[BioPython] Problem with blastx output parsing =~
Italo Maia
italo.maia at gmail.com
Mon Jun 4 16:36:21 UTC 2007
Well, i have a perfectly fine blastx output that throws an error when parsed
by biopython.
It gives me this output:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/var/lib/python-support/python2.5/Bio/Blast/NCBIStandalone.py", line
624, in parse
self._scanner.feed(handle, self._consumer)
File "/var/lib/python-support/python2.5/Bio/Blast/NCBIStandalone.py", line
99, in feed
self._scan_parameters(uhandle, consumer)
File "/var/lib/python-support/python2.5/Bio/Blast/NCBIStandalone.py", line
570, in _scan_parameters
has_re=re.compile(r"[Ll]ength of \s*[Dd]atabase"))
File "/var/lib/python-support/python2.5/Bio/ParserSupport.py", line 300,
in read_and_call
raise SyntaxError, errmsg
SyntaxError: Line does not match regex '[Ll]ength of \s*[Dd]atabase':
Number of HSP's gapped: 136690
What could i do??? I'm using ubuntu feisty here.
--
"A arrogância é a arma dos fracos."
===========================
Italo Moreira Campelo Maia
Ciência da Computação - UECE
Desenvolvedor WEB
Programador Java, Python
Meu blog ^^ http://eusouolobomal.blogspot.com/
===========================
More information about the Biopython
mailing list