bio 1.4.0 → 1.4.1

data/test/unit/bio/test_tree.rb

@@ -1,8 +1,9 @@
 #
 # = test/bio/test_tree.rb - unit test for Bio::Tree
 #
-# Copyright::   Copyright (C) 2006
+# Copyright::   Copyright (C) 2006, 2010
 #               Naohisa Goto <ng@bioruby.org>
+#               Copyright (C) 2010 Kazuhiro Hayashi <k.hayashi.info@gmail.com>
 # License::     The Ruby License
 #
 # $Id:$
@@ -587,6 +588,264 @@ module Bio
     def test_remove_edge_nonexistent
       assert_raise(IndexError) { @tree.remove_edge(@mouse, @rat) }
     end
+
+    def test_remove_edge_if
+      ret = nil
+      assert_nothing_raised {
+        ret = @tree.remove_edge_if do |source, target, edge|
+          [ source.name, target.name ].sort == [ 'mouse', 'rodents' ]
+        end
+      }
+      assert_equal(@tree, ret)
+      assert_nil(@tree.get_edge(@mouse, @rodents))
+    end
+
+    def test_remove_edge_if_nothing_removed
+      ret = nil
+      by_id_2 = Proc.new { |x,y| x[2].__id__ <=> y[2].__id__ }
+      orig_edges = @tree.edges.sort(&by_id_2)
+      assert_nothing_raised {
+        ret = @tree.remove_node_if { |edge| false }
+      }
+      assert_equal(@tree, ret)
+      assert_equal(orig_edges, @tree.edges.sort(&by_id_2))
+    end
+
+    def test_collect_node!
+      ret = nil
+      newmouse = Bio::Tree::Node.new('MOUSE')
+      newhuman = Bio::Tree::Node.new('HUMAN')
+      assert_nothing_raised {
+        ret = @tree.collect_node! do |node|
+          case node.name
+          when 'mouse'
+            newmouse
+          when 'human'
+            newhuman
+          else
+            node
+          end
+        end
+      }
+      assert_equal(@tree, ret)
+      assert(@tree.include?(newmouse))
+      assert(!@tree.include?(@mouse))
+      assert(@tree.include?(newhuman))
+      assert(!@tree.include?(@human))
+      nodes = [ newmouse, @rat, @rodents, newhuman,
+                @chimpanzee, @primates, @mammals ].sort(&@by_id)
+      assert_equal(nodes, @tree.nodes.sort(&@by_id))
+    end
+
+    def test_collect_edge!
+      ret = nil
+      newedge_rodents_mouse  = Bio::Tree::Edge.new(100.0)
+      newedge_primates_human = Bio::Tree::Edge.new(200.0)
+      assert_nothing_raised {
+        ret = @tree.collect_edge! do |source, target, edge|
+          case [ source.name, target.name ].sort
+          when [ 'mouse', 'rodents' ]
+            newedge_rodents_mouse
+          when [ 'human', 'primates' ]
+            newedge_primates_human
+          else
+            edge
+          end
+        end
+      }
+      assert_equal(@tree, ret)
+      assert_equal(newedge_rodents_mouse, @tree.get_edge(@mouse, @rodents))
+      assert_equal(newedge_primates_human, @tree.get_edge(@human, @primates))
+      expected = [ newedge_rodents_mouse,
+                   @edge_rodents_rat,
+                   @edge_mammals_rodents,
+                   newedge_primates_human,
+                   @edge_primates_chimpanzee,
+                   @edge_mammals_primates ].sort(&@by_id)
+      assert_equal(expected, @tree.edges.collect { |x| x[-1] }.sort(&@by_id))
+    end
+
+    def test_get_edge_merged
+      edge1 = Bio::Tree::Edge.new(12.34)
+      edge2 = Bio::Tree::Edge.new(56.78)
+      merged_edge = @tree.get_edge_merged(edge1, edge2)
+      # struggle to avoid possible float problem
+      expected = 12.34 + 56.78
+      assert_equal(expected, merged_edge.distance)
+    end
+
+    def test_get_node_bootstrap
+      node = Bio::Tree::Node.new("test")
+      node.bootstrap = 1
+      assert_equal(1, @tree.get_node_bootstrap(node))
+    end
+
+    def test_get_node_bootstrap_string=
+      node = Bio::Tree::Node.new("test")
+      node.bootstrap_string = "0.75"
+      assert_equal(0.75, @tree.get_node_bootstrap(node))
+    end
+
+    def test_subtree
+      newtree = nil
+      assert_nothing_raised {
+        newtree = @tree.subtree([ @mouse, @rodents, @human ])
+      }
+      assert_equal(3, newtree.number_of_nodes)
+      assert_equal(1, newtree.number_of_edges)
+      nodes = [ @mouse, @rodents, @human ].sort(&@by_id)
+      assert_equal(nodes, newtree.nodes.sort(&@by_id))
+      edges = [ @edge_rodents_mouse ].sort(&@by_id)
+      assert_equal(edges, newtree.edges.collect { |x| x[-1] }.sort(&@by_id))
+    end
+
+    def test_subtree_with_all_paths
+      newtree = nil
+      assert_nothing_raised {
+        newtree = @tree.subtree_with_all_paths([ @mouse, @rodents, @human ])
+      }
+      assert_equal(5, newtree.number_of_nodes)
+      assert_equal(4, newtree.number_of_edges)
+      nodes = [ @mouse, @rodents, @mammals, @primates, @human ].sort(&@by_id)
+      assert_equal(nodes, newtree.nodes.sort(&@by_id))
+      edges = [ @edge_rodents_mouse,
+                @edge_mammals_rodents,
+                @edge_mammals_primates,
+                @edge_primates_human ].sort(&@by_id)
+      assert_equal(edges, newtree.edges.collect { |x| x[-1] }.sort(&@by_id))
+    end
+
+    def test_concat
+      tree2 = Bio::Tree.new
+      node1 = Bio::Tree::Node.new('node1')
+      node2 = Bio::Tree::Node.new('node2')
+      edge0 = Bio::Tree::Edge.new(0.1)
+      tree2.add_edge(node1, node2, edge0)
+      ret = nil
+      assert_nothing_raised {
+        ret = @tree.concat(tree2)
+      }
+      assert_equal(@tree, ret)
+      assert_equal(9, @tree.number_of_nodes)
+      assert_equal(7, @tree.number_of_edges)
+      nodes = (@nodes + [ node1, node2 ]).sort(&@by_id)
+      assert_equal(nodes, @tree.nodes.sort(&@by_id))
+      edges = (@edges.collect { |x| x[-1] } + [ edge0 ]).sort(&@by_id)
+      assert_equal(edges, @tree.edges.collect { |x| x[-1] }.sort(&@by_id))
+    end
+
+    def test_path
+      expected = [ @mouse, @rodents, @mammals, @primates, @human ]
+      assert_equal(expected, @tree.path(@mouse, @human))
+    end
+
+    #Passed cache_* methods because of internal methods
+
+    def test_parent
+      assert_equal(@rodents, @tree.parent(@mouse, @mammals))
+    end
+
+    def test_children
+      expected = [ @primates, @rodents ].sort(&@by_id)
+      assert_equal(expected,
+                   @tree.children(@mammals, @mammals).sort(&@by_id))
+    end
+
+    def test_descendents
+      expected = [ @primates, @rodents, @human, @chimpanzee,
+                   @mouse, @rat ].sort(&@by_id)
+      assert_equal(expected,
+                   @tree.descendents(@mammals, @mammals).sort(&@by_id))
+    end
+
+    def test_leaves_noargs
+      expected = [ @chimpanzee, @human, @mouse, @rat ].sort(&@by_id)
+      @tree.root = @mammals
+      assert_equal(expected, @tree.leaves.sort(&@by_id))
+    end
+
+    def test_leaves
+      expected = [ @chimpanzee, @human, @mouse, @rat ].sort(&@by_id)
+      assert_equal(expected, @tree.leaves(@mammals, @mammals).sort(&@by_id))
+    end
+
+    def test_ancestors
+      expected = [ @rodents, @mammals ].sort(&@by_id)
+      assert_equal(expected, @tree.ancestors(@mouse, @mammals).sort(&@by_id))
+    end
+
+    def test_lowest_common_ancestor
+      assert_equal(@rodents,
+                   @tree.lowest_common_ancestor(@mouse, @rat, @mammals))
+    end
+
+    def test_total_distance
+      assert_equal("0.7777", sprintf("%.15g", @tree.total_distance))
+    end
+
+    def test_distance_matrix
+      mat = @tree.distance_matrix([ @mouse, @rat, @human, @chimpanzee ])
+      assert_instance_of(Matrix, mat)
+      assert_equal([ "0",      "0.2093", "0.6149", "0.6266" ],
+                   mat.row(0).map { |x| sprintf("%.15g", x) }.to_a)
+      assert_equal([ "0.2093", "0",      "0.6306", "0.6423" ],
+                   mat.row(1).map { |x| sprintf("%.15g", x) }.to_a)
+      assert_equal([ "0.6149", "0.6306", "0",      "0.0889" ],
+                   mat.row(2).map { |x| sprintf("%.15g", x) }.to_a)
+      assert_equal([ "0.6266", "0.6423", "0.0889", "0" ],
+                   mat.row(3).map { |x| sprintf("%.15g", x) }.to_a)
+    end
+     
+    def test_adjacency_matrix
+      a =
+        [ [ 0,  nil, @edge_rodents_mouse, nil, nil, nil, nil ],
+          [ nil, 0, @edge_rodents_rat, nil, nil, nil, nil ],
+          [ @edge_rodents_mouse, @edge_rodents_rat, 0, nil,
+            nil, nil, @edge_mammals_rodents ],
+          [ nil, nil, nil, 0, nil, @edge_primates_human, nil ],
+          [ nil, nil, nil, nil, 0, @edge_primates_chimpanzee, nil ],
+          [ nil, nil, nil, @edge_primates_human,
+            @edge_primates_chimpanzee, 0, @edge_mammals_primates ],
+          [ nil, nil, @edge_mammals_rodents, nil,
+            nil, @edge_mammals_primates, 0 ]
+        ]
+      expected = Matrix.rows(a, false)
+      assert_equal(expected, @tree.adjacency_matrix(@nodes, nil, 0))
+    end
+
+    def test_adjacency_matrix_with_block
+      a =
+        [ [ 0,  nil, "0.0968", nil, nil, nil, nil ],
+          [ nil, 0, "0.1125", nil, nil, nil, nil ],
+          [ "0.0968", "0.1125", 0, nil, nil, nil, "0.256" ],
+          [ nil, nil, nil, 0, nil, "0.0386", nil ],
+          [ nil, nil, nil, nil, 0, "0.0503", nil ],
+          [ nil, nil, nil, "0.0386", "0.0503", 0, "0.2235" ],
+          [ nil, nil, "0.256", nil, nil, "0.2235", 0 ]
+        ]
+      expected = Matrix.rows(a, false)
+      assert_equal(expected,
+                   @tree.adjacency_matrix(@nodes, nil, 0) { |src, tgt, edge|
+                     sprintf("%.15g", edge.distance)
+                   })
+    end
+
+    def test_remove_nonsense_nodes
+      assert_equal([ @mammals ], @tree.remove_nonsense_nodes)
+    end
+
+    def test_insert_node
+      node1 = Bio::Tree::Node.new('node1')
+      ret = nil
+      assert_nothing_raised {
+        ret = @tree.insert_node(@mouse, @rodents, node1, 0.0123)
+      }
+      assert_equal(@tree, ret)
+      distance_mouse_node1 = @tree.get_edge(@mouse, node1).distance
+      assert_equal("0.0123", sprintf("%.15g", distance_mouse_node1))
+      distance_node1_rodents = @tree.get_edge(node1, @rodents).distance
+      assert_equal("0.0845", sprintf("%.15g", distance_node1_rodents))
+    end
   end #class TestTree2
 
 end #module Bio

data/test/unit/bio/util/test_contingency_table.rb

@@ -74,20 +74,20 @@ module Bio #:nodoc:
 
 
       #assert_equal(2.4, results[0][2])
-      assert_equal('2.4', results[0][2].to_s)
-      assert_equal('0.534522483824849', results[0][3].to_s)
+      assert_in_delta(2.4, results[0][2], 1e-13)
+      assert_in_delta(0.534522483824849, results[0][3], 1e-15)
 
-      assert_equal('12.0', results[5][2].to_s)
-      assert_equal('0.816496580927726', results[5][3].to_s)
+      assert_in_delta(12.0, results[5][2], 1e-13)
+      assert_in_delta(0.816496580927726, results[5][3], 1e-15)
 
-      assert_equal('2.4', results[9][2].to_s)
-      assert_equal('0.534522483824849', results[9][3].to_s)
+      assert_in_delta(2.4, results[9][2], 1e-13)
+      assert_in_delta(0.534522483824849, results[9][3], 1e-15)
 
       ctable = Bio::ContingencyTable.new
       ctable.table['a']['t'] = 4
       ctable.table['a']['g'] = 2
       ctable.table['g']['t'] = 3
-      assert_equal('1.28571428571429', ctable.chi_square.to_s)
+      assert_in_delta(1.28571428571429, ctable.chi_square, 1e-14)
       assert_equal(ctable.column_sum_all, ctable.row_sum_all)
       assert_equal(ctable.column_sum_all, ctable.table_sum_all)
     end

metadata

@@ -1,7 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.4.0
+  prerelease: false
+  segments: 
+  - 1
+  - 4
+  - 1
+  version: 1.4.1
 platform: ruby
 authors: 
 - BioRuby project
@@ -9,7 +14,7 @@ autorequire: bio
 bindir: bin
 cert_chain: []
 
-date: 2009-12-28 00:00:00 +09:00
+date: 2010-10-22 00:00:00 +09:00
 default_executable: bioruby
 dependencies: []
 
@@ -30,6 +35,7 @@ extra_rdoc_files:
 - README_DEV.rdoc
 - RELEASE_NOTES.rdoc
 - doc/Changes-1.3.rdoc
+- doc/RELEASE_NOTES-1.4.0.rdoc
 files: 
 - COPYING
 - COPYING.ja
@@ -54,6 +60,7 @@ files:
 - doc/Changes-1.3.rdoc
 - doc/KEGG_API.rd
 - doc/KEGG_API.rd.ja
+- doc/RELEASE_NOTES-1.4.0.rdoc
 - doc/Tutorial.rd
 - doc/Tutorial.rd.html
 - doc/Tutorial.rd.ja
@@ -141,6 +148,7 @@ files:
 - lib/bio/db/fasta/format_fasta.rb
 - lib/bio/db/fasta/format_qual.rb
 - lib/bio/db/fasta/qual.rb
+- lib/bio/db/fasta/qual_to_biosequence.rb
 - lib/bio/db/fastq.rb
 - lib/bio/db/fastq/fastq_to_biosequence.rb
 - lib/bio/db/fastq/format_fastq.rb
@@ -164,7 +172,9 @@ files:
 - lib/bio/db/kegg/glycan.rb
 - lib/bio/db/kegg/keggtab.rb
 - lib/bio/db/kegg/kgml.rb
+- lib/bio/db/kegg/module.rb
 - lib/bio/db/kegg/orthology.rb
+- lib/bio/db/kegg/pathway.rb
 - lib/bio/db/kegg/reaction.rb
 - lib/bio/db/kegg/taxonomy.rb
 - lib/bio/db/lasergene.rb
@@ -236,6 +246,7 @@ files:
 - lib/bio/sequence/generic.rb
 - lib/bio/sequence/na.rb
 - lib/bio/sequence/quality_score.rb
+- lib/bio/sequence/sequence_masker.rb
 - lib/bio/shell.rb
 - lib/bio/shell/core.rb
 - lib/bio/shell/demo.rb
@@ -387,7 +398,17 @@ files:
 - test/data/KEGG/G00024.glycan
 - test/data/KEGG/G01366.glycan
 - test/data/KEGG/K02338.orthology
+- test/data/KEGG/M00118.module
 - test/data/KEGG/R00006.reaction
+- test/data/KEGG/T00005.genome
+- test/data/KEGG/T00070.genome
+- test/data/KEGG/b0529.gene
+- test/data/KEGG/ec00072.pathway
+- test/data/KEGG/hsa00790.pathway
+- test/data/KEGG/ko00312.pathway
+- test/data/KEGG/map00030.pathway
+- test/data/KEGG/map00052.pathway
+- test/data/KEGG/rn00250.pathway
 - test/data/SOSUI/sample.report
 - test/data/TMHMM/sample.report
 - test/data/aaindex/DAYM780301
@@ -400,6 +421,7 @@ files:
 - test/data/blast/b0002.faa.m7
 - test/data/blast/b0002.faa.m8
 - test/data/blast/blastp-multi.m7
+- test/data/clustalw/example1.aln
 - test/data/command/echoarg2.bat
 - test/data/embl/AB090716.embl
 - test/data/embl/AB090716.embl.rel89
@@ -458,13 +480,23 @@ files:
 - test/data/fastq/wrapping_original_sanger.fastq
 - test/data/gcg/pileup-aa.msf
 - test/data/genscan/sample.report
+- test/data/go/selected_component.ontology
+- test/data/go/selected_gene_association.sgd
+- test/data/go/selected_wikipedia2go
 - test/data/iprscan/merged.raw
 - test/data/iprscan/merged.txt
+- test/data/medline/20146148_modified.medline
 - test/data/meme/db
 - test/data/meme/mast
 - test/data/meme/mast.out
 - test/data/meme/meme.out
 - test/data/paml/codeml/control_file.txt
+- test/data/paml/codeml/models/aa.aln
+- test/data/paml/codeml/models/aa.dnd
+- test/data/paml/codeml/models/aa.ph
+- test/data/paml/codeml/models/alignment.phy
+- test/data/paml/codeml/models/results0-3.txt
+- test/data/paml/codeml/models/results7-8.txt
 - test/data/paml/codeml/output.txt
 - test/data/paml/codeml/rates
 - test/data/phyloxml/apaf.xml
@@ -496,6 +528,7 @@ files:
 - test/unit/bio/appl/blast/test_ncbioptions.rb
 - test/unit/bio/appl/blast/test_report.rb
 - test/unit/bio/appl/blast/test_rpsblast.rb
+- test/unit/bio/appl/clustalw/test_report.rb
 - test/unit/bio/appl/gcg/test_msf.rb
 - test/unit/bio/appl/genscan/test_report.rb
 - test/unit/bio/appl/hmmer/test_report.rb
@@ -506,6 +539,7 @@ files:
 - test/unit/bio/appl/meme/test_motif.rb
 - test/unit/bio/appl/paml/codeml/test_rates.rb
 - test/unit/bio/appl/paml/codeml/test_report.rb
+- test/unit/bio/appl/paml/codeml/test_report_single.rb
 - test/unit/bio/appl/paml/test_codeml.rb
 - test/unit/bio/appl/sim4/test_report.rb
 - test/unit/bio/appl/sosui/test_report.rb
@@ -525,13 +559,18 @@ files:
 - test/unit/bio/db/embl/test_embl_to_bioseq.rb
 - test/unit/bio/db/embl/test_sptr.rb
 - test/unit/bio/db/embl/test_uniprot.rb
+- test/unit/bio/db/fasta/test_defline.rb
+- test/unit/bio/db/fasta/test_defline_misc.rb
 - test/unit/bio/db/fasta/test_format_qual.rb
 - test/unit/bio/db/kegg/test_compound.rb
 - test/unit/bio/db/kegg/test_drug.rb
 - test/unit/bio/db/kegg/test_enzyme.rb
 - test/unit/bio/db/kegg/test_genes.rb
+- test/unit/bio/db/kegg/test_genome.rb
 - test/unit/bio/db/kegg/test_glycan.rb
+- test/unit/bio/db/kegg/test_module.rb
 - test/unit/bio/db/kegg/test_orthology.rb
+- test/unit/bio/db/kegg/test_pathway.rb
 - test/unit/bio/db/kegg/test_reaction.rb
 - test/unit/bio/db/pdb/test_pdb.rb
 - test/unit/bio/db/sanger_chromatogram/test_abif.rb
@@ -540,6 +579,7 @@ files:
 - test/unit/bio/db/test_fasta.rb
 - test/unit/bio/db/test_fastq.rb
 - test/unit/bio/db/test_gff.rb
+- test/unit/bio/db/test_go.rb
 - test/unit/bio/db/test_lasergene.rb
 - test/unit/bio/db/test_medline.rb
 - test/unit/bio/db/test_newick.rb
@@ -565,6 +605,7 @@ files:
 - test/unit/bio/sequence/test_dblink.rb
 - test/unit/bio/sequence/test_na.rb
 - test/unit/bio/sequence/test_quality_score.rb
+- test/unit/bio/sequence/test_sequence_masker.rb
 - test/unit/bio/shell/plugin/test_seq.rb
 - test/unit/bio/test_alignment.rb
 - test/unit/bio/test_command.rb
@@ -598,6 +639,8 @@ files:
 - test/unit/bio/util/test_sirna.rb
 has_rdoc: true
 homepage: http://bioruby.org/
+licenses: []
+
 post_install_message: 
 rdoc_options: 
 - --main
@@ -611,23 +654,27 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
 rubyforge_project: bioruby
-rubygems_version: 1.3.1
+rubygems_version: 1.3.7
 signing_key: 
-specification_version: 2
+specification_version: 3
 summary: Bioinformatics library
 test_files: []