sequence_logo 1.1.1 → 1.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2411aa5c78c5efae4860eafaa8743acbbc526f04
-  data.tar.gz: b4451fceda9c126ed40a8db058b649f626a0ba7a
+  metadata.gz: a53d6d681797aec870766358a55b460aa10a87f1
+  data.tar.gz: 43c4712e2b1bbef50ac8de24626c115c5492dfaf
 SHA512:
-  metadata.gz: 32b810e2ed04ede3d15face6e91cf9fe677a30217f24c9f535fdd97f681028fd706d8c0f488d3198d984ab455bce982de0717367c6fc315462e8ff7f2419bb1c
-  data.tar.gz: fcf545d611c2ce7fd9b449273e25fac6fe094b158b9c676b39b934f8e84f480f4a4697e54779263832594e1b26f59b87f0585133cf89226309631c62ebf18f44
+  metadata.gz: 4331c46e148cb21342e7cb5d39ab635ff633086974a3e87d20a8d1efd1534f5590d6df7ccd50f0a5e7eea1d6222fc8a03709a2200f90432083a63a016bf3f9fa
+  data.tar.gz: 7b1013ed36a55848884760f55bb2418789e98fd9cd040e846a8748360889c3bcf34d0a92d520b3e034d501eb21ec2df3948a5d3be41b1b1f22aad699a7546e3b

data/TODO.txt

@@ -1,3 +1,7 @@
+Fix word count to calculate column-wise word-counts where possible! Selex logos are bad
+
+Make use of bioinform gem
+
 AssetsPath shouldn't be used at draw_logo level because it makes it impossible to change scheme on one folder that is outside the gem
 And how to make possible use schemes inside the assets path
 

data/lib/sequence_logo/alignment.rb

@@ -48,7 +48,7 @@ module SequenceLogo
       items_normalized.each do |item|
         canvas.add_image item.render(canvas_factory)
       end
-      canvas.background(Magick::HatchFill.new('white', 'white'))
+      canvas.background(canvas_factory.background_fill)
       canvas.image
     end
 

data/lib/sequence_logo/canvas_factory.rb

@@ -3,7 +3,7 @@ require_relative 'canvases'
 
 module SequenceLogo
   class CanvasFactory
-    attr_reader :x_unit, :y_unit, :text_size, :logo_shift
+    attr_reader :x_unit, :y_unit, :text_size, :logo_shift, :background_fill
     attr_reader :letter_images
 
     def initialize(letter_images, options = {})
@@ -12,6 +12,7 @@ module SequenceLogo
       @x_unit = options[:x_unit] || 30
       @y_unit = options[:y_unit] || 60
       @text_size = options[:text_size] || 24
+      @background_fill = options[:background_fill] || Magick::SolidFill.new('transparent')
     end
 
     def text_image(text, img_height = y_unit)

data/lib/sequence_logo/cli.rb

@@ -14,6 +14,7 @@ module SequenceLogo
     end
     def parser
       @parser ||= OptionParser.new do |opts|
+        opts.version = ::SequenceLogo::VERSION
         opts.on('-x', '--x-unit X_UNIT', 'Single letter width') do |v|
           options[:x_unit] = v.to_i
         end

data/lib/sequence_logo/data_models/ppm_logo.rb

@@ -36,15 +36,11 @@ module SequenceLogo
 
     def render(canvas_factory)
       canvas = LogoCanvas.new(canvas_factory)
-      if icd_mode == :discrete
-        canvas.background(Magick::HatchFill.new('white', 'white'))
-        if enable_threshold_lines
-          canvas.draw_threshold_line(ppm.get_line(ppm.icd2of4))
-          canvas.draw_threshold_line(ppm.get_line(ppm.icdThc))
-          canvas.draw_threshold_line(ppm.get_line(ppm.icdTlc))
-        end
-      else
-        canvas.background(Magick::HatchFill.new('white', 'bisque'))
+      canvas.background(canvas_factory.background_fill)
+      if icd_mode == :discrete && enable_threshold_lines
+        canvas.draw_threshold_line(ppm.get_line(ppm.icd2of4))
+        canvas.draw_threshold_line(ppm.get_line(ppm.icdThc))
+        canvas.draw_threshold_line(ppm.get_line(ppm.icdTlc))
       end
 
       logo_matrix.each do |position|

data/lib/sequence_logo/data_models/predefined_logo.rb

@@ -23,7 +23,10 @@ module SequenceLogo
     end
 
     def render(canvas_factory)
-      @direct_image
+      layers = Magick::ImageList.new
+      layers.put_image_at(@direct_image, 0, 0)
+      layers.unshift Magick::Image.new(@direct_image.columns, @direct_image.rows, canvas_factory.background_fill)
+      layers.flatten_images
     end
   end
 end

data/lib/sequence_logo/data_models/sequence.rb

@@ -19,7 +19,7 @@ module SequenceLogo
 
     def render(canvas_factory)
       canvas = LogoCanvas.new(canvas_factory)
-      canvas.background(Magick::HatchFill.new('white', 'white'))
+      canvas.background(canvas_factory.background_fill)
       sequence.each_char do |letter|
         canvas.add_letter(letter)
       end

data/lib/sequence_logo/data_models/sequence_with_snp.rb

@@ -30,7 +30,7 @@ module SequenceLogo
 
     def render(canvas_factory)
       canvas = LogoCanvas.new(canvas_factory)
-      canvas.background(Magick::HatchFill.new('white', 'white'))
+      canvas.background(canvas_factory.background_fill)
       left.each_char{|letter| canvas.add_letter(letter) }
       canvas.add_position_ordered(snp_position_heights)
       right.each_char{|letter| canvas.add_letter(letter) }

data/lib/sequence_logo/exec/glue_logos.rb

@@ -78,7 +78,9 @@ begin
 
   argv = ARGV
   total_orientation = :direct
-  default_options = {x_unit: 30, y_unit: 60, words_count: nil, icd_mode: :discrete, threshold_lines: false, scheme: 'nucl_simpa', logo_shift: 300, text_size: 24}
+  default_options = { x_unit: 30, y_unit: 60, logo_shift: 300, scheme: 'nucl_simpa',
+                      words_count: nil, icd_mode: :discrete, threshold_lines: false,
+                      text_size: 24, background_color: 'white' }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -93,6 +95,14 @@ begin
       raise ArgumentError, 'Orientation can be either direct or revcomp or both'  unless [:direct, :revcomp, :both].include?(v)
       total_orientation = v
     end
+
+    parser.on('--bg-fill FILL', 'Background fill. Specify either `transparent` or `color` or `color,hatch_color`') do |v|
+      if v.match(/^\w+,\w+$/)
+        options[:background_fill] = Magick::HatchFill.new(*v.split(','))
+      else
+        options[:background_fill] = Magick::SolidFill.new(v)
+      end
+    end
   end
   options = cli.parse_options!(argv)
 
@@ -105,8 +115,9 @@ begin
 
   scheme_dir = File.join(SequenceLogo::AssetsPath, options[:scheme])
   letter_images = SequenceLogo::CanvasFactory.letter_images(scheme_dir)
-  canvas_factory = SequenceLogo::CanvasFactory.new(letter_images, x_unit: options[:x_unit], y_unit: options[:y_unit],
-                                                    text_size: options[:text_size], logo_shift: options[:logo_shift])
+  canvas_factory = SequenceLogo::CanvasFactory.new( letter_images, x_unit: options[:x_unit], y_unit: options[:y_unit],
+                                                    text_size: options[:text_size], logo_shift: options[:logo_shift],
+                                                    background_fill: options[:background_fill] )
 
   case total_orientation
   when :direct

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -44,7 +44,9 @@ begin
   EOS
 
   argv = ARGV
-  default_options = {x_unit: 30, y_unit: 60, words_count: nil, orientation: :direct, logo_folder: '.', icd_mode: :discrete, threshold_lines: true, scheme: 'nucl_simpa'}
+  default_options = { x_unit: 30, y_unit: 60, scheme: 'nucl_simpa',
+                      words_count: nil, orientation: :direct, icd_mode: :discrete, threshold_lines: true,
+                      logo_folder: '.', background_color: 'white' }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -63,6 +65,13 @@ begin
     parser.on('--sequence', 'Specify sequence (like ATCTCGCCTAAT) instead of motif filenames') do
       options[:sequence] = true
     end
+    parser.on('--bg-fill FILL', 'Background fill. Specify either `transparent` or `color` or `color,hatch_color`') do |v|
+      if v.match(/^\w+,\w+$/)
+        options[:background_fill] = Magick::HatchFill.new(*v.split(','))
+      else
+        options[:background_fill] = Magick::SolidFill.new(v)
+      end
+    end
   end
   options = cli.parse_options!(argv)
 
@@ -71,7 +80,8 @@ begin
 
   scheme_dir = File.join(SequenceLogo::AssetsPath, options[:scheme])
   letter_images = SequenceLogo::CanvasFactory.letter_images(scheme_dir)
-  canvas_factory = SequenceLogo::CanvasFactory.new(letter_images, x_unit: options[:x_unit], y_unit: options[:y_unit])
+  canvas_factory = SequenceLogo::CanvasFactory.new( letter_images, x_unit: options[:x_unit], y_unit: options[:y_unit],
+                                                    background_fill: options[:background_fill] )
 
   raise "Specify either sequence or sequence with SNP or none of them, but not both"  if options[:sequence] && options[:sequence_w_snp]
 

data/lib/sequence_logo/magick_support.rb

@@ -1,14 +1,27 @@
 require 'RMagick'
 
-class Magick::ImageList
-  def put_image_at(image, x, y)
-    self << image
-    cur_image.page = Magick::Rectangle.new(0, 0, x, y)
+module Magick
+  class ImageList
+    def put_image_at(image, x, y)
+      self << image
+      cur_image.page = Magick::Rectangle.new(0, 0, x, y)
+    end
+
+    # add transparent layer so that full canvas size can't be less than given size
+    def set_minimal_size(x_size, y_size)
+      empty_image = Magick::Image.new(x_size, y_size){ self.background_color = 'transparent'}
+      self.unshift(empty_image)
+    end
   end
 
-  # add transparent layer so that full canvas size can't be less than given size
-  def set_minimal_size(x_size, y_size)
-    empty_image = Magick::Image.new(x_size, y_size){ self.background_color = 'transparent'}
-    self.unshift(empty_image)
+  class SolidFill
+    def initialize(bgcolor)
+      @bgcolor = bgcolor
+    end
+
+    def fill(img)
+      img.background_color = @bgcolor
+      img.erase!
+    end
   end
 end

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.1.1"
+  VERSION = "1.1.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.1.1
+  version: 1.1.2
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-26 00:00:00.000000000 Z
+date: 2014-06-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick