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

Lincoln Stein lstein@cshl.org
Fri, 22 Nov 2002 11:24:38 -0500


I'm all done with the following modules:

	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deprecate Aaron Mackey's get_Stream_by_batch() methods, which are superseded 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 


Lincoln Stein