From: kipling.houston.tx@...
Date: 2007-03-25T04:30:04+09:00
Subject: bioruby ent function

Hello,

I can use the function "ent" from interactive bioruby environment

###################################################
$ bioruby
Loading config (session/config) ... done
Loading object (session/object) ... done
Loading history (session/history) ... done

. . . B i o R u b y   i n   t h e   s h e l l . . .

  Version : BioRuby 1.0.0 / Ruby 1.8.5

bioruby> ss = ent('genbank:AB169639')
Retrieving entry from KEGG API (genbank:AB169639)
###################################################

but from the regular ruby environment, it does not recognize the
function even after calling the library with

require 'bio'

although all other functions of bioruby can be used in this way.

###################################################
$ irb
irb(main):001:0> require 'bio'
=> true
irb(main):002:0> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
=> "atgcatgcaaaa"
irb(main):003:0> puts seq.complement
ttttgcatgcat
=> nil
irb(main):004:0> ss = ent('genbank:AB169639')
NoMethodError: undefined method `ent' for main:Object
        from (irb):4
        from :0
irb(main):005:0> exit
###################################################

The same is true when I try to run a script that uses "ent" function
--- it crushes because it does not recognize the ent function although
all other bioruby functions seem to work fine. This occurs under two
different installations (linux and cygwin).

Could you tell me how to get around of this problem?

Thank you.
Kipling