[Bioperl-l] remoteblast xml problem

Hubert Prielinger hubert.prielinger at gmx.at
Fri Jun 2 20:49:15 EDT 2006


hi,
input database: swissprot
         matrix: pam30
         count: 1
         gapcosts: 9 1

I know that there are  a lot of sequences, but that doesn't matter, you 
can delete all of them except one, the amount of the sequences is not 
the problem, the script reads one line and submits it.....then the 
second line and so on.....I have tried it with only one sequence either 
and I got the same result.... the script run at that time for more than 
20 minutes!!!!!! .....and that should be enough time to retrieve the 
results for ONE sequence, I guess

regards
Hubert



Chris Fields wrote:
> 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
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
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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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