# Bioruby ent function

**URL:** <https://www.ruby-forum.com/t/bioruby-ent-function/89996>\
**Category:** Ruby\
**Created:** [March 24, 2007, 8:30pm UTC](https://www.ruby-forum.com/t/bioruby-ent-function/89996 "2007-03-24T20:30:50Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![unknown](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/u/4bbf92/32.png) [@unknown](https://www.ruby-forum.com/u/unknown)\
**Post date:** [March 24, 2007, 8:30pm UTC](https://www.ruby-forum.com/t/bioruby-ent-function/89996/1 "2007-03-24T20:30:50Z")

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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

---

<div class="post-metadata">

**Author:** ![unknown](https://www.ruby-forum.com/letter_avatar_proxy/v4/letter/u/4bbf92/32.png) [@unknown](https://www.ruby-forum.com/u/unknown)\
**Post date:** [March 24, 2007, 8:43pm UTC](https://www.ruby-forum.com/t/bioruby-ent-function/89996/2 "2007-03-24T20:43:06Z")

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Kipling wrote:

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

Hmm. I’ll take a look today or tomorrow.

Evan W.