[BioRuby] bioruby shell

[Davide Rambaldi]

Hello,
	I have posted as a reply in another thread a small modification to  
lib/bio/shell/plugin/entry.rb that resolve the demo problem (die  
after trying to download a genbank from KeggAPI):

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


I have some other ideas for the shell:

- adding a method to remove all saved objects
- making an help (at least for demo, ls and rm commands)
- adding an OptionParser

In general I want to propose some other simple modification to this  
part of the bioruby library.

I am losing my time? there is another person on this?

or I can go on?

Many thanks for feedback

P.S: my simple BLAT application blatanalyzer is now accessible via  
svn at
svn checkout svn://rubyforge.org/var/svn/blatanalyzer/trunk

any feedback is really appreciated


thanks again



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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