[Bioperl-l] swiss fix

[Ewan Birney]

On Wed, 6 Sep 2000, Jason Stajich wrote:

> Okay, so the reason I added the (incorrect) Bio::SeqIO::swiss fix stemmed
> back from the original problem, downloading using Bio::DB::GenPept,
> outputting the data as swissprot.
> 
> Of course this is just the stream handler, data is downloaded
> from ncbi as GenPept (which we handle with the GenBank format) 
> and display_id() is filled in via SeqIO::genbank, which doesn't
> add the _$div to the display_id.  One solution is to check in swissprot
> before writing out the record that the display_id indeed follows the
> locus_div format, if it doesn't then add the _$div to the display_id.

Messy. But better than it not working.

hilmar's definitely right about the id stuff...


> 
> -jason
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office) 
> (919)684-2275 (fax) 
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/ 
> 
> 
> 
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