[BioRuby] Remote blast not working?

[Michael Barton]

I know the EBI maintains a REST API for blast. They have an example ruby script
for accessing it as well. Building a bio-gem around this could solve the
problem of keeping up with Genomenet in bio core. A bio-gem could also use
Nokogiri for faster XML parsing too.

I think this could be a good student project perhaps.

On Sat, Jun 23, 2012 at 05:09:43AM +0900, Naohisa GOTO wrote:

> 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')
> >
par error:
Word too long: /Users/mike/.gem/gems/bio-1.4.2/lib/bio/appl/blast/genomenet.rb:251:in