[Biopython-dev] [Bug 2412] NCBIXML. fails parsing with blast 2.2.15 in special cases (Karlin-Altschul)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2412





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2007-12-04 14:43 EST -------
The fact that your example gives an empty XML file is essentially due to some
problem with Blast.  I agree that the Biopython error message you quoted is
very unhelpful in this situation.

Are you using Biopython 1.43 (as suggested by the strack trace in the error
report), or Biopython 1.44 as reported in the bug details?

What does this do on your setup?

from StringIO import StringIO
from Bio.Blast import NCBIXML
handle = StringIO("")
for record in NCBIXML.parse(handle) :
    print record

If you are using Biopython 1.44 or later you should get a helpful error
message, "ValueError: Your XML file was empty". You can catch this, and inspect
the contents of the error handle if you want to deal with this in your
application.

i.e. I think this bug has already been fixed in Biopython 1.44


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