sequence_logo 1.3.2 → 1.3.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,15 +1,15 @@
 PATH
   remote: .
   specs:
-    sequence_logo (1.3.0)
+    sequence_logo (1.3.3)
       bioinform (~> 0.3.1)
-      rmagick (~> 2.13)
+      rmagick (>= 3.2.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
     bioinform (0.3.1)
-    rmagick (2.16.0)
+    rmagick (4.1.2)
 
 PLATFORMS
   ruby
@@ -18,4 +18,4 @@ DEPENDENCIES
   sequence_logo!
 
 BUNDLED WITH
-   1.16.1
+   1.17.2

data/README.md

@@ -35,10 +35,11 @@ SequenceLogo consists of two tools:
     * --orientation <direct|revcomp|both> - create logo for a direct, reverse-complement or both orientations of motif
     * --scheme FOLDER - name of folder containing nucleotide images
     * --threshold-lines - draw lines on specific levels
+    * --output-file - Specify filename for resulting image
 
 * Tool **glue_logos** generates a single image of aligned motifs.
 
-      ```glue_logos <output file> <file with alignment infos>```
+      glue_logos <output file> <file with alignment infos>
 
   or
       

data/lib/sequence_logo/canvas_factory.rb

@@ -16,7 +16,7 @@ module SequenceLogo
     end
 
     def text_image(text, img_height = y_unit)
-      text_img = Magick::Image.new(logo_shift, img_height){ self.background_color = 'transparent' }
+      text_img = Magick::Image.new(logo_shift, img_height){|img| img.background_color = 'transparent' }
       annotation = Magick::Draw.new
       annotation.pointsize(text_size)
       annotation.text(10, img_height / 2, text)
@@ -26,7 +26,7 @@ module SequenceLogo
 
     def shifted_logo(image, shift)
       canvas = HorizontalGluingCanvas.new
-      canvas.add_image Magick::Image.new(shift * x_unit, image.rows){ self.background_color = 'transparent' }
+      canvas.add_image Magick::Image.new(shift * x_unit, image.rows){|img| img.background_color = 'transparent' }
       canvas.add_image image
       canvas.image
     end
@@ -74,7 +74,12 @@ module SequenceLogo
       else
         index = letter_index(letter)
       end
-      letter_images[index].dup.resize(x_size, y_size)
+      letter_clone = letter_images[index].dup
+      channels_clone = letter_clone.separate(Magick::AllChannels)
+      channels_clone.each{|channel|
+        channel.resize!(x_size, y_size)
+      }
+      channels_clone.combine
     end
 
     def letter_index(letter)

data/lib/sequence_logo/magick_support.rb

@@ -9,7 +9,7 @@ module Magick
 
     # 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'}
+      empty_image = Magick::Image.new(x_size, y_size){|img| img.background_color = 'transparent' }
       self.unshift(empty_image)
     end
   end

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.3.2"
+  VERSION = "1.3.4"
 end

data/sequence_logo.gemspec

@@ -3,7 +3,7 @@ require File.expand_path('../lib/sequence_logo/version', __FILE__)
 
 Gem::Specification.new do |gem|
   gem.authors       = ["Ilya Vorontsov"]
-  gem.email         = ["prijutme4ty@gmail.com"]
+  gem.email         = ["vorontsov.i.e@gmail.com"]
   gem.description   = %q{SequenceLogo is a tool for drawing sequence logos of motifs. It gets Positional Count Matrices(PCMs) or IUPAC sequences as input and generates png-logos for a motif. Also one can create logo for reverse complement or even generate logos for a whole collection of motifs.
   Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence (see http://weblogo.berkeley.edu/)
 }
@@ -17,6 +17,6 @@ Gem::Specification.new do |gem|
   gem.require_paths = ["lib"]
   gem.version       = SequenceLogo::VERSION
   
-  gem.add_dependency('rmagick', '~> 2.13')
+  gem.add_dependency('rmagick', '>= 3.2.0')
   gem.add_dependency('bioinform', '~> 0.3.1')
 end

metadata

@@ -1,29 +1,28 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.3.2
+  version: 1.3.4
 platform: ruby
 authors:
 - Ilya Vorontsov
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-07 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '2.13'
+        version: 3.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '2.13'
+        version: 3.2.0
 - !ruby/object:Gem::Dependency
   name: bioinform
   requirement: !ruby/object:Gem::Requirement
@@ -42,7 +41,7 @@ description: |
   SequenceLogo is a tool for drawing sequence logos of motifs. It gets Positional Count Matrices(PCMs) or IUPAC sequences as input and generates png-logos for a motif. Also one can create logo for reverse complement or even generate logos for a whole collection of motifs.
     Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence (see http://weblogo.berkeley.edu/)
 email:
-- prijutme4ty@gmail.com
+- vorontsov.i.e@gmail.com
 executables:
 - glue_logos
 - sequence_logo
@@ -106,7 +105,6 @@ files:
 homepage: ''
 licenses: []
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -121,9 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
-signing_key: 
+rubygems_version: 3.6.9
 specification_version: 4
 summary: Tool for drawing sequence logos of motifs
 test_files: