[BioRuby] Remote blast not working?

[Michael Barton]

Hi Toshiaki,

Thank you for the patch. That worked perfectly. I sometimes get unusual parsing
errors which I think are originating from raxml. Has anyone else experienced
something similar?

Cheers

Mike

On Thu, Mar 17, 2011 at 10:28:21AM +0900, Toshiaki Katayama wrote:
> As for the GenomeNet part, it is already fixed but not yet released.
> 
> https://github.com/bioruby/bioruby/blob/master/lib/bio/appl/blast/genomenet.rb#L241
> 
> You can replace your installation with the above file for quick fix.
> 
> Thanks,
> Toshiaki
> 
> On 2011/03/17, at 6:12, Michael Barton wrote:
> 
> > Hi,
> > 
> > I'm struggling to use the remote blast part of bioruby. I get errors using
> > either the ddbj or genomenet versions. With genomenet I get an error about
> > a nil response and with genomenet I get an error for 'cannot understand
> > response'. I've tried different combinations of databases and options but keep
> > getting the same problems.
> > 
> > Bio::Blast::Remote.ddbj('blastp', 'nr-aa', '-e 0.001')
> > 
> > Can anyone offer any suggestions?
> > 
> > Cheers
> > 
> > Mike
> > _______________________________________________
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>