test/rbbt/sources/test_organism.rb in rbbt-sources-3.0.34 vs test/rbbt/sources/test_organism.rb in rbbt-sources-3.0.35

@@ -3,41 +3,41 @@
 require 'test/unit'
 require 'rbbt/sources/ensembl_ftp'
 
 class TestOrganism < Test::Unit::TestCase
 
-  def _test_known_ids
+  def test_known_ids
     assert Organism.known_ids("Hsa").include?("Associated Gene Name")
   end
 
-  def _test_location
+  def test_location
     assert_equal "share/organisms/Sce/identifiers", Organism.identifiers('Sce')
   end
 
-  def _test_identifiers
+  def test_identifiers
     assert Organism.identifiers('Hsa').tsv(:key_field => "Entrez Gene ID", :persist => true)['1020']["Associated Gene Name"].include?('CDK5')
     assert Organism.identifiers('Sce').tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
     assert Organism.identifiers("Sce").tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
   end
 
-  def _test_lexicon
+  def test_lexicon
     assert TSV.open(Organism.lexicon('Sce'))['S000006120'].flatten.include?('YPL199C')
   end
 
-  def _test_guess_id
+  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 "Associated Gene Name", Organism.guess_id("Sce", gene_name).first
     assert_equal "Ensembl Gene ID", Organism.guess_id("Sce", ensembl).first
   end
 
-  def _test_organisms
+  def test_organisms
     assert Organism.organisms.include? "Hsa"
     assert_equal "Hsa", Organism.organism("Homo sapiens")
   end
 
-  def _test_attach_translations
+  def test_attach_translations
     tsv = TSV.setup({"1020" => []}, :type => :list)
     tsv.key_field = "Entrez Gene ID"
     tsv.fields = []
     tsv.namespace = "Hsa"
     
@@ -45,11 +45,11 @@
     Organism.attach_translations "Hsa", tsv, "Ensembl Gene ID"
 
     assert_equal "CDK5", tsv["1020"]["Associated Gene Name"]
   end
 
-  def _test_entrez_taxids
+  def test_entrez_taxids
     assert_equal "Hsa", Organism.entrez_taxid_organism('9606')
   end
 
   def test_lift_over
     mutation_19 = "19:21131664:T"
@@ -59,25 +59,25 @@
 
     assert_equal mutation_18, Organism.liftOver([mutation_19], source_build, target_build).first
     assert_equal mutation_19, Organism.liftOver([mutation_18], target_build, source_build).first
   end
 
-  def _test_orhtolog
+  def test_orhtolog
     require 'rbbt/entity/gene'
     assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog(Organism.default_code("Hsa"))
   end
 
-  #def _test_genes_at_chromosome
+  #def test_genes_at_chromosome
   #  pos = [12, 117799500]
   #  assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
   #end
 
-  #def _test_genes_at_chromosome_array
+  #def test_genes_at_chromosome_array
   #  pos = [12, [117799500, 106903900]]
   #  assert_equal ["ENSG00000089250", "ENSG00000013503"], Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
   #end
  
-  #def _test_genes_at_genomic_positions
+  #def test_genes_at_genomic_positions
   #  pos = [[12, 117799500], [12, 106903900], [1, 115259500]]
   #  assert_equal ["ENSG00000089250", "ENSG00000013503", "ENSG00000213281"], Organism::Hsa.genes_at_genomic_positions(pos)
   #end
 
 end