[BioPython] What to do with BLAST XML syntax error?
Chris Fields
cjfields at uiuc.edu
Sun Jun 17 19:01:48 UTC 2007
Very likely what is returned is not XML at all, but HTML or a server
error code (thus triggering the XML error since it isn't XML). IIRC
you have to loop every x seconds to check the RID, then retrieve the
results; every server check could theoretically have some unforeseen
server error.
With BioPerl this is checked using the response object returned from
every RID request:
if ($response->is_error) {
# throw some relevant error
}
Hate to say but I'm not sure how this would be handled via Python.
chris
On Jun 17, 2007, at 1:34 PM, Jolanda Reek wrote:
> ...
> Can anyone help me think up a solution? And what is causing those
> faulty XML
> files? (Avoiding the problem altogether is better than fixing it.)
>
> Thank you.
>
> Chiko.
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