[BioPython] Does biopython have a 'WORKING' blastparser and where ?
Chris
chrisf at fagmed.uit.no
Fri Nov 11 05:20:32 EST 2005
*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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