[BioPython] plain txt blast output - xml instead

[Rohini Damle]

So what do one need to do to make biopython working?  Make changes in the
XML  parser so that it will consider one iteration for one result out put?
-Rohini


On 6/15/06, Michiel Jan Laurens de Hoon <mdehoon at c2b2.columbia.edu> wrote:
>
> Peter wrote:
> > According to the XML file, it is from BLASTP 2.2.14 [May-07-2006], maybe
> > they changed the XML format without telling anyone?
> >
> It appears that the XML format did change.
> With Blastp 2.2.14, multiple searches generate multiple
> <Iteration>...</Iteration> blocks, one for each search.
> With an older Blastp, multiple searches effectively generate multiple
> XML files (each with one <Iteration>...</Iteration> block). These files
> are then concatenated into one output file. Biopython then parses this
> file by looking for the beginning of each XML file in this output file.
>
> The new output is in a sense better because the output file is a valid
> XML file. It may be that Biopython's XML parser ignores the <Iteration>
> tags, since in the old format there was only one <Iteration> block
> anyway, and therefore fails with the new format.
>
> --Michiel.
>
> --
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1130 St Nicholas Avenue
> New York, NY 10032
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