[Bioperl-l] remoteblast xml problem

Hubert Prielinger hubert.prielinger at gmx.at
Fri Jun 2 21:36:42 EDT 2006


hi chris,
thanks but I never intended to run the remoteblast with so much, only a 
few of them, acutally I goal is to run the phiblast with regular 
expression, so that i just don't need that
file anymore.

another question for parsing the xml output....is there a xml parser 
available for blast xml output or how to start.....
I have looked up at the wikiperl and cpan Bio::SearchIO::blastxml, but 
I'm not sure how to start....sorry, I guess I'm too stupid....
is their maybe another introduction or an example.

thanks
Hubert


Chris Fields wrote:
> Yes, I see the same error you do.  But I have a similar script  
> (blastp, XML blast report, XML parsing, similar loop structure) that  
> works fine.  I'm trying to dissect the problem but I think it may be  
> something logically wrong here (something not so obvious) and not a  
> bug...
>
> What I'm trying to say is, when you send sequences using remoteblast  
> like, this you are essentially spamming the NCBI BLAST server with  
> ~1600 requests.  This script wasn't set up with that intent in mind;  
> you should really try to set up your own local blast database if  
> possible.  If you can't, try running this script in off-hours  
> (10pm-6am EST or something like that).
>
>
> Chris
>
> On Jun 2, 2006, at 7:49 PM, Hubert Prielinger wrote:
>
>   
>> 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
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>>
>>>>>>>>
>>>>>>>>                 
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>             
>>>>>
>>>>>           
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>         
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>>       
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>   



More information about the Bioperl-l mailing list