[Bioperl-l] All done with Bio::DB::Query

Hilmar Lapp hlapp@gnf.org
Sun, 24 Nov 2002 13:46:09 -0800

Cool Lincoln.

Can't get_stream_by_batch rewritten to use the new code? Sorry if 
the answer is obvious.

I should have said that Bio::DB::Query is the namespace that I also 
use in bioperl-db for object-relational query modules. There's no 
clash yet of module names, and the chance for one is probably fairly 
low; I just thought I mention this here. If you or anyone else feels 
we need to better protect from possible future clashes, we need to 
rename either in bioperl-live or bioperl-db.


On Friday, November 22, 2002, at 08:24 AM, Lincoln Stein wrote:

> Hi,
> I'm all done with the following modules:
> 	Bio::DB::QueryI
> 	Bio::DB::Query::WebDBQuery  # web utilities
> 	Bio::DB::Query::GenBank   # the only "real" one
> I have tested on a variety of Unix systems, but I need a Windows 
> tester.  I
> used fork() in a couple of places in order to make SeqIO streaming
> pipelineable (otherwise it has to download the whole set of records 
> before it
> can start processing the first one).  The code should detect that 
> it is not
> on a platform that supports fork-and-pipe and automatically fall 
> back to the
> old way of doing things, but I'm not 100% certain it will work as 
> advertised.
> I've also done a touch up here and there on the Bio::DB:: modules, 
> mostly to
> deprecate Aaron Mackey's get_Stream_by_batch() methods, which are 
> superseded
> by the eutils interface.
> Let us all be glad that NCBI has committed to maintain eutils as 
> its official
> interface.
> Lincoln
> --
> Lincoln Stein
> lstein@cshl.org
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757