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

[Ewan Birney]

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

> Ewan,

cc'ing this straight back to bioperl ;) 

> 
> I'd be glad to write something for you. How would you like it to look? Right
> now these methods accept single arguments, the "id". Proposal 1, accept a
> second argument, (protein|p) or (nucleotide|n), for example (default is
> nucleotide?). This assumes the person knows what they want, probably true
> almost all of the time. Proposal 2, if not found in "nucleotide", try
> "protein". Nicer, I think. 
> 

My bias is that DNA stuff happens in the Bio::DB::GenBank and protein in
Bio::DB::Genpept. That's why there are two different modules

> Related matter, and this was discussed in one of the groups. This module
> uses IO::Socket. My module uses LWP and HTTP. It's easy to see how to go
> from one to the other, but which would you rather use? I can't intelligently
> compare them myself. Just from reading TPJ I'd say the combination of LWP
> and HTTP is used far more often when one talking about HTTP requests.
> Anyway...
> 

Moving this to LWP is the preferred method at the moment, to allow access
through firewalls

> Doesn't Aaron want to do this? Isn't this stepping on his toes a bit?
> 

I am sure Aaron is cool with this. 


Forge forwards - this will be something for the 0.7 release. As soon as
you have something serious, post it to me and, assumming it looks ok, I'll
set you up with cvs access so you can just hack on the code base directly.


thanks for offering.


> Brian O.
> 
> 
> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Thursday, October 05, 2000 2:22 PM
> To: Osborne, Brian
> Cc: 'Bioperl-l@bioperl.org'
> Subject: Re: [Bioperl-l] clarification on Bio::DB::GenBank
> 
> 
> 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
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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