[BioPython] plain txt blast output - xml instead
Peter
biopython at maubp.freeserve.co.uk
Thu Jun 15 18:38:54 UTC 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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