[BioRuby] Remote blast not working?

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Fri Jun 22 20:09:43 UTC 2012


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
> >>
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