[BioRuby] test and bioruby shell questions

[Ben Woodcroft]

Hi,

Using the edge version of bioruby I get 7 errors as well, although
they are slightly different. I wouldn't be too worried.

$ ruby runner.rb
Loaded suite .
Started
.....FF..F.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FFE................................................
Finished in 133.52153 seconds.

  1) Failure:
test_gff_exportview(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:95]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  2) Failure:
test_gff_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:121]:
<"4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tgene_id=ENSG00000206158;
transcript_id=ENST00000382964; exon_id=ENSE00001494097;
gene_type=KNOWN_protein_coding\n"> expected but was
<"">.

  3) Failure:
test_tab_exportview_with_named_args(Bio::FuncTestEnsemblHuman)
[./functional/bio/io/test_ensembl.rb:180]:
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n4\tEnsembl\tGene\t1148366\t1151952\t.\t+\t1\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n">
expected but was
<"seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\n">.

  4) Failure:
test_id_line_sequence_version(Bio::TestEMBL)
[./unit/bio/db/embl/test_embl_rel89.rb:45]:
<"1"> expected but was
<nil>.

  5) Failure:
test_left_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:43]:
<"nnnnnnn"> expected but was
<"">.

  6) Failure:
test_right_padding(Bio::TestStringFormatting)
[./unit/bio/util/restriction_enzyme/test_string_formatting.rb:50]:
<"nn"> expected but was
<"">.

  7) Error:
test_strip_padding(Bio::TestStringFormatting):
NoMethodError: undefined method `[]' for nil:NilClass
    ../lib/bio/util/restriction_enzyme/string_formatting.rb:64:in
`strip_padding'
    ./unit/bio/util/restriction_enzyme/test_string_formatting.rb:33:in
`test_strip_padding'

1867 tests, 4049 assertions, 6 failures, 1 errors






Can't help with the bioruby shell, sorry, as I don't use it. Why would
you want to remove objects, though?

Thanks,
ben

2008/8/30 Davide Rambaldi <davide.rambaldi at ifom-ieo-campus.it>:
> 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.
> -----------------------------------------------------
> 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)
>
> -----------------------------------------------------
>
>
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



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