require File.expand_path(File.dirname(__FILE__) + '/../../test_helper') require 'rbbt/sources/organism' require 'test/unit' class TestEntrez < Test::Unit::TestCase def test_identifiers assert TSV.new(Organism.identifiers('Sce'))['S000006120']["Ensembl Gene ID"].include?('YPL199C') assert TSV.new(Organism::Sce.identifiers)['S000006120']["Ensembl Gene ID"].include?('YPL199C') assert TSV.new(Organism.identifiers('Hsa'))['1020']["Associated Gene Name"].include?('CDK5') end def test_lexicon assert TSV.new(Organism.lexicon('Sce'))['S000006120'].flatten.include?('YPL199C') end def test_guess_id ensembl = %w(YOL044W YDR289C YAL034C YGR246C ARS519 tH(GUG)E2 YDR218C YLR002C YGL224C) gene_name = %w(SNR64 MIP1 MRPS18 TFB2 JEN1 IVY1 TRS33 GAS3) assert_equal "Ensembl Gene ID", Organism::Sce.guess_id(ensembl).first assert_equal "Associated Gene Name", Organism::Sce.guess_id(gene_name).first end def test_organisms assert Organism.organisms.include? "Hsa" assert_equal "Hsa", Organism.organism("Homo sapiens") end end