rbbt-util 3.2.0 → 3.2.1

data/test/rbbt/util/test_bed.rb

@@ -1,136 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/util/bed'
-require 'rbbt/util/tmpfile'
-
-class TestBed < Test::Unit::TestCase
-  def load_data(data)
-    Log.debug("Data:\n#{Open.read(data)}")
-    tsv = TSV.new(data, :list, :sep=>":", :cast => proc{|e| e =~ /(\s*)(_*)/; ($1.length..($1.length + $2.length - 1))})
-    tsv.add_field "Start" do |key, values|
-      values["Range"].first
-    end
-    tsv.add_field "End" do |key, values|
-      values["Range"].last
-    end
- 
-    tsv
-  end
-
-  def test_point
-    data =<<-EOF
-#ID Pos
-a 1
-b 10
-c 20
-d 12
-e 26
-f 11
-g 25
-    EOF
-
-    TmpFile.with_file(data) do |f|
-      bed = Bed.new TSV.new(f, :list, :sep=>" "), :key => "Pos" , :value => "ID"
-
-      assert_equal %w(), bed[0].sort
-      assert_equal %w(b), bed[10].sort
-      assert_equal %w(a b c d f), bed[(0..20)].sort
-    end
-  end
-
-  def test_range
-    data =<<-EOF
-#ID:Range
-#:012345678901234567890
-a:   ______
-b: ______
-c:    _______
-d:  ____
-e:    ______
-f:             ___
-g:         ____
-    EOF
-
-    TmpFile.with_file(data) do |f|
-      bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID"
-
-      assert_equal %w(), bed[0].sort
-      assert_equal %w(b), bed[1].sort
-      assert_equal %w(), bed[20].sort
-      assert_equal %w(), bed[(20..100)].sort
-      assert_equal %w(a b d), bed[3].sort
-      assert_equal %w(a b c d e), bed[(3..4)].sort
-    end
-  end
-
-  def test_format
-    entry = Bed::Entry.new "Hola", 0, 10, nil
-    format = Bed::FixWidthTable.format(entry,1, 100)
-    assert_equal entry, Bed::FixWidthTable.unformat(format, 100)
-  end
-
-  def test_table
-    TmpFile.with_file do |f|
-      table = Bed::FixWidthTable.new(f, 100, false)
-      table.add Bed::Entry.new("Entry1", 0, 10, nil), 0
-      table.add Bed::Entry.new("Entry2", 10, 20, nil), 10
-      table.add Bed::Entry.new("Entry3", 10, 20, nil), 10
-
-      table.read 
-
-      assert_equal "Entry1", table[0].value
-      assert_equal "Entry2", table[1].value
-      assert_equal "Entry3", table[2].value
-    end
-
-  end
-
-  def test_range_point
-     data =<<-EOF
-#ID Pos
-a 1
-b 10
-c 20
-d 12
-e 26
-f 11
-g 25
-    EOF
-
-    TmpFile.with_file(data) do |f|
-      bed = Bed.new TSV.new(f,:list, :sep=>" "), :key => "Pos" , :value => "ID", :persistence => true
-
-      bed = Bed.new TSV.new(f,:list, :sep=>" "), :key => "Pos" , :value => "ID", :persistence => true
-
-      assert_equal %w(), bed[0].sort
-      assert_equal %w(a b c d f), bed[(0..20)].sort
-      assert_equal %w(b), bed[10].sort
-    end
-   end
-
-  def test_range_persistence
-    data =<<-EOF
-#ID:Range
-#:012345678901234567890
-a:   ______
-b: ______
-c:    _______
-d:  ____
-e:    ______
-f:             ___
-g:         ____
-    EOF
-
-    TmpFile.with_file(data) do |f|
-      bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID", :persistence => true
-
-      bed = Bed.new load_data(f), :range => ["Start" , "End"], :value => "ID", :persistence => true
-      
-      assert_equal %w(), bed[0].sort
-      assert_equal %w(b), bed[1].sort
-      assert_equal %w(), bed[20].sort
-      assert_equal %w(), bed[(20..100)].sort
-      assert_equal %w(a b d), bed[3].sort
-      assert_equal %w(a b c d e), bed[(3..4)].sort
-    end
-  end
-end