bio-graphics 1.2 → 1.4

data/lib/feature.rb

@@ -0,0 +1,204 @@
+module Bio
+class Feature
+  def initialize(feature, position, qualifiers = [], parent = nil, subfeatures = [])
+    @feature, @position, @qualifiers, @parent = feature, position, qualifiers, parent
+    @subfeatures = Array.new
+    subfeatures.each {|sf| add_subfeature(sf) }
+    @locations = Bio::Locations.new(@position)
+  end
+
+  # Returns type of feature in String (e.g 'CDS', 'gene')
+  attr_accessor :feature
+
+  # Returns position of the feature in String (e.g. 'complement(123..146)')
+  attr_accessor :position
+  
+  # Returns position of the feature as a Bio::Locations object
+  attr_accessor :locations
+
+  # Returns an Array of Qualifier objects.
+  attr_accessor :qualifiers
+
+  # Returns parent of Bio::Feature is it is a subfeature of another one
+  attr_accessor :parent
+  
+  # Returns an Array of Bio::Feature objects
+  attr_accessor :subfeatures
+
+  # Adds a Bio::Feature as a subfeature.
+  # *Arguments*:
+  # * (required) _feature_: Bio::Feature object
+  # *Returns*:: Bio::Feature object
+  def add_subfeature(sf)
+    sf.parent = self
+    @subfeatures.push(sf)
+    return self
+  end
+  
+  # Adds a Qualifier object to the Feature.
+  # 
+  # *Arguments*:
+  # * (required) _qualifier_: Bio::Feature::Qualifier object
+  # *Returns*:: Bio::Feature object
+  def add_qualifier(a)
+    @qualifiers.push(a) if a.is_a? Qualifier
+    return self
+  end
+  alias :append_qualifier :add_qualifier
+
+  # Iterates on each subfeature object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over subfeatures of this type
+  def each_subfeature(arg = nil)
+    @subfeatures.each do |x|
+      next if arg and x.feature != arg
+      yield x
+    end
+  end
+  alias :each :each_subfeature
+
+  # Iterates on each qualifer object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over qualifiers with this key
+  def each_qualifier(arg = nil)
+    @qualifiers.each do |x|
+      next if arg and x.qualifier != arg
+      yield x
+    end
+  end
+
+#  # Returns a Hash constructed from qualifier objects.
+#  def assoc
+#    STDERR.puts "Bio::Feature#assoc is deprecated, use Bio::Feature#to_hash instead" if $DEBUG
+#    hash = Hash.new
+#    @qualifiers.each do |x|
+#      hash[x.qualifier] = x.value
+#    end
+#    return hash
+#  end
+#
+#  # Returns a Hash constructed from qualifier objects.
+#  def to_hash
+#    hash = Hash.new
+#    @qualifiers.each do |x|
+#      hash[x.qualifier] ||= []
+#      hash[x.qualifier] << x.value
+#    end
+#    return hash
+#  end
+#
+#  # Short cut for the Bio::Feature#to_hash[key]
+#  def [](key)
+#    self.to_hash[key]
+#  end
+
+  # Container for qualifier-value pairs for sequence features.
+  class Qualifier
+    # Creates a new Bio::Feature::Qualifier object
+    #
+    # *Arguments*:
+    # * (required) _key_: key of the qualifier (e.g. "gene")
+    # * (required) _value_: value of the qualifier (e.g. "CYP2D6")
+    # *Returns*:: Bio::Feature::Qualifier object
+    def initialize(key, value)
+      @qualifier, @value = key, value
+    end
+
+    # Qualifier name in String
+    attr_reader :qualifier
+
+    # Qualifier value in String
+    attr_reader :value
+
+  end #Qualifier
+
+end #Feature
+
+
+# = DESCRIPTION
+# Container for a list of Feature objects.
+#
+# = USAGE
+#  # First, create some Bio::Feature objects
+#  feature1 = Bio::Feature.new('intron','3627..4059')
+#  feature2 = Bio::Feature.new('exon','4060..4236')
+#  feature3 = Bio::Feature.new('intron','4237..4426')
+#  feature4 = Bio::Feature.new('CDS','join(2538..3626,4060..4236)',
+#                   [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
+#                     Bio::Feature::Qualifier.new('translation','MGXXTVMHLL...')
+#                   ])
+#
+#  # And create a container for them
+#  feature_container = Bio::Features.new([ feature1, feature2, feature3, feature4 ])
+#
+#  # Iterate over all features and print
+#  feature_container.each do |feature|
+#    puts feature.feature + "\t" + feature.position
+#    feature.each do |qualifier|
+#      puts "- " + qualifier.qualifier + ": " + qualifier.value
+#    end
+#  end
+#
+#  # Iterate only over CDS features and extract translated amino acid sequences
+#  features.each("CDS") do |feature|
+#    hash = feature.to_hash
+#    name = hash["gene"] || hash["product"] || hash["note"] 
+#    aaseq  = hash["translation"]
+#    pos  = feature.position
+#    if name and seq
+#      puts ">#{gene} #{feature.position}"
+#      puts aaseq
+#    end
+#  end
+class Features
+  # Create a new Bio::Features object.
+  #
+  # *Arguments*:
+  # * (optional) _list_ _of_ _features_: list of Bio::Feature objects
+  # *Returns*:: Bio::Features object
+  def initialize(ary = [])
+    @features = ary
+  end
+
+  # Returns an Array of Feature objects.
+  attr_accessor :features
+
+  # Appends a Feature object to Features.
+  # 
+  # *Arguments*:
+  # * (required) _feature_: Bio::Feature object
+  # *Returns*:: Bio::Features object
+  def append(a)
+    @features.push(a) if a.is_a? Feature
+    return self
+  end
+
+  # Iterates on each feature object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over features with this key
+  def each(arg = nil)
+    @features.each do |x|
+      next if arg and x.feature != arg
+      yield x
+    end
+  end
+
+  # Short cut for the Features#features[n]
+  def [](*arg)
+    @features[*arg]
+  end
+
+  # Short cut for the Features#features.first
+  def first
+    @features.first
+  end
+
+  # Short cut for the Features#features.last
+  def last
+    @features.last
+  end
+end
+end

data/samples/arkdb_features.rb

@@ -2,13 +2,15 @@ require File.dirname(__FILE__) + '/../lib/bio-graphics'
 
 #Initialize graphic for a nucleotide sequence of 4173015 bp, zooming in on the
 #region 11111..3333333
-my_panel = Bio::Graphics::Panel.new(4173015, 800, true, 11111, 3333333)
+my_panel = Bio::Graphics::Panel.new(4173015, :width => 600, :clickable => true,
+                                    :display_range => 11111..3333333,
+                                    :vertical => true)
 #my_panel = Bio::Graphics::Panel.new(4173015, 800, false, 1, 4173015)
 
 #Create and configure tracks
-scaffold_track = my_panel.add_track('scaffold', false)
-marker_track = my_panel.add_track('marker', true)
-clone_track = my_panel.add_track('clone', false)
+scaffold_track = my_panel.add_track('scaffold', :label => false)
+marker_track = my_panel.add_track('marker')
+clone_track = my_panel.add_track('clone', :label => false)
 
 scaffold_track.colour = [1,0,0]
 marker_track.colour = [0,1,0]
@@ -21,15 +23,15 @@ File.open('data.txt').each do |line|
   accession, type, start, stop = line.split(/\t/)
   if type == 'scaffold'
     if start.nil?
-      scaffold_track.add_feature(accession)
+      scaffold_track.add_feature(Bio::Feature.new('scaffold', '1..4173015'), :label => accession)
     else
-      scaffold_track.add_feature(accession, start + '..' + stop)
+      scaffold_track.add_feature(Bio::Feature.new('scaffold', start + '..' + stop), :label => accession, :link => 'http://www.google.com/search?q=' + accession)
     end
     
   elsif type == 'marker'
-    marker_track.add_feature(accession, ((start.to_i + stop.to_i)/2).to_s, 'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=' + accession)
+    marker_track.add_feature(Bio::Feature.new('marker', ((start.to_i + stop.to_i)/2).to_s), :label => accession, :link => 'http://www.thearkdb.org/arkdb/do/getMarkerDetail?accession=' + accession)
   elsif type == 'clone'
-    clone_track.add_feature(accession, start + '..' + stop)
+    clone_track.add_feature(Bio::Feature.new('clone', start + '..' + stop), :label => accession)
   end
 end
 

data/samples/glyph_showcase.rb

@@ -1,33 +1,69 @@
 require '../lib/bio-graphics'
 
-my_panel = Bio::Graphics::Panel.new(500, 1000, false)
+my_panel = Bio::Graphics::Panel.new(500, :width => 1000, :format => :svg)
 
-generic_track = my_panel.add_track('generic', false)
-line_track = my_panel.add_track('line', false, [0,0,1], :line)
-directed_track = my_panel.add_track('directed', false, [0,1,0], :directed_generic)
-triangle_track = my_panel.add_track('triangle', false, [1,0,0], :triangle)
-spliced_track = my_panel.add_track('spliced', false, [1,0,0], :spliced)
-directed_spliced_track = my_panel.add_track('directed_spliced', false, [1,0,1], :directed_spliced)
+generic_track = my_panel.add_track('generic', :label => false)
+box_track = my_panel.add_track('box', :label => false, :glyph => :box)
+line_track = my_panel.add_track('line', :label => false, :glyph => :line, :colour => [0,0,1])
+line_with_handles_track = my_panel.add_track('line_with_handles', :label => false, :glyph => :line_with_handles, :colour => [1,0,0])
+directed_track = my_panel.add_track('directed', :label => false, :glyph => :directed_generic, :colour => [0,1,0])
+directed_box_track = my_panel.add_track('directed_box', :label => false, :glyph => :directed_box, :colour => [0,1,0])
+triangle_track = my_panel.add_track('triangle', :label => false, :glyph => :triangle, :colour => [1,0,0])
+spliced_track = my_panel.add_track('spliced', :label => false, :glyph => :spliced, :colour => [1,0,0])
+directed_spliced_track = my_panel.add_track('directed_spliced', :label => false, :glyph => :directed_spliced, :colour => [1,0,1])
+composite_track = my_panel.add_track('composite_features', :label => false, :glyph => { 'utr5' => :line, 'utr3' => :line, 'cds' => :directed_spliced})
+transcript_track = my_panel.add_track('transcripts', :label => true, :glyph => :transcript)
 
-generic_track.add_feature('clone1','250..375', 'http://www.newsforge.com')
-generic_track.add_feature('clone2','54..124', 'http://www.thearkdb.org')
-generic_track.add_feature('clone3','100..449', 'http://www.google.com')
+generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :label => 'clone1', :link => 'http://www.newsforge.com', :colour => [0.5,0.8,0.2])
+generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :label => 'clone2', :link => 'http://www.thearkdb.org')
+generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :label => 'clone3', :link => 'http://www.google.com')
 
-line_track.add_feature('primer1','complement(200..320)')
-line_track.add_feature('primer2','355..480', 'http://www.zdnet.co.uk')
+line_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'), :label => 'some_utr')
+line_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
 
-directed_track.add_feature('marker1','50..60', 'http://www.google.com')
-directed_track.add_feature('marker2','complement(80..120)', 'http://www.sourceforge.net')
+line_with_handles_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
+line_with_handles_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
 
-triangle_track.add_feature('snp1','56')
-triangle_track.add_feature('snp2','103','http://digg.com')
+directed_track.add_feature(Bio::Feature.new('primer', '50..60'), :link => 'http://www.google.com')
+directed_track.add_feature(Bio::Feature.new('primer', 'complement(80..120)'), :link => 'http://www.sourceforge.net')
 
-spliced_track.add_feature('gene1','join(34..52,109..183)','http://news.bbc.co.uk')
-spliced_track.add_feature('gene2','complement(join(170..231,264..299,350..360,409..445))')
-spliced_track.add_feature('gene3','join(134..152,209..283)')
+directed_box_track.add_feature(Bio::Feature.new('primer', '50..60'), :link => 'http://www.google.com')
+directed_box_track.add_feature(Bio::Feature.new('primer', 'complement(80..120)'), :link => 'http://www.sourceforge.net')
 
-directed_spliced_track.add_feature('gene4','join(34..52,109..183)', 'http://www.vrtnieuws.net')
-directed_spliced_track.add_feature('gene5','complement(join(170..231,264..299,350..360,409..445))', 'http://bioinformatics.roslin.ac.uk')
-directed_spliced_track.add_feature('gene6','join(134..152,209..283)')
+triangle_track.add_feature(Bio::Feature.new('snp', '56'))
+triangle_track.add_feature(Bio::Feature.new('snp', '103'), :link =>'http://digg.com')
 
+spliced_track.add_feature(Bio::Feature.new('spliced', 'join(34..52,109..183)'), :link =>'http://news.bbc.co.uk')
+spliced_track.add_feature(Bio::Feature.new('spliced', 'complement(join(170..231,264..299,350..360,409..445))'), :label => 'anonymous')
+spliced_track.add_feature(Bio::Feature.new('spliced', 'join(134..152,209..283)'))
+
+directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(34..52,109..183)'), :link => 'http://www.vrtnieuws.net')
+directed_spliced_track.add_feature(Bio::Feature.new('cds', 'complement(join(170..231,264..299,350..360,409..445))'), :link => 'http://bioinformatics.roslin.ac.uk')
+directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(134..152,209..283)'))
+
+box_track.add_feature(Bio::Feature.new('clone', '250..375'), :link  => 'http://www.newsforge.com')
+box_track.add_feature(Bio::Feature.new('clone', '54..124'), :link  => 'http://www.thearkdb.org')
+box_track.add_feature(Bio::Feature.new('clone', '100..449'), :link  => 'http://www.google.com')
+
+transcript1_utr5 = Bio::Feature.new('utr5', '100..150')
+transcript1_cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
+transcript1_utr3 = Bio::Feature.new('utr3', '330..375')
+transcript2_utr5 = Bio::Feature.new('utr5', 'complement(330..375)')
+transcript2_cds = Bio::Feature.new('cds', 'complement(join(150..225, 250..275, 310..330))')
+transcript2_utr3 = Bio::Feature.new('utr3', 'complement(100..150)')
+
+transcript1 = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [transcript1_utr5,transcript1_cds,transcript1_utr3])
+transcript2 = Bio::Feature.new('transcript', 'complement(join(100..150, 150..225, 250..275, 310..330, 330..375))', [], nil, [transcript2_utr5,transcript2_cds,transcript2_utr3])
+
+composite_track.add_feature(transcript1, :label => 'my_transcript')
+composite_track.add_feature(transcript2, :label => 'my_reverse_transcript')
+transcript_track.add_feature(transcript1, :label => 'my_transcript')
+transcript_track.add_feature(transcript2, :label => 'my_reverse_transcript')
+
+my_panel.draw('glyph_showcase.svg')
+my_panel.format = :png
 my_panel.draw('glyph_showcase.png')
+my_panel.format = :pdf
+my_panel.draw('glyph_showcase.pdf')
+my_panel.format = :ps
+my_panel.draw('glyph_showcase.ps')

data/samples/protein_domains.rb

@@ -0,0 +1,19 @@
+# Data from http://pfam.sanger.ac.uk/protein?id=Q8C6V9_MOUSE
+require '../lib/bio-graphics'
+my_panel = Bio::Graphics::Panel.new(700, :width => 600)
+
+track = my_panel.add_track('Q8C6V9_MOUSE')
+track.glyph = :generic
+
+# First make the Bio::Feature objects and then create a Bio::Graphics feature
+cimr_1 = Bio::Feature.new('CIMR', '3..142')
+fn2 = Bio::Feature.new('fn2', '151..190')
+cimr_2 = Bio::Feature.new('CIMR', '194..331')
+cimr_3 = Bio::Feature.new('CIMR', '485..527')
+
+track.add_feature(cimr_1, :label => 'CIMR', :colour => [0,1,0])
+track.add_feature(fn2, :label => 'fn2', :colour => [1,0,0])
+track.add_feature(cimr_2, :label => 'CIMR', :colour => [0,1,0])
+track.add_feature(cimr_3, :label => 'CIMR', :colour => [0,1,0])
+
+my_panel.draw('protein_domains.png')

data/samples/subfeatures.rb

@@ -0,0 +1,31 @@
+require '../lib/bio-graphics'
+my_panel = Bio::Graphics::Panel.new(700, :width => 600)
+
+track = my_panel.add_track('transcripts')
+track.glyph = :directed_spliced
+
+# First make the Bio::Feature objects
+# Arguments are:
+# * type
+# * location
+# * qualifiers
+# * parent
+# * subfeatures
+utr5 = Bio::Feature.new('utr', '100..150')
+cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
+utr3 = Bio::Feature.new('utr', '330..375')
+
+transcript = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [utr5,cds,utr3])
+
+# And then create the Bio::Graphics feature
+# Arguments are:
+# * Bio::Feature object
+# * name
+# * colour
+# * glyphs
+track.add_feature(transcript, :label => 'my_label_a', :glyph => { 'utr' => :line, 'cds' => :directed_spliced })
+
+# Or do it all in one go, but then we can't do subfeatures.
+track.add_feature(Bio::Feature.new('mrna', 'complement(join(120..250, 300..350, 375..390))'), :label => 'my_label_b', :colour => [0,1,0])
+
+my_panel.draw('subfeatures.png')

data/test/unit/custom_glyph_in_file.rb

@@ -0,0 +1,12 @@
+module Bio::Graphics::Glyph
+  class Bio::Graphics::Glyph::CustomTestGlyphInFile < Bio::Graphics::Glyph::Common
+    
+    def draw
+      (self.left_pixel..self.right_pixel).step(20) do |pos|
+        @feature_context.move_to(pos, 0)
+        @feature_context.line_to(pos, Bio::Graphics::FEATURE_HEIGHT)
+        @feature_context.close_path.stroke
+      end
+    end
+  end
+end

data/test/unit/data.txt

@@ -0,0 +1,32 @@
+test	scaffold
+ARKSCA00000496	scaffold	1766280	3140306
+ARKSCA00000495	scaffold	1454125	1756279
+ARKMKR00050962	marker	1547565	1547116
+ARKMKR00049743	marker	1467043	1467548
+ARKMKR00049753	marker	1293787	1294437
+ARKMKR00033347	marker	976330	976530
+ARKMKR00049788	marker	959182	959941
+ARKMKR00049746	marker	3030496	3031106
+ARKCLN00574951	clone	1454125	1743183
+ARKCLN00580755	clone	1115673	1332008
+ARKCLN00734502	clone	2680312	2880020
+ARKCLN00637391	clone	1291903	1444124
+ARKCLN00733777	clone	554351	745744
+ARKCLN00516431	clone	1766280	2053569
+ARKCLN00734156	clone	1973620	2155335
+ARKCLN00605941	clone	1576502	1756279
+ARKCLN00608810	clone	672169	860914
+ARKCLN00565213	clone	348808	418529
+ARKCLN00679752	clone	2321244	2563972
+ARKCLN00538485	clone	2851750	3078918
+ARKCLN00581628	clone	2966855	3140306
+ARKCLN00511832	clone	1034205	1213124
+ARKCLN00734700	clone	2566852	2709684
+ARKCLN00534126	clone	1043517	1290570
+ARKCLN00734007	clone	951813	1154597
+ARKCLN00733988	clone	140268	332409
+ARKCLN00589095	clone	800155	1015201
+ARKCLN00635737	clone	265756	445381
+ARKCLN00573316	clone	2226636	2363631
+ARKCLN00494906	clone	2130193	2314107
+ARKCLN00515356	clone	81435	254456

data/test/unit/test_class_extensions.rb

@@ -0,0 +1,23 @@
+require 'test/unit'
+require File.dirname(__FILE__) + '/../../lib/bio-graphics'
+
+class TestExtensions < Test::Unit::TestCase
+  def test_range
+    r = (1..5)
+    assert_equal(1, r.begin)
+    assert_equal(5, r.end)
+    assert_equal(1, r.lend)
+    assert_equal(5, r.rend)
+  end
+  
+  def test_string
+    snake = 'this_is_a_string'
+    assert_equal('ThisIsAString', snake.camel_case)
+    
+    camel = 'ThisIsAnotherString'
+    assert_equal('this_is_another_string', camel.snake_case)
+    
+    class_name = 'Bio::Graphics::Glyph::Generic'
+    assert(class_name.to_class == Bio::Graphics::Glyph::Generic)
+  end
+end