Sunday, June 20, 2010


There are 5 files witch don't have the files for unit test.

I skipped Bio::KEGG::Brite, It probably has the same methods as KEGGDB.

Bio::TestBioKEGGEXPRESSION outputs the following result now.
12 tests, 7 assertions, 6 failures, 5 errors
I checked the following error of them.
4) Error:
Errno::EDOM: Numerical argument out of domain - log10
    ./lib/bio/db/kegg/expression.rb:128:in `log10'
    ./lib/bio/db/kegg/expression.rb:128:in `logy_minus_logx'
    ./lib/bio/db/kegg/expression.rb:127:in `each'
    ./lib/bio/db/kegg/expression.rb:127:in `logy_minus_logx'
    ./lib/bio/db/kegg/expression.rb:99:in `down_regulated'
    test/unit/bio/db/kegg/test_expression.rb:77:in `test_down_regulated'
The reason is that test_down_regulated gives a negative value to Math.log10.

I skipped Bio::KEGG::KGML because it is just a wrapper class of REXML.

I haven't written Bio::KEGG::Common, Bio::KEGG::KEGGTAB and Bio::KEGG::Taxonomy (the latter two classes may not be so important.).

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