[BioPython] BLAST XML problem?

[Iddo Friedberg]

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