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

[Aaron J. Mackey]

This is what I do to distinguish intermediate pages from , and it  
seems to be stable (at least so far):

   if ($html =~ m/Status=WAITING/iso)

-Aaron

On Jul 20, 2005, at 9:23 PM, Jason Stajich wrote:

> 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
>> SciTegic Inc.                       mobile: +1 858 205 3653
>> 9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
>> San Diego, CA 92123                 fax:    +1 858 279 8804
>> USA                                 web:    http://www.scitegic.com
>>
>>
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>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12/
>
>
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