bio 1.1.0 → 1.2.0

data/lib/bio/sequence/common.rb

@@ -6,7 +6,7 @@
 #               Ryan Raaum <ryan@raaum.org>
 # License::     The Ruby License
 #
-# $Id: common.rb,v 1.4 2007/04/05 23:35:41 trevor Exp $
+# $Id: common.rb,v 1.5 2007/12/03 06:19:12 nakao Exp $
 #
 
 module Bio
@@ -91,10 +91,13 @@ module Common
   #   puts s                                  #=> "atgcatgcatgcatgc"
   # ---
   # *Returns*:: current Bio::Sequence::NA/AA object (modified)
-  def <<(*arg)
+  def concat(*arg)
     super(self.class.new(*arg))
   end
-  alias concat <<
+
+  def <<(*arg)
+    concat(*arg)
+  end
 
   # Create a new sequence by adding to an existing sequence.
   # The existing sequence is not modified.

data/lib/bio/shell/interface.rb

@@ -5,7 +5,7 @@
 #               Toshiaki Katayama <k@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: interface.rb,v 1.18 2007/06/26 08:38:38 k Exp $
+# $Id: interface.rb,v 1.19 2007/11/15 07:08:49 k Exp $
 #
 
 module Bio::Shell
@@ -152,7 +152,7 @@ module Bio::Shell
     datadir = Bio::Shell.data_dir
     message = "Save file '#{file}' in '#{datadir}' directory? [y/n] "
     if ! file[/^#{datadir}/] and Bio::Shell.ask_yes_or_no(message)
-      file = datadir + file
+      file = File.join(datadir, file)
     end
     if File.exists?(file)
       message = "Overwrite existing '#{file}' file? [y/n] "

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb

@@ -5,7 +5,7 @@ class BiorubyGenerator < Rails::Generator::Base
       m.directory 'app/helpers'
       m.directory 'app/views/bioruby'
       m.directory 'app/views/layouts'
-      m.directory 'public/images'
+      m.directory 'public/images/bioruby'
       m.directory 'public/stylesheets'
       m.file 'bioruby_controller.rb', 'app/controllers/bioruby_controller.rb'
       m.file 'bioruby_helper.rb',     'app/helpers/bioruby_helper.rb'
@@ -18,10 +18,10 @@ class BiorubyGenerator < Rails::Generator::Base
       m.file 'history.rhtml',         'app/views/bioruby/history.rhtml'
       m.file 'index.rhtml',           'app/views/bioruby/index.rhtml'
       m.file 'bioruby.rhtml',         'app/views/layouts/bioruby.rhtml'
-      m.file 'bioruby-gem.png',       'public/images/bioruby-gem.png'
-      m.file 'bioruby-link.gif',      'public/images/bioruby-link.gif'
-      m.file 'bioruby-bg.gif',        'public/images/bioruby-bg.gif'
-      m.file 'bioruby-console.png',   'public/images/bioruby-console.png'
+      m.file 'spinner.gif',           'public/images/bioruby/spinner.gif'
+      m.file 'bioruby-gem.png',       'public/images/bioruby/gem.png'
+      m.file 'bioruby-link.gif',      'public/images/bioruby/link.gif'
+      m.file 'bioruby-bg.gif',        'public/images/bioruby/bg.gif'
       m.file 'bioruby.css',           'public/stylesheets/bioruby.css'
     end
   end

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css

@@ -3,7 +3,7 @@
 body {
 	margin: 0;
 	color: #555555;
-	background: url("/images/bioruby-bg.gif") repeat-y center;
+	background: url("/images/bioruby/bg.gif") repeat-y center;
 	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
 	font-size: 12px;
 }
@@ -22,7 +22,7 @@ div#title {
 	padding-right: 200px;
 	margin-bottom: 20px;
 	text-align: left;
-	background: url("/images/bioruby-gem.png") no-repeat left bottom;
+	background: url("/images/bioruby/gem.png") no-repeat left bottom;
 }
 
 div#title .titletop {
@@ -169,6 +169,11 @@ div#side li {
 
 div#side img {
 	padding: 5px;
+	/* centering */
+	display: block;
+	margin-left: auto;
+	margin-right: auto;
+	border: 0px;
 }
 
 /* history */
@@ -198,11 +203,6 @@ div#command {
 /* image */
 
 img {
-	/* centering */
-	display: block;
-	margin-left: auto;
-	margin-right: auto;
-	border: 0px;
 }
 
 /* em */
@@ -335,7 +335,6 @@ input[type=submit] {
 /* textarea */
 
 textarea {
-	background: url("/images/bioruby-console.png") no-repeat center;
 	background-color: #eaedeb;
 	font-family: monospace;
 	font-size: 12px;

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml

@@ -28,7 +28,7 @@
   <%= render :partial => "variables" %>
 
   <br>
-  <a href="http://bioruby.org/"><img src="/images/bioruby-link.gif" border=0></a>
+  <a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
  </div><!-- side -->
 
  <div id="title">

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml

@@ -1,22 +1,26 @@
 <div id="console">
-<%- if flash[:notice] -%>
-<div id="notice"><p><%= flash[:notice] %></p></div><br>
-<%- end -%>
-<%= form_remote_tag(:url => {:action => "evaluate"}, :position => "top") %>
-<b>BioRuby script:</b>
-<textarea id="script" name="script" rows=10 cols=80></textarea><br>
-<input type="submit" value="Evaluate">
-<input type="reset" value="Clear">
-&nbsp;&nbsp;
-Show [
-<%= link_to_remote "All",      :url => {:action => "results", :limit => 0} %> |
-<%= link_to_remote "Last 5",   :url => {:action => "results", :limit => 5} %> |
-<%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
-] or
-<%= link_to "Hide", :action => "index" %>
-results<br>
-<%= end_form_tag %>
+ <%- if flash[:notice] -%>
+  <div id="notice"><p><%= flash[:notice] %></p></div><br>
+ <%- end -%>
+ <% form_remote_tag(:url => {:action => "evaluate"}, :position => "top",
+      :before => %(Element.show('spinner')),
+      :complete => %(Element.hide('spinner'))) do %>
+  <img id="spinner" src="/images/bioruby/spinner.gif" style="display:none">
+  <b>BioRuby script:</b>
+  <br/>
+  <textarea id="script" name="script" rows=10 cols=80></textarea>
+  <br/>
+  <input type="submit" value="Evaluate">
+  <input type="reset" value="Clear">
+  &nbsp;&nbsp;
+  Show [
+  <%= link_to_remote "All",    :url => {:action => "results", :limit => 0} %> |
+  <%= link_to_remote "Last 5", :url => {:action => "results", :limit => 5} %> |
+  <%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
+  ] or <%= link_to "Hide", :action => "index" %> results<br/>
+ <% end %>
 </div>
+
 <div id="logs">
 </div>
 

data/test/functional/bio/io/test_ensembl.rb

@@ -5,7 +5,7 @@
 #               Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-#  $Id: test_ensembl.rb,v 1.4 2007/04/05 23:35:42 trevor Exp $
+#  $Id: test_ensembl.rb,v 1.5 2007/11/10 16:57:43 nakao Exp $
 #
 
 require 'pathname'
@@ -73,13 +73,47 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
   end
 
    def test_gff_exportview
-     line = "chromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tgene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"
+     line = ["chromosome:NCBI36:4:1149206:1149209:1", 
+             "Ensembl", 
+             "Gene", 
+             "-839",
+             "2747", 
+             ".", 
+             "+",
+             ".",
+             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"].join("\t")  + "\n"
+     line = ["4", 
+             "Ensembl", 
+             "Gene", 
+             "1148366", 
+             "1151952", 
+             ".", 
+             "+", 
+             "1", 
+             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
      gff = @serv.exportview(4, 1149206, 1149209, ['gene'])
      assert_equal(line, gff)
    end
 
    def test_gff_exportview_with_named_args
-     line = "chromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tgene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding\n"
+     line = ["chromosome:NCBI36:4:1149206:1149209:1",
+             "Ensembl",
+             "Gene",
+             "-839",
+             "2747",
+             ".",
+             "+",
+             ".",
+             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
+     line = ["4", 
+             "Ensembl", 
+             "Gene", 
+             "1148366", 
+             "1151952", 
+             ".", 
+             "+", 
+             "1", 
+             "gene_id=ENSG00000206158; transcript_id=ENST00000382964; exon_id=ENSE00001494097; gene_type=KNOWN_protein_coding"].join("\t") + "\n"
      gff = @serv.exportview(:seq_region_name => 4,
                             :anchor1 => 1149206,
                             :anchor2 => 1149209, 
@@ -88,7 +122,56 @@ class FuncTestEnsemblHuman < Test::Unit::TestCase
    end 
 
    def test_tab_exportview_with_named_args
-     line = "seqname\tsource\tfeature\tstart\tend\tscore\tstrand\tframe\tgene_id\ttranscript_id\texon_id\tgene_type\nchromosome:NCBI36:4:1149206:1149209:1\tEnsembl\tGene\t-839\t2747\t.\t+\t.\tENSG00000206158\tENST00000382964\tENSE00001494097\tKNOWN_protein_coding\n"
+     line = [["seqname",
+             "source",
+             "feature",
+             "start",
+             "end",
+             "score",
+             "strand",
+             "frame",
+             "gene_id",
+             "transcript_id",
+             "exon_id",
+             "gene_type"].join("\t"),
+             ["chromosome:NCBI36:4:1149206:1149209:1",
+              "Ensembl",
+              "Gene",
+              "-839",
+              "2747",
+              ".",
+              "+",
+              ".",
+              "ENSG00000206158",
+              "ENST00000382964",
+              "ENSE00001494097",
+              "KNOWN_protein_coding"].join("\t") + "\n"
+     ].join("\n")
+     line = [["seqname",
+             "source",
+             "feature",
+             "start",
+             "end",
+             "score",
+             "strand",
+             "frame",
+             "gene_id",
+             "transcript_id",
+             "exon_id",
+             "gene_type"].join("\t"),
+             ["4",
+              "Ensembl",
+              "Gene",
+              "1148366",
+              "1151952",
+              ".",
+              "+",
+              "1",
+              "ENSG00000206158",
+              "ENST00000382964",
+              "ENSE00001494097",
+              "KNOWN_protein_coding"].join("\t") + "\n"
+     ].join("\n")
      gff = @serv.exportview(:seq_region_name => 4,
                             :anchor1 => 1149206,
                             :anchor2 => 1149209, 

data/test/unit/bio/db/test_newick.rb

@@ -6,7 +6,7 @@
 #               Naohisa Goto <ng@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: test_newick.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
+# $Id: test_newick.rb,v 1.6 2007/12/12 16:06:22 ngoto Exp $
 #
 
 require 'test/unit'
@@ -53,4 +53,241 @@ module Bio
     end
 
   end #class TestNewick
+
+  class TestNewick2 < Test::Unit::TestCase
+
+    TREE_STRING = <<-END_OF_TREE_STRING
+    (
+      (
+        'this is test':0.0625,
+        'test2 (abc, def)':0.125
+      ) 'internal node''s name' : 0.25,
+      (
+        '''':0.03125,
+        (
+          'ABCAC_HUMAN [ABC superfamily]':0.015625,
+          hypothetical_protein:0.5
+        ) ABC : 0.25 [99]
+      ) test3 :0.5
+    )root;
+    END_OF_TREE_STRING
+
+    def test_string_tree
+      newick = Bio::Newick.new(TREE_STRING)
+      tree = newick.tree
+      assert_equal('root', tree.root.name)
+      assert_equal([ 
+                    "this is test",
+                    "test2 (abc, def)",
+                    "internal node\'s name",
+                    "\'",
+                    "ABCAC_HUMAN [ABC superfamily]",
+                    "hypothetical protein",
+                    "ABC",
+                    "test3",
+                    "root"
+                   ].sort,
+                   tree.nodes.collect { |x| x.name }.sort)
+
+      assert_equal(tree.children(tree.root).collect { |x| x.name }.sort,
+                   [ "internal node\'s name", "test3" ])
+
+      node = tree.get_node_by_name('ABC')
+      assert_equal(99, node.bootstrap)
+
+      assert_equal(1.5625,
+                   tree.distance(tree.get_node_by_name('hypothetical protein'),
+                                 tree.get_node_by_name('this is test')))
+    end
+
+  end #class TestNewick2
+
+  class TestNewickPrivate < Test::Unit::TestCase
+    def setup
+      @newick = Bio::Newick.new('') # dummy data
+    end
+
+    def test_parse_newick_leaf
+      leaf_tokens = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
+                      "&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]" ]
+      node = Bio::Tree::Node.new
+      edge = Bio::Tree::Edge.new
+      options = {}
+
+      assert_equal(true,
+                   @newick.instance_eval do
+                     __parse_newick_leaf(leaf_tokens, node, edge, options)
+                   end)
+
+      assert_equal(:nhx, @newick.options[:original_format])
+      assert_equal("A:B _C(D,E)F\'s G[H]", node.name)
+      assert_equal("human", node.scientific_name)
+      assert_equal("1.1.1.1", node.ec_number)
+      assert_equal(0.5, edge.distance)
+    end
+
+    def test_parse_newick_get_tokens_for_leaf
+      input = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
+                "&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
+                :",", :"(", "bbb", :":", "0.2", :")" ]
+      leaf_should_be = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
+                "&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]" ]
+      rest_should_be = [ :",", :"(", "bbb", :":", "0.2", :")" ]
+
+      assert_equal(leaf_should_be, 
+                   @newick.instance_eval do
+                     __parse_newick_get_tokens_for_leaf(input)
+                   end)
+
+      assert_equal(rest_should_be, input)
+    end
+
+    def test_parse_newick_tokenize
+      examples =
+        [
+         [ 
+          '(a,b);', # input
+          [ :"(", 'a', :",", 'b', :")" ], # normal parser result
+          [ :"(", 'a', :",", 'b', :")" ], # naive parser result
+         ],
+         [
+          # input
+          "(\'A:B _C(D,E)F\'\'s G[H]\':0.5[&&NHX:S=human:E=1.1.1.1], \n(bbb:0.2, c_d_e[&&NHX:B=100]);",
+            # normal parser result
+            [ :"(", "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
+            "&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
+            :",", :"(", "bbb", :":", "0.2", :",", 
+            "c d e", :"[", "&&NHX", :":", "B=100", :"]", :")" ],
+            # naive parser result
+            [ :"(", "\'A", :":", "B _C", :"(", "D", :",", "E",
+            :")", "F\'\'s G", :"[", "H", :"]", "\'", :":", '0.5', :"[",
+            "&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
+            :",", :"(", "bbb", :":", "0.2", :",", 
+            "c_d_e", :"[", "&&NHX", :":", "B=100", :"]", :")" ]
+          ]
+        ]
+
+      examples.each do |a|
+        # normal parser
+        assert_equal(a[1],
+                     @newick.instance_eval do
+                       __parse_newick_tokenize(a[0], {})
+                     end)
+
+        # naive parser
+        assert_equal(a[2],
+                     @newick.instance_eval do
+                       __parse_newick_tokenize(a[0], { :parser => :naive })
+                     end)
+      end
+    end
+  end #class TestNewickPrivate
+
+  class TestBioTreeOutputPrivate < Test::Unit::TestCase
+
+    def setup
+      @tree = Bio::Tree.new
+    end
+
+    def test_to_newick_format_label
+      # unquoted_label
+      assert_equal('ABC', @tree.instance_eval do
+                     __to_newick_format_label('ABC', {})
+                   end)
+
+      # unquoted_label, replaces blank to underscore
+      assert_equal('A_B_C', @tree.instance_eval do
+                     __to_newick_format_label('A B C', {})
+                   end)
+
+      # quoted_label example 1
+      assert_equal("\'A B_C\'", @tree.instance_eval do
+                     __to_newick_format_label('A B_C', {})
+                   end)
+
+      # quoted_label example 2
+      assert_equal("\'A(B),C\'", @tree.instance_eval do
+                     __to_newick_format_label('A(B),C', {})
+                   end)
+
+      # normal formatter
+      assert_equal("\'A_B_C\'", @tree.instance_eval do
+                     __to_newick_format_label('A_B_C', {})
+                   end)
+      # naive formatter
+      assert_equal("A_B_C", @tree.instance_eval do
+                     __to_newick_format_label('A_B_C',
+                                              { :parser => :naive })
+                   end)
+    end
+
+
+    def test_to_newick_format_leaf
+      node = Bio::Tree::Node.new('ABC')
+      edge = Bio::Tree::Edge.new(0.5)
+
+      assert_equal('ABC:0.5', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge, {})
+                   end)
+
+      # disable branch length
+      assert_equal('ABC', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge,
+                                             { :branch_length_style =>
+                                               :disabled })
+                   end)
+
+      node.bootstrap = 98
+      # default: molphy style bootstrap
+      assert_equal('ABC:0.5[98]', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge, {})
+                   end)
+      # force molphy style bootstrap
+      assert_equal('ABC:0.5[98]', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge,
+                                             { :bootstrap_style => :molphy })
+                   end)
+      # disable bootstrap output
+      assert_equal('ABC:0.5', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge,
+                                             { :bootstrap_style =>
+                                               :disabled })
+                   end)
+
+      # force traditional bootstrap style
+      assert_equal('ABC98:0.5', @tree.instance_eval do
+                     __to_newick_format_leaf(node, edge,
+                                             { :bootstrap_style =>
+                                               :traditional })
+                   end)
+      # normally, when traditional style, no node name allowed for the node
+      node2 = Bio::Tree::Node.new
+      node2.bootstrap = 98
+      assert_equal('98:0.5', @tree.instance_eval do
+                     __to_newick_format_leaf(node2, edge,
+                                             { :bootstrap_style =>
+                                               :traditional })
+                   end)
+      
+    end
+
+    def test_to_newick_format_leaf_NHX
+      node = Bio::Tree::Node.new('ADH')
+      edge = Bio::Tree::Edge.new(0.5)
+      node.bootstrap = 98
+      node.ec_number = '1.1.1.1'
+      node.scientific_name = 'human'
+      node.taxonomy_id = '9606'
+      node.events.push :gene_duplication
+      edge.log_likelihood = 1.5
+      edge.width = 3
+
+      str = 'ADH:0.5[&&NHX:B=98:D=Y:E=1.1.1.1:L=1.5:S=human:T=9606:W=3]'
+      assert_equal(str, @tree.instance_eval do
+                     __to_newick_format_leaf_NHX(node, edge, {})
+                   end)
+    end
+
+  end #class TestBioTreeOutputPrivate
+
 end #module Bio