[BioPython] plain txt blast output - xml instead

Peter biopython at maubp.freeserve.co.uk
Thu Jun 15 14:38:54 EDT 2006


Michiel Jan Laurens de Hoon wrote:
> Peter wrote:
> 
>>Looking at the raw XML file by hand, I could only see references to P1, 
>>the first protein.
>>
>>If the file had results for all four proteins I would expect to see:
>>
>><?xml version="1.0"?>
>>... results for P1 ...
>><?xml version="1.0"?>
>>... results for P2 ...
>><?xml version="1.0"?>
>>... results for P3 ...
>><?xml version="1.0"?>
>>... results for P4 ...
>>
> 
> There are results for all four proteins in the XML file, but they look 
> like this:
> 
>   <Iteration>
>     <Iteration_iter-num>2</Iteration_iter-num>
>     <Iteration_query-ID>2_20304</Iteration_query-ID>
>     <Iteration_query-def>p2</Iteration_query-def>
>     ...
>   </Iteration>
> 
> and so on.

Oh yeah.  I should have seen that, sorry.

According to the XML file, it is from BLASTP 2.2.14 [May-07-2006], maybe 
they changed the XML format without telling anyone?

I couldn't see anything obvious on this page:

http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml

This looks like the source code here:

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi.tar.gz

And you can view their CVS here:

http://www.ncbi.nlm.nih.gov/cvsweb/index.cgi/ncbi/algo/blast/

There is nothing in the check-in comments that leaps out at me regarding 
XML iterations...

 >
 > Could you let us know how this XML file was generated?
 >

e.g. Standalone or online?

Peter



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