[Bioperl-l] remoteblast xml problem

Hubert Prielinger hubert.prielinger at gmx.at
Fri Jun 2 17:11:41 EDT 2006


hi,
sorry, but I have updated the remoteblast module and I have run several 
attempts with the same results as before. It didn't work.
I didn't get any results.

regards
Hubert


Chris Fields wrote:
> Sendu, Hubert,
>
>
> Hubert, your code looks fine so Sendu's patch should fix the problem (break
> out of that infinite loop).  I applied Sendu's patch to RemoteBlast in CVS;
> it passed all tests in RemoteBlast.t.  Try updating from CVS to see if it
> works.  
>
> Chris
>
>   
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
>> Sent: Friday, June 02, 2006 4:04 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>
>> Hubert Prielinger wrote:
>>     
>>> hi,
>>> I have the following program and it worked quite well, for retrieving
>>> remoteblast results in a textfile,
>>> now I have altered it to to xml, and it didn't work anymore.....
>>> it takes all the parameter at the commandline, submits the query, but I
>>> don't retrieve any results file anymore.....
>>>
>>> it seems that it hangs in a endless loop......
>>> the only output I get is:  $rc is not a ref! over and over..... it
>>> doesn't enter the else term anymore....
>>>       
>> There is no problem with your code. The problem is with the NCBI server
>> and should be reported to them. You can visit the site and do a blast,
>> requesting xml format, and you will typically get one normal 'waiting'
>> message and the promise that it will be updated in x seconds, but
>> subsequent attempts to get progress information result in an xml error
>> page because the NCBI server doesn't actually send any data.
>>
>> Unfortunately the way that the bioperl code is written, it treats no
>> data as 'waiting' instead of an error. I've offered a patch to fix this
>> at this bug page:
>> http://bugzilla.bioperl.org/show_bug.cgi?id=2015
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>>     
>
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