[BioPython] Problem with blastx output parsing =~

[Christof Winter]

Hi Maia:

Could you post the begin and end of your blastx output? I think you can omit the 
query and hits in between...

Cheers,
Christof


Italo Maia wrote:
> 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.
> 
>