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

[Julius Lucks]

Why not wrap the try/except block in a while loop:

done = 0
while not done:
     #wait some time
     try:
         #your code
         done = 1
     except SyntaxError:
         #your code

Julius

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On Jun 17, 2007, at 2:34 PM, Jolanda Reek wrote:

> Hello,
>
> I'm using BioPython to send some protein sequences to the NCBI  
> WWWBlast
> server and parse the output. Sometimes, like once every few  
> minutes, instead
> of giving the output, BLAST returns a XML syntax error. It states  
> something
> along the lines of 'SyntaxError: This XML doesn't start with...'.  
> and then
> BioPython can't parse the output (duh). I've written a try/except  
> statement
> to resend the protein query when this problem occurs,however,  
> sometimes the
> problem occurs multiple times in a row, leaving me with no other  
> option then
> to nest try/except statements (= ugly code).
>
>      print "BLAST search: "+proteinLijst[x].id
>      try:
>       acNr, evalueNr = blast(proteinLijst[x].sequentie)
>       idList.append(acNr)
>      except SyntaxError:
>       print "SyntaxError: BLAST server send incomplete results.  
> Resubmitting
> query..."
>       try:
>        acNr, evalueNr = blast(proteinLijst[x].sequentie)
>        idList.append(acNr)
>       except SyntaxError:
>        print "SyntaxError: BLAST server send incomplete results.
> Resubmitting query..."
>        try:
>         acNr, evalueNr = blast(proteinLijst[x].sequentie)
>         idList.append(acNr)
>        except SyntaxError:
>         print "SyntaxError: BLAST server send incomplete results.
> Resubmitting query..."
>         acNr, evalueNr = blast(proteinLijst[x].sequentie)
>         idList.append(acNr)
>
> << Etc. Yuck. It works, but it is still yuck. :)
>
> 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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