[Bioperl-l] remoteblast xml problem

Chris Fields cjfields at uiuc.edu
Fri Jun 2 20:33:48 EDT 2006


You need to add the input conditions as well (you have several  
<STDIN> lines which may play a role; I would like to know what you  
normally enter for those).

How long did you let the script run?  I ran a quick check on your  
sequences; you have almost 1600, so you have to expect that you'll  
run into some problems here!  Most here (including me) would suggest  
you try installing a local blast setup for something like this.

Chris

On Jun 2, 2006, at 6:19 PM, Hubert Prielinger wrote:

> hi,
> I have submitted the bug -> Bug 2017
> with the script and input file, just start it from command line
>
> thank you very much
> greetings
>
> Hubert
>
> Chris Fields wrote:
>> Hubert,
>>
>> I have a script that's using blastxml and XML output which seems  
>> to work.
>> I'll try looking at it to get a better idea this weekend.
>>
>> Chris
>>
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Hubert Prielinger
>>> Sent: Friday, June 02, 2006 4:12 PM
>>> To: Chris Fields; bioperl-l at bioperl.org; Chris Fields; 'Sendu Bala'
>>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>>
>>> 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
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
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>>>>
>>>>
>>>>
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>>
>>
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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