[BioRuby] Remote blast not working?

[Naohisa GOTO]

Hi,

It seems that the Genomenet BLAST site is modified again
by the Genomenet site administrators.
Currently, it is not easy to catch up their changes.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp

On Fri, 22 Jun 2012 12:27:12 -0400
Michael Barton <mail at michaelbarton.me.uk> wrote:

> Hi,
> 
> I appear to be having a similar problem again using ruby 1.9.3 and bio 1.4.2.
> 
> blast = Bio::Blast.remote('blastp', 'nr-aa', '-e 0.001', 'genomenet')
> 
> /Users/mike/.gem/gems/bio-1.4.2/lib/bio/appl/blast/genomenet.rb:251:in
> `exec_genomenet': cannot understand response (RuntimeError)
> 	from /Users/mike/.gem/gems/bio-1.4.2/lib/bio/appl/blast.rb:368:in `query'
> 	from bin/blast:17:in `<main>'
> 
> I've tried downloading the latest version of genomenet.rb but this did
> not appear to solve the problem this time.
> 
> Thank you
> 
> Michael Barton
> 
> 
> 
> On 20 March 2011 16:56, Michael Barton <mail at michaelbarton.me.uk> wrote:
> > 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
> >> > _______________________________________________
> >> > BioRuby Project - http://www.bioruby.org/
> >> > BioRuby mailing list
> >> > BioRuby at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby