sequence_logo 1.3.3 → 1.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: eaa5c95e4d2e0823719f5a9db61b95e42283fe656b65577cb5fe192df562699c
-  data.tar.gz: df60aa00113e82ab99fcd149e53e2c9818004f2a10bf04a543ef4e43746d26e5
+  metadata.gz: c619eecefa46220873c431f87a9c8d20a9a8d8d26093c213df04c366d19c0434
+  data.tar.gz: a587739504949d122f6cf13691db350bf566bd9089c45b3c59035e6c78aa16e3
 SHA512:
-  metadata.gz: e4f977a3f7c0a276f3e6468a707153d62f0173f1fc5997606e894936991fb2e02275459799a4657806175ca5f202284975a4822df0807c252362580e49266a78
-  data.tar.gz: '068f555ffaabe14d92b472c0ad3e7638f4358d9a1fabfd6b0cd73e0283b0b5eb5cc2f5df38d95597d9bb1c0de3f3a933783a1a2063c1881a12cd54100d09e6a1'
+  metadata.gz: a8b8cfe480444b5aa07e07577ba4911827fcb36ddbb18c1b6e55c27fb0ea2aad796ccdd6c7bf5df810389850b342ed539d5751dcad3fe6592b86b0a672e435c8
+  data.tar.gz: ff374cc30952e3c124b8ac8b2673e2f64ed1a15f4b31a37bc9eaae26e7ececaf330c7dac27b62b1780568675b6b89ee4def1636be27c382b1ca568a839510ba6

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

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -82,6 +82,8 @@ begin
     }
 
     parser.on('--dinucleotide'){ options[:from_dinucleotide] = true }
+
+    parser.on('--ppm-count N', 'Multiply PPM by N to get PCM'){|value| options[:ppm_count] = Float(value) }
   end
   options = cli.parse_options!(argv)
 
@@ -123,6 +125,14 @@ begin
         ppm = Bioinform::MotifModel::PCM.from_file(filename, validator: Bioinform::MotifModel::PCM::DIFFERENT_COUNTS_VALIDATOR)
       end
 
+      if options[:ppm_count]
+        new_matrix = ppm.matrix.map{|position|
+          sum = position.sum(0.0)
+          position.map{|el| el * options[:ppm_count] / sum}
+        }
+        ppm = Bioinform::MotifModel::PCM.new(new_matrix)
+      end
+
       logo = SequenceLogo::PPMLogo.new( ppm,
                                         icd_mode: options[:icd_mode],
                                         enable_threshold_lines: options[:threshold_lines])

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 = "1.3.3"
+  VERSION = "1.3.5"
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.3.3
+  version: 1.3.5
 platform: ruby
 authors:
 - Ilya Vorontsov
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-08-20 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
@@ -106,7 +105,6 @@ files:
 homepage: ''
 licenses: []
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -121,8 +119,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key: 
+rubygems_version: 3.6.9
 specification_version: 4
 summary: Tool for drawing sequence logos of motifs
 test_files: