[BioRuby] test and bioruby shell questions

[Davide Rambaldi]

On Aug 30, 2008, at 2:16 PM, Toshiaki Katayama wrote:

> The demo above was designed to utilize the KEGG API, which is a  
> SOAP based web service,
> so we need to change the default data source to obtain this entry.
> We can fix this by switching to use NCBI's efetch method instead.



I manage to write a fix for this... is really horrible actually (but  
it works)
I have inserted my code in the nested if/else that retrieve the  
entry, so after the KEGG API try, the shell try NCBI::REST.efetch

Oni:~/src/bioruby tucano$ git diff lib/bio/shell/plugin/entry.rb
diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/ 
entry.rb
index 6d36fb5..0a45ecd 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,16 @@ module Bio::Shell

        # KEGG API at http://www.genome.jp/kegg/soap/
        else
-        puts "Retrieving entry from KEGG API (#{arg})"
          entry = bget(arg)
+        if $?.exitstatus == 0 and str.length != 0
+          puts "Retrieving entry from KEGG API (#{arg})"
+        else
+          # efetch from NCBI
+          puts "Retrieving entry from NCBI (#{arg})"
+          require 'bio/io/ncbirest.rb'
+          fetch = Bio::NCBI::REST.efetch("AF237819",  
{"db"=>"nuccore", "rettype"=>"gb"})
+          entry = fetch.to_s
+        end
        end
      end



So the questions/comments:

1. I have added the require 'bio/io/ncbirest.rb' beacuse in bio.rb  
ncbirest.rb is not loaded (only SOAP). Is a bug or a feature?

2. the standard demo command now is able to retrieve the genbank  
entry, but generate an error in the MIDI file generation:

bioruby> midifile("data/AF237819.mid", kuma.naseq)
Saving MIDI file (data/AF237819.mid) ... Error: Failed to save (data/ 
AF237819.mid) : No such file or directory - data/AF237819.mid

  any clue for this FAil?

by the way: wow a module to translate a sequence in music? I really  
wont to test it also! I have made a software that do something similar:

http://recipient.cc/playgene/

Is made with a perl (?!) script to efetch sequence from NCBI, and a  
flash application for the interface and to load the music library... :-)

Best Regards




Davide Rambaldi,
Bioinformatics PhD student.
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Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
(homepage)
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)

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