[BioPython] plain txt blast output - xml instead

[Rohini Damle]

I used online ncbi blast to generate the xml output
Rohini


On 6/15/06, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> 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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