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require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
require 'rbbt/util/tmpfile'
require 'test/unit'
require 'rbbt/knowledge_base'
require 'rbbt/knowledge_base/query'
class TestKnowledgeBaseQuery < Test::Unit::TestCase
EFFECT =StringIO.new <<-END
#: :sep=" "#:type=:double
#SG TG Effect
MDM2 TP53 inhibition
TP53 NFKB1|GLI1 activation|activation true|true
END
EFFECT_OPTIONS = {
:source => "SG=~Associated Gene Name=>Ensembl Gene ID",
:target => "TG=~Associated Gene Name=>Ensembl Gene ID",
:persist => false,
:identifiers => datafile_test('identifiers'),
:undirected => true,
:namespace => "Hsa"
}
EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup
KNOWLEDGE_BASE = KnowledgeBase.new Rbbt.tmp.test.kb_foo2, "Hsa"
KNOWLEDGE_BASE.format = {"Gene" => "Ensembl Gene ID"}
KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup
def test_subset_all_persist
Misc.benchmark(1000) do
assert_equal 6, KNOWLEDGE_BASE.subset(:effects, :all).length
assert_equal 4, KNOWLEDGE_BASE.subset(:effects, :all).target_entity.uniq.length
assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys
end
end
def _test_subset_all_persist_format
assert KNOWLEDGE_BASE.subset(:effects, :all).target_entity.reject{|e| e =~ /^ENS/}.empty?
end
end
Version data entries
139 entries across 139 versions & 1 rubygems