[BioPython] NCBIXML error

[Peter]

On Wed, May 7, 2008 at 10:29 PM,  <gbastian at pasteur.fr> wrote:
> Dear all,
>
>  I have been using a script to blast sequences for days without a
>  problem, then, after 2/3 hours it started giving me this error
>  and never worked again...did they change xml blast format?

Looking at the XML snippet, the version is "BLASTP 2.2.18+" (with a
plus but no date) so it looks like the may well have updated
something.  Its possible that they'll make further tweaks in the next
couple of days, so it would be worth retesting.  The Biopython code
expects something like "BLASTP 2.2.12 [Aug-07-2005]", and its the
missing date that is causing this error for you.

On a different note, if you have really been running BLASTP for days
over the internet, it would probably be faster and more efficient to
install standalone blast and the nr database on your local machine.
You can still ask for XML output, so the parsing side of your script
shouldn't change.

Peter