rbbt-util 5.43.0 → 5.44.0

data/test/rbbt/tsv/test_accessor.rb

@@ -1,319 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt/tsv'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-class TestTSVAccessor < Test::Unit::TestCase
-
-  def test_to_hash
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      hash = tsv.to_hash
-      assert hash.methods.select{|m| m =~ /#{ TSV::KEY_PREFIX }/}.empty?
-    end
-  end
-
-  def test_zip_new
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b|bb|bbb    Id1|Id2|Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      tsv.zip_new("row1", %w(aaaa bbbb Id4))
-      assert_equal %w(b bb bbb bbbb), tsv["row1"]["ValueB"]
-    end
-  end
-
-  def test_tsv
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal 2, tsv.keys.length
-      assert_equal 2, tsv.values.length
-      assert_equal 2, tsv.collect.length
-    end
-  end
-
-  def test_named_values
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal ["A"], tsv["row2"]["ValueA"]
-    end
-  end
-
-  def test_to_s
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert tsv.to_s =~ /row1\ta|aa|aaa/
-      assert tsv.to_s =~ /:type=:double/
-    end
-  end
-  
-  def test_to_s_no_preable
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    target =<<-EOF
-Id,ValueA,ValueB,OtherID
-row1,a|aa|aaa,b,Id1|Id2
-row2,A,B,Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal tsv.to_s(preamble: false, header_hash: '').gsub(/\t/, ','), target
-    end
-  end
-  
-  def test_entries
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal filename, tsv.options[:filename]
-    end
- 
-  end
-
-  def test_marshal
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :persist_serializer => :marshal, :persist => true)
-      assert_equal 2, tsv.size
-      assert_equal filename, tsv.options[:filename]
-    end
-  end
-
-  def test_zip_fields
-    a = [%w(1 2), %w(a b)]
-    assert_equal a, TSV.zip_fields(TSV.zip_fields(a))
-  end
-
-  def test_indentify_fields
-    content =<<-EOF
-#ID ValueA ValueB Comment
-row1 a b c
-row2 A B C
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(File.open(filename), :double, :sep => /\s/)
-      assert_equal :key, tsv.identify_field("ID")
-    end
-  end
-
-  def test_sort
-    content =<<-EOF
-#ID ValueA ValueB Comment
-row1 a B c
-row2 A b C
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(File.open(filename), :double, :sep => /\s/)
-      assert_equal %w(row2 row1), tsv.tsv_sort{|a,b|
-        a[1]["ValueA"] <=> b[1]["ValueA"]
-      }.collect{|k,v| k}
-      assert_equal %w(row1 row2), tsv.tsv_sort{|a,b|
-        a[1]["ValueB"] <=> b[1]["ValueB"]
-      }.collect{|k,v| k}
-    end
-  end
-
-  def test_sort_by
-    content =<<-EOF
-#ID ValueA ValueB Comment
-row1 a B c
-row2 A b C
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(File.open(filename), :list, :sep => /\s/)
-      assert_equal %w(row2 row1), tsv.sort_by("ValueA").collect{|k,v| k}
-      assert_equal %w(row1 row2), tsv.sort_by("ValueB").collect{|k,v| k}
-    end
-  end
-
-
-  def test_page
-    content =<<-EOF
-#ID ValueA ValueB Comment
-row1 a B f
-row2 A b e
-row3 A b d
-row4 A b c
-row5 A b b
-row6 A b a
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(File.open(filename), :list, :sep => /\s/)
-      assert_equal 3, tsv.page(1,3).size
-      assert_equal %w(row1 row2 row3).sort, tsv.page(1,3).keys.sort
-      assert_equal %w(row6 row5 row4).sort, tsv.page(1,3, "Comment").keys.sort
-      assert_equal %w(row4 row3).sort, tsv.page(2,2, "Comment").keys.sort
-    end
-  end
-
-
-  def test_sort_by_with_proc
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID    Pos
-row1    a|aa|aaa    b    Id1|Id2    2
-row2    aA    B    Id3    1
-row3    A|AA|AAA|AAA    B    Id3    3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(File.open(filename), :sep => /\s+/)
-      assert_equal %w(row3 row1 row2), (tsv.sort_by("ValueA") do |key, value| value.length end).collect{|k,v| k}.reverse
-    end
-  end
-
-  def test_chunked_values_at
-    tsv = TSV.setup({})
-    10.times do |i|
-      tsv[i] = i
-    end
-    pos = tsv.chunked_values_at (0..10-1).to_a, 2
-    assert_equal (0..10-1).to_a, pos
-  end
-
-  def test_unzip
-    content =<<-EOF
-#: :type=:list
-#PMID:Sentence number:TF:TG	Transcription Factor (Associated Gene Name)	Target Gene (Associated Gene Name)	Sign	Negation	PMID
-24265317:3:NR1H3:FASN	NR1H3	FASN			24265317
-17522048:0:NR1H3:FASN	NR1H3	FASN	+		17522048
-19903962:0:NR1H3:FASN	NR1H3	FASN			19903962
-19903962:7:NR1H3:FASN	NR1H3	FASN			19903962
-22183856:4:NR1H3:FASN	NR1H3	FASN			22183856
-22641099:4:NR1H3:FASN	NR1H3	FASN	+		22641099
-23499676:8:NR1H3:FASN	NR1H3	FASN	+		23499676
-11790787:5:NR1H3:FASN	NR1H3	FASN			11790787
-11790787:7:NR1H3:FASN	NR1H3	FASN	+		11790787
-11790787:9:NR1H3:FASN	NR1H3	FASN	+		11790787
-11790787:11:NR1H3:FASN	NR1H3	FASN			11790787
-17522048:1:NR1H3:FASN	NR1H3	FASN	+		17522048
-17522048:3:NR1H3:FASN	NR1H3	FASN			17522048
-22160584:1:NR1H3:FASN	NR1H3	FASN			22160584
-22160584:5:NR1H3:FASN	NR1H3	FASN	+		22160584
-22160584:8:NR1H3:FASN	NR1H3	FASN	+		22160584
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Transcription Factor (Associated Gene Name)", :fields => ["Target Gene (Associated Gene Name)", "Sign", "PMID"], :merge => true, :type => :double)
-      unzip = tsv.unzip(0,true)
-      assert_equal unzip["NR1H3:FASN"][0].length, unzip["NR1H3:FASN"][1].length
-    end
-  end
-
-  def test_to_s_unmerge
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|A    b|B    Id1|Id2
-row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal 6, CMD.cmd('grep -v "#" | cut -f 1', :in => tsv.to_s(nil, false, true)).read.split("\n").length
-    end
-  end
-
-  def test_to_s_no_fields
-    file1 =<<-EOF
-row6 dd dd ee
-row1 a b c
-row2 A B C
-row3 1 2 3
-   EOF
-    tsv1 = TSV.open StringIO.new(file1), :sep => " "
-    assert tsv1.to_s(:sort, true).include?('dd')
-  end
-
-  def test_to_s_unmerge_expand
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|A    b|B    Id1
-row2    aa|aa|AA|AA    b1|b2|B1|B2    Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      text = tsv.to_s(nil, false, :expand)
-      assert text =~ /row2\taa\tb2\tId2/
-    end
-  end
-
-  def test_remove_duplicates
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|A|a|a    b|B|b|    Id1|Id2|Id1|Id1
-row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal %w(a A a), tsv.remove_duplicates["row1"]["ValueA"]
-      assert tsv.remove_duplicates["row1"]["ValueB"].include?("")
-    end
-
-  end
-
-  def test_unzip_zip
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|A|a|a    b|B|b|    Id1|Id2|Id1|Id1
-row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal ["b", "b", ""], tsv.unzip("ValueA", true)["row1:a"]["ValueB"]
-      assert_equal ["b", "b", "", "B"].sort, tsv.unzip("ValueA", true).zip(true)["row1"]["ValueB"].sort
-    end
-
-  end
-
-  def test_identifier_files
-    assert_include datadir_test.CollecTRI.identifier_files.first, "test/data"
-  end
-end