[BioRuby] test and bioruby shell questions

[Davide Rambaldi]

Greetings,
  I am a new user of ruby and bioruby and I really like it especially  
for the opportunity to test interactively with irb and BioRuby shell

  I have some question please:

- TESTING (bioruby 1.2.1 and ruby 1.8.7 on a Power PC G4 osx)
   during testing

  I got 7 errors:

  	test_gff_exportview(Bio::FuncTestEnsemblHuman) [./functional/bio/ 
io/test_ensembl.rb:95]:
	test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:121]:
	test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman) [./ 
functional/bio/io/test_ensembl.rb:180]:
	test_list_falsenegative(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1304]:
	test_list_falsepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1356]:
	test_list_potentialhit(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1408]:
	test_list_truepositive(Bio::TestPROSITE) [./unit/bio/db/ 
test_prosite.rb:1236]:

   Is a know problem or related with my computer?


- BioRuby SHELL
   during shell demo (demo command) there is a crash after:
kuma = getobj("gb:AF237819")
Retrieving entry from KEGG API (gb:AF237819)
   ==> nil
bioruby> kuma.definition
NoMethodError: undefined method `definition' for nil:NilClass
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52:in  
`irb_binding'
         from /usr/local/lib/ruby/1.8/irb/workspace.rb:52
Maybe IRB bug!!

   crash because kuma is empty? irb can reach the sequence?
bioruby> kuma
   ==> nil


- SHELL OBJECTS and HELP

   there is a way to delete shell objects (.bioruby/shell/session/ 
object) directly from the shell?
   a "rm" command?
   there is an help in the BioRuby shell? (help give me => nil,  ./ 
bioruby --help give unrecognized option )


Thanks and 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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