[Bioperl-l] Fw: Inquiry about a prog written by [MAJ]

[Mark A. Jensen]

Thought this should be archived to the list. 
MAJ

----- Original Message ----- 
From: Mark A. Jensen 
To: Ross KK Leung 
Sent: Thursday, June 25, 2009 8:46 AM
Subject: Re: Inquiry about a prog written by you


Hi Ross-
Yes, you can specify the recombinants, as "A/C/G[subtype]" in the query string. Unfortunately, the 10000 record limit is imposed by the Los Alamos site that my program accesses. You might be able to work around this if you're willing to write your own script using the BioPerl modules that are the basis for the hivq.PLS -- by using the modules to perform multiple queries, and collecting the the entire set of sequences over that series of queries. 
You might look at the documentation for the modules for ideas; try looking at http://www.bioperl.org/wiki/Module:Bio::DB::HIV and http://www.bioperl.org/wiki/Module:Bio::DB::Query::HIVQuery . 
best regards- 
Mark
  ----- Original Message ----- 
  From: Ross KK Leung 
  To: maj at fortinbras.us 
  Sent: Thursday, June 25, 2009 6:09 AM
  Subject: Inquiry about a prog written by you


  Dear Mark A. Jensen,

   

  A google search returns your program (http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/DB-HIV/hivq.PLS)

   

  I wonder whether the program is able to search recombinants (e.g. B incl. recombinants) and retrieve results more than 50000 records. This limitation is a bottleneck by the web-based search.

   

  Thanks for your advice, Ross