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

[Jolanda Reek]

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.