[BioPython] BLAST XML problem?

[Iddo Friedberg]

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
>
> Huh?
>
> [idoerg at hotdog:~/results/jafa]> ./try_blast.py star_human.fasta
> /home/idoerg/biopy_cvs/biopython/Bio/Blast/NCBIWWW.py:1070: 
> UserWarning: qblast works only with blastn and blastp for now.
>  warnings.warn("qblast works only with blastn and blastp for now.")
> Traceback (most recent call last):
>  File "./try_blast.py", line 19, in ?
>    b_record = b_parser.parse(open('my_blast.out'))
>  File "/home/idoerg/biopy_cvs/biopython/Bio/Blast/NCBIXML.py", line 
> 112, in parse
>    self._parser.parse(handler)
>  File "/usr/lib/python2.3/xml/sax/expatreader.py", line 107, in parse
>    xmlreader.IncrementalParser.parse(self, source)
>  File "/usr/lib/python2.3/xml/sax/xmlreader.py", line 123, in parse
>    self.feed(buffer)
>  File "/usr/lib/python2.3/xml/sax/expatreader.py", line 211, in feed
>    self._err_handler.fatalError(exc)
>  File "/usr/lib/python2.3/xml/sax/handler.py", line 38, in fatalError
>    raise exception
> xml.sax._exceptions.SAXParseException: my_blast.out:6:81: not 
> well-formed (invalid token)
>
>
>
> Iddo
>


-- 

Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: (858) 646 3100 x3516
Fax: (858) 713 9949
http://iddo-friedberg.org