[BioRuby] Bio::Fetch issue - biofetch.rb not found
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Thu Sep 22 06:12:07 UTC 2011
Hello Marc,
Sorry for late response.
> http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at
> that location?
The service is down for years, due to the server trouble,
and it is currently difficult to restore the service
because of the internal structure of bioruby.org.
Please use other server, e.g.
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
bf =Bio::Fetch.new('http://www.ebi.ac.uk/Tools/dbfetch/dbfetch')
str = bf.fetch('embl', 'AE014292')
print str
Alternatively, some other classes provide similar function.
str = Bio::TogoWS::REST.entry('genbank', 'AF237819')
print str
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
On Mon, 19 Sep 2011 10:57:14 +0200
"Marc P. Hoeppner" <mphoeppner at gmail.com> wrote:
> Hi,
>
> when trying to fetch entries from remote databases via Bio::Fetch, I
> receive the following error:
>
> /usr/lib/ruby/1.8/open-uri.rb:277:in `open_http': 404 Not Found
> (OpenURI::HTTPError)
>
> It appears the default entry for Fetch.new searches for
> http://bioruby.org/cgi-bin/biofetch.rb - which does not seem to exist at
> that location?
>
> Am I doing anything wrong?
>
> Using gem version 1.4.2 and ruby 1.8.7 on Ubuntu 11.04
>
> /Marc
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