[Bioperl-l] clarification on Bio::DB::GenBank

[Ewan Birney]

On Thu, 5 Oct 2000, Osborne, Brian wrote:

> To the group,
> 
> First, congratulations to the developers on the exceptional work they
> continue to do on bioperl. It's been my pleasure to watch the traffic as it
> passes and see the graceful progress of this project. 


Graceful? Hmmmmmmmmm. Not the phrase that springs to mind

> 
> My question relates to get_Seq_by_id() from Bio::DB::GenBank (I'm using the
> latest version, "pre3"). It looks like this works for nucleotide gi numbers
> (4,5,7,9,1147, etc.) but not protein gi numbers (125109,124343,125074,
> etc.). This doesn't surprise me given that entrez/query.fcgi can query
> Nucleotide or Protein, apparently not both simultaneously
> (query.fcgi?cmd=Search&db=Nucleotide&term="125074"&doptcmdl=GenPept works,
> query.fcgi?cmd=Search&db=Nucleotide&db=Protein&term="125074"&doptcmdl=GenPep
> t. doesn't, for example). The same is true of the older entrez CGIs, I
> believe.
> 
> Is there a plan to implement the retrieval of protein sequences using gi
> numbers, say through the use of an additional argument, "protein" or
> "nucleotide", or with additional methods or by catching the error and
> requerying? Please bear in mind that "no" means I'll have to use my own
> significantly-less-beautiful modules !

We're happy to accept patches... <hint>



> 
> Thanks again,
> 
> Brian O.
> 
> Brian Osborne, Information Technology
> OSI Pharmaceuticals
> 777 Old Saw Mill River Rd.
> Tarrytown NY 10591
> brian.osborne@osip.com
> TEL 914 467 6291
> FAX 914 345 3565
> 
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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