[BioPython] Does biopython have a 'WORKING' blastparser and where ?

[Chris]

*output for blast out.html and out.xml attached


NCBIWWW.BlastParser(): *


/usr/local/lib/python2.4/site-packages/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 "/usr/bin/npw_blast2tab", line 93, in ?
    blast()
  File "/usr/bin/npw_blast2tab", line 14, in __init__
    self.parse_blast(opts)
  File "/usr/bin/npw_blast2tab", line 51, in parse_blast
    b_record     = blast_parser.parse(b_results)
  File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py", 
line 47, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py", 
line 98, in feed
    has_re=re.compile(r'<b>.?BLAST'))
  File "/usr/local/lib/python2.4/site-packages/Bio/ParserSupport.py", 
line 335, in read_and_call_until
    line = safe_readline(uhandle)
  File "/usr/local/lib/python2.4/site-packages/Bio/ParserSupport.py", 
line 411, in safe_readline
    raise SyntaxError, "Unexpected end of stream."
SyntaxError: Unexpected end of stream.

*
NCBIXML.BlastParser():*

/usr/local/lib/python2.4/site-packages/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 "/usr/bin/npw_blast2tab", line 93, in ?
    blast()
  File "/usr/bin/npw_blast2tab", line 14, in __init__
    self.parse_blast(opts)
  File "/usr/bin/npw_blast2tab", line 51, in parse_blast
    b_record     = blast_parser.parse(b_results)
  File "/usr/local/lib/python2.4/site-packages/Bio/Blast/NCBIXML.py", 
line 112, in parse
    self._parser.parse(handler)
  File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 107, in parse
    xmlreader.IncrementalParser.parse(self, source)
  File "/usr/local/lib/python2.4/xml/sax/xmlreader.py", line 125, in parse
    self.close()
  File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 217, in close
    self.feed("", isFinal = 1)
  File "/usr/local/lib/python2.4/xml/sax/expatreader.py", line 211, in feed
    self._err_handler.fatalError(exc)
  File "/usr/local/lib/python2.4/xml/sax/handler.py", line 38, in fatalError
    raise exception
xml.sax._exceptions.SAXParseException: <unknown>:1:0: no element found

 




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