bio-svgenes 0.2.2 → 0.2.3

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/bio-svgenes.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-svgenes"
-  s.version = "0.2.2"
+  s.version = "0.2.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Dan MacLean"]
-  s.date = "2013-01-18"
+  s.date = "2013-01-30"
   s.description = "This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data."
   s.email = "maclean.daniel@gmail.com"
   s.extra_rdoc_files = [
@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
     "examples/example_config.json",
     "examples/gene.gff",
     "examples/get_coverage_in_windows.rb",
+    "examples/make_example.rb",
     "examples/transcripts.gff",
     "lib/.DS_Store",
     "lib/bio-svgenes.rb",
@@ -54,7 +55,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/danmaclean/bioruby-svgenes"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.11"
+  s.rubygems_version = "1.8.10"
   s.summary = "Create pretty SVG-format images of features, gene models and data tracks"
 
   if s.respond_to? :specification_version then

data/examples/draw_from_json.rb

@@ -27,7 +27,6 @@ end
 optparse.parse!
 
 
-
 require 'bio-svgenes'
 
 Bio::Graphics::Page.from_json(:json => options[:json], :outfile => options[:svg] )

data/examples/make_example.rb

@@ -0,0 +1,291 @@
+#!/usr/bin/env ruby
+#
+#  untitled
+#
+#  Created by Dan MacLean (TSL) on 2013-01-18.
+#  Copyright (c)  . All rights reserved.
+###################################################
+
+##to do:
+## background colour
+## single nt features : minimum size on circles, squares, triangles, diamonds, span (t bar)
+## label sizes
+## label positions 
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-svgenes'
+
+
+
+page = Bio::Graphics::Page.new(
+      :width => 800, 
+      :height => 200, 
+      :number_of_intervals => 10,
+      :background_color => "#F8F8F8"
+      )
+
+
+def new_gene_track_on page
+  page.add_track(
+    :glyph => :directed,
+    :height => 15,
+    :name => "Genes", 
+    :label => true, 
+    :stroke => :green,
+    :fill_color => :green_white_h
+  )
+end
+
+def new_mRNA_track_on page
+  page.add_track(
+    :glyph => :transcript,
+    :name => "mRNA", 
+    :height => 15,    
+    :label => true,
+    :exon_stroke => :black,
+    :exon_stroke_width => 1, 
+    :exon_fill_color => :blue,
+    :utr_fill_color => :purple,
+    :utr_stroke => :black,
+    :utr_stroke_width => 1,
+    :gap_marker => 'angled',
+    :line_color => :black,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+def new_te_insertion_site_track_on page
+  page.add_track(
+    :glyph => :circle,
+    :name => "TE Insertions", 
+    :label => true, 
+    :fill_color => :blue,
+    :radius => 3,
+    :stroke => :blue,
+    :stroke_width => 0.5,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+def new_cDNA_match_track_on page
+  page.add_track(
+    :glyph => :directed,
+    :name => "cDNA matches", 
+    :label => true, 
+    :stroke => :red,
+    :height => 15,
+    :fill_color => :red_white_h
+  )
+end
+
+
+def new_microarray_probe_track_on page
+  page.add_track(
+    :glyph => :generic,
+    :height => 15,
+    :name => "Microarray probes", 
+    :label => true, 
+    :fill_color => 'green',
+    :stroke_width => 0,
+    :style => "fill-opacity:1.0;"
+  )
+end
+
+def new_insertion_track_on page
+  page.add_track(
+    :glyph => :down_triangle,
+    :name => "Insertions", 
+    :label => true, 
+    :min_width => 6,
+    :fill_color => :red,
+    :stroke_width => 0,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+
+def new_deletion_track_on page
+  page.add_track(
+    :glyph => :up_triangle,
+    :name => "Deletions", 
+    :label => true, 
+    :fill_color => :green,
+    :min_width => 6,
+    :stroke_width => 0,
+    :style => "fill-opacity:0.4;"
+  )
+end
+
+def new_marker_track_on page
+  page.add_track(
+    :glyph => :span,
+    :height => 20,
+    :name => "Markers", 
+    :label => true, 
+    :stroke => :orange,
+    :stroke_width => 15
+  )
+end
+
+
+all_features = Bio::Graphics::Page.parse_gff( ARGV[0] )
+puts all_features.length
+#all_features.collect {|f| f.feature }.uniq.each do | feature_type |
+['gene', 'mRNA','cDNA_match', 'microarray_probe', 'insertion','deletion','substitution','transposable_element_insertion_site'].each do |feature_type|
+#['gene', 'mRNA','cDNA_match', 'microarray_probe','transposable_element_insertion_site'].each do |feature_type|
+  puts "rendering #{feature_type}"
+    case feature_type
+    when 'gene'
+      track = new_gene_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end,
+                                        :strand => feature.strand,
+                                        :id => feature.attributes.select {|a| a.first == 'Name'}.first.last
+                                        )
+       track.add(mf)
+      end 
+    when 'cDNA_match'
+      track = new_cDNA_match_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :strand => feature.strand,
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end  
+    when 'mRNA'
+      track = new_mRNA_track_on page
+      five_utrs = all_features.select {|x| x.feature_type == 'five_prime_UTR'} 
+      three_utrs = all_features.select {|z| z.feature_type == 'three_prime_UTR'}
+      all_exons = all_features.select {|z| z.feature_type == 'CDS'}
+      require 'pp'
+      pp all_exons
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+
+        feature_id = feature.attributes.select {|y| y.first == "ID"}.first.last
+        five_utr = five_utrs.select {|x|  x.attributes_to_hash["Parent"] == feature_id  }.first
+        three_utr = three_utrs.select {|z| z.attributes_to_hash["Parent"] == feature_id }.first
+        utrs = []
+        if not five_utr.nil? and not three_utr.nil?
+          utrs = [five_utr.start,five_utr.end, three_utr.start,three_utr.end]
+                  require 'pp'
+          utrs.sort!
+          
+        end
+        exons = []
+        exons = all_exons.select {|x|  x.attributes_to_hash["Parent"] == feature_id  }
+        exons = exons.collect {|x| [x.start, x.end] }.flatten
+        #if not exons.empty?
+        #  exons = exons.sort
+        #end
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end,
+                                        :utrs => utrs,
+                                        :exons => exons,
+                                        :strand => feature.strand      
+        )
+        track.add(mf)
+      end
+    when 'microarray_probe'
+      track = new_microarray_probe_track_on page
+            all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :strand => feature.strand,
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end
+    when 'transposable_element_insertion_site'
+      track = new_te_insertion_site_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :strand => feature.strand,
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end
+    when 'insertion'
+      track = new_insertion_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end
+     when 'deletion'
+      track = new_deletion_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end
+     when 'marker'
+      track = new_marker_track_on page
+      all_features.select {|f| f.feature == feature_type }.each do |feature|
+        mf = Bio::Graphics::MiniFeature.new(
+                                        :start => feature.start, 
+                                        :end => feature.end      
+        )
+        track.add(mf)
+      end
+    end
+    
+    
+end
+
+data_track1 = page.add_track(:glyph => :histogram,  #might also be :density or heatmap  ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
+                        :stroke_color => 'black',
+                        :fill_color => :blue,
+                        :track_height => 75,
+                        :name => 'Simulated NGS coverage (transformed sine function)', 
+                        :label => true, 
+                        :stroke_width => 0,
+                        :style => "fill-opacity:0.6;"
+                        
+                        )
+##generate a load of data, each data point becomes a feature...                         
+data = (19597235..19637234).step(10) do |start|
+#data = (19616011..19618459).step(1) do |start|
+  height = Math::sin(start)
+  height = height * -1 if height < 0
+  height = Math::log(height)
+  height = height * -1 if height < 0
+  data_feature = Bio::Graphics::MiniFeature.new(:start => start,
+                       :end => start + 30,
+                       :segment_height => height * 10
+                     )
+  data_track1.add(data_feature)
+  
+end
+
+data_track2 = page.add_track(:glyph => :histogram,  #might also be :density or heatmap  ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
+                        :stroke_color => 'black',
+                        :fill_color => :yellow,
+                        :track_height => 75,
+                        :name => 'Random bar height', 
+                        :label => true, 
+                        :stroke_width => 1,
+                        :style => "fill-opacity:0.4;"
+                        
+                        )
+##generate a load of data, each data point becomes a feature...                         
+data = (19597235..19637234).step(200) do |start|
+#data = (19616011..19618459).step(30) do |start|
+  data_feature = Bio::Graphics::MiniFeature.new(:start => start,
+                       :end => start + 200,
+                       :segment_height => rand(30)
+                     )
+  data_track2.add(data_feature)
+  
+end
+
+page.write( "out.svg" )

data/lib/bio/graphics/glyph.rb

@@ -3,7 +3,7 @@ module Bio
 class Glyph
   attr_reader :glyphs
   #holds a load of definitions for glyphs .. a glyph is an array of primitives... 
-  @glyphs = [:generic, :directed, :transcript, :scale, :label, :histogram]
+  @glyphs = [:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
   
   def self.generic(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height, 
     args = { 
@@ -17,6 +17,20 @@ class Glyph
     [Bio::Graphics::Primitive.new(:rectangle, args)]
   end 
   
+  def self.circle(args) 
+    args = { 
+      :radius => 10, 
+      :fill_color => 'red', 
+      :stroke => "black", 
+      :stroke_width => 1, 
+      :style => ""}.merge!(args)
+      args[:x_center] = args[:x]
+      args[:y_center] = args[:y]
+      [:x, :y].each {|e| args.delete(e)}
+    [Bio::Graphics::Primitive.new(:circle, args)]
+  end 
+  
+  
   def self.directed(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
     args = {
       
@@ -34,6 +48,44 @@ class Glyph
     [Bio::Graphics::Primitive.new(:polygon, args)]
   end
   
+  def self.down_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
+    args = {
+      
+      :height => 10, 
+      :fill_color => 'red', 
+      :stroke => "black", 
+      :stroke_width => 1, 
+      :style => "fill-opacity:0.4;"}.merge!(args)
+      args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }"
+    [Bio::Graphics::Primitive.new(:polygon, args)]
+  end
+  
+  def self.up_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
+    args = {
+      :height => 10, 
+      :fill_color => 'red', 
+      :stroke => "black", 
+      :stroke_width => 1, 
+      :style => "fill-opacity:0.4;"}.merge!(args)
+      args[:points] = "#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }"
+    [Bio::Graphics::Primitive.new(:polygon, args)]
+  end
+  
+  def self.span(args)
+    args = {
+      :height => 10,
+      :fill_color => 'red',
+      :stroke => "black",
+      :stroke_width => 1,
+      :style => "fill-opacity:1;"
+    }.merge!(args)
+    args[:x1] = args[:x]
+    args[:x2] = args[:x] + args[:width]
+    args[:y1] = args[:y]
+    args[:y2] = args[:y]
+    [Bio::Graphics::Primitive.new(:line, args)]
+  end
+  
   def self.transcript(args)
       args = {
       :height => 10, 

data/lib/bio/graphics/page.rb

@@ -5,6 +5,7 @@ class Page
   def initialize(args)
     @height = args[:height]
     @width = args[:width]
+    args[:style] = "background-color:#{args[:background_color]};" if args[:background_color]
     @svg = SVGEE.new(args)
     @scale_start = 1.0/0.0
     @scale_stop = -1.0/0.0
@@ -25,7 +26,6 @@ class Page
   def self.from_json(args)
     require 'rubygems'
     require 'json'
-    puts "memememe"
     data = JSON.parse(File.open(args[:json], 'r').read)
     p = Page.new(:width => data["Page"]["width"], 
                  :height => data["Page"]["height"], 
@@ -64,6 +64,8 @@ class Page
         end
           #now flick through the parentless features and add any exons / UTRs
           parentless_features.each do |plf|
+            require 'pp'
+            pp parentless_features
             gff_id = plf.attributes.select {|a| a.first == 'ID'}
             gff_id = gff_id.first.last
             exons = []
@@ -146,6 +148,10 @@ class Page
       Glyph.directed(args).each {|g| @svg.add_primitive(g) }
   end
   
+  def draw_circle(args)
+      Glyph.circle(args).each {|g| @svg.add_primitive(g) }
+  end
+  
   def draw_transcript(args)
     Glyph.transcript(args).each {|g| @svg.add_primitive(g) }
   end
@@ -154,6 +160,18 @@ class Page
     Glyph.generic(args).each {|g| @svg.add_primitive(g) }
   end
   
+  def draw_up_triangle(args)
+    Glyph.up_triangle(args).each {|g| @svg.add_primitive(g) }
+  end
+
+  def draw_down_triangle(args)
+    Glyph.down_triangle(args).each {|g| @svg.add_primitive(g) }
+  end
+
+  def draw_span(args)
+    Glyph.span(args).each {|g| @svg.add_primitive(g) }
+  end
+  
   def draw_features(track) #sort out the input information into a user friendly format..
     if [:histogram, "histogram"].include?(track.glyph) #do different stuff for data tracks...
 
@@ -219,7 +237,9 @@ class Page
         end
 
         width = to_px( (f.end - @scale_start) - (f.start - @scale_start) )
-
+        if track.min_width and width < track.min_width
+          width = track.min_width
+        end
         y = @track_top + (track.feature_rows[index] * 2 * track.feature_height)
 
         self.send("draw_#{track.glyph}", {:x => x, 

data/lib/bio/graphics/track.rb

@@ -2,7 +2,7 @@ module Bio
   class Graphics
 
 class Track
-  attr_reader :glyph, :name, :label, :args, :track_height, :scale, :max_y
+  attr_reader :glyph, :name, :label, :args, :track_height, :scale, :max_y, :min_width
   attr_accessor :features, :feature_rows, :name, :number_rows, :feature_height
   def initialize(args)
     @args = {:glyph => :generic, 
@@ -20,6 +20,7 @@ class Track
     @feature_height = @args[:feature_height]
     @number_of_rows = 1
     @max_y = args[:max_y]
+    @min_width = args[:min_width]
     
 
   end

metadata

@@ -1,108 +1,80 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-svgenes
-version: !ruby/object:Gem::Version 
-  hash: 19
+version: !ruby/object:Gem::Version
+  version: 0.2.3
   prerelease: 
-  segments: 
-  - 0
-  - 2
-  - 2
-  version: 0.2.2
 platform: ruby
-authors: 
+authors:
 - Dan MacLean
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-01-18 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  type: :development
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id001
+date: 2013-01-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: shoulda
-- !ruby/object:Gem::Dependency 
+  requirement: &70232196114400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *70232196114400
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &70232196113480 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 23
-        segments: 
-        - 1
-        - 0
-        - 0
+      - !ruby/object:Gem::Version
         version: 1.0.0
-  version_requirements: *id002
-  name: bundler
-- !ruby/object:Gem::Dependency 
   type: :development
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: *70232196113480
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &70232196112820 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 1
-        - 6
-        - 4
+      - !ruby/object:Gem::Version
         version: 1.6.4
-  version_requirements: *id003
-  name: jeweler
-- !ruby/object:Gem::Dependency 
   type: :development
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
-  version_requirements: *id004
+  version_requirements: *70232196112820
+- !ruby/object:Gem::Dependency
   name: rcov
-- !ruby/object:Gem::Dependency 
+  requirement: &70232196111740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: *70232196111740
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &70232196111080 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 1
-        - 4
-        - 2
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.2
-  version_requirements: *id005
-  name: bio
-description: This bio-gem facilitates the creation of pretty, publication quality SVG images from feature data.
+  type: :development
+  prerelease: false
+  version_requirements: *70232196111080
+description: This bio-gem facilitates the creation of pretty, publication quality
+  SVG images from feature data.
 email: maclean.daniel@gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .DS_Store
 - .document
 - Gemfile
@@ -124,6 +96,7 @@ files:
 - examples/example_config.json
 - examples/gene.gff
 - examples/get_coverage_in_windows.rb
+- examples/make_example.rb
 - examples/transcripts.gff
 - lib/.DS_Store
 - lib/bio-svgenes.rb
@@ -137,37 +110,31 @@ files:
 - test/helper.rb
 - test/test_bio-svgenes.rb
 homepage: http://github.com/danmaclean/bioruby-svgenes
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 1694400785006489552
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: Create pretty SVG-format images of features, gene models and data tracks
 test_files: []
-