[Bioperl-l] HTTP response size check in Bio::Tools::Run::RemoteBlast

[Jason Stajich]

I got a email from Guido to the same effect.  Guido - best to post to  
the mailing list in the future so I am not the bottleneck.

I just haven't had time to actually make the changes.

Really need someone else to maintain this module to be honest.

Anyways, any ways to make the module more robust to NCBI changes  
would be appreciated - it really started as a simple hack - I don't  
know if it needs to mirror more closely the example code that NCBI  
provides for submitting remote blasts.

-jason
On Jul 20, 2005, at 5:19 PM, Scott Markel wrote:

> Sometime last week NCBI made a change to the HTTP response
> for remote BLAST requests.  Based on when my regressions
> started to fail, I think it was on the 14th.
>
> The if( $size > 1000 ) check in retrieve_blast() now passes
> when it shouldn't, meaning that intermediate pages are assumed
> to be final results.  I'm now seeing response sizes of just
> under 2000 for the intermediate pages.  A customer of mine is
> getting about the same.
>
> If this check is changed to 2000, then we're back in business.
> We can't make the number too big or we'll start missing small
> result sets.  A request for a single BLASTp hit gives me a
> result size of about 3400.
>
> Has anyone else seen this problem?  Is this a reasonable fix
> to propose?  I'm a little concerned that whatever the number
> is, it's very susceptible to changes at NCBI.
>
> Scott
>
> -- 
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/