[BioPython] What to do with BLAST XML syntax error?

[Chris Fields]

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.