[Bioperl-l] remoteblast xml problem

Chris Fields cjfields at uiuc.edu
Mon Jun 5 23:42:18 EDT 2006


Hubert,

I had no trouble getting this to work; the script scans through each  
sequence and save the XML output to a file on both Windows and Mac OS  
X, both using bioperl-live.  The older RemoteBlast would only save  
text; otherwise it saved an empty file.  Using your script I get  
several XML BLAST output files (1.xml, 2.xml, etc) based on a  
counter, each about 1 MB.  All were parseable by SearchIO.

I did notice that if certain parameters weren't entered in correctly  
then you will get no data (such as setting the database to 'swiss'  
instead of 'swissprot').  A warning pops up stating that no data was  
returned when this occurs (it doesn't tell you what was wrong, just  
that no data came back from NCBI).  If you see this then that is  
likely the problem.  Besides that, I don't know what else it can be.

Chris

On Jun 5, 2006, at 2:12 PM, Hubert Prielinger wrote:

> hi chris,
> sorry, I have tried it with the latest CVS version:
>
> # $Id: RemoteBlast.pm,v 1.33 2006/06/03 06:26:41 cjfields Exp $
>
> but it still doesn't work.
>
> Hubert
>
> Chris Fields wrote:
>> Hubert,
>>
>> Make sure you have the latest Bio::Tools::Run::RemoteBlast from  
>> CVS.  The
>> option to save XML was committed relatively recently (last month  
>> or so).
>>
>> Chris
>>

...

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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