Jason Stajich]

> > Now I think there is a bug because spliced seq is sorting the locations
> > before processing on them which has been reported but not fixed
> > (I am really hoping for some more bugfixing developers out there folks!)
> > but it should work through that system once that bug is fixed.
>
> I'm using spliced_seq, and its returning sequence w/ N's for the
> segments derived form joins outside the current accession.

Just fixed this in the CVS live.  We have to trust the location order when
it is mixed with remote locations.  There may be a couple more special
cases which the code I put won't catch, so those who have problems, please
submit them so we can add tests.


>
> >
> > I would just use a Bio::DB::Fasta/Bio::Index::Fasta where you have the
> > accessions indexed instead of reading in all the possible seqs and storing
> > in a hash to keep the memory requirements down.  You can also use the
> > DB::Failover + DB::FileCache to cache local/remote calls if you need to
> > mix local and remote dbs.
>
> I'll try this -thanks.
>
> Charles
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu