[BioPython] BLAST XML problem?

[Peter]

Iddo Friedberg wrote:
> Slight correction to my previous email: using biopython from CVS, and 
> python 2.3 as you can see from the stack dump
> 
> Iddo Friedberg wrote:
> 
>> Not sure what we're doing wrong here...
>>
>> Using the cookbook example, biopython 1.41, python 2.2 (our Zope needs 
>> that Python version, sorry):
>>
>> from Bio.Blast import NCBIXML
>>
>> b_parser = NCBIXML.BlastParser()
>> b_record = b_parser.parse(blast_out)
>>
>>
>> Breaks on "Alejandro Schäefer",  in the XML <BlastOutput_reference> 
>> tag. The ä seems to cause the error. Replace it with a regular "a" 
>> everything is hunky-dory

Is the lower-case a with umlaut in the XML file as ä, or using an 
encoding like &auml; or &#228; instead? (ampersand characters, aka 
character entities)

Also, what character set does the blast_out XML file claim to be in? 
And does that fit with the inclusion of an a-umlaut as a character?

It may be the NCBI's fault for producing a bad XML file...

Peter