sequence_logo 1.2.2 → 1.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
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-  data.tar.gz: bd8990d9f2ae74d63a2565152ef5f9a32044c4b2
+SHA256:
+  metadata.gz: eaa5c95e4d2e0823719f5a9db61b95e42283fe656b65577cb5fe192df562699c
+  data.tar.gz: df60aa00113e82ab99fcd149e53e2c9818004f2a10bf04a543ef4e43746d26e5
 SHA512:
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-  data.tar.gz: 51dd020446c145136fad74b845cd6711423439bfa41a3d4cd895b2fb2fbd910f307d175fd83aaeb5d828377bf897c173141ab01a7032e762b25e66f418591f12
+  metadata.gz: e4f977a3f7c0a276f3e6468a707153d62f0173f1fc5997606e894936991fb2e02275459799a4657806175ca5f202284975a4822df0807c252362580e49266a78
+  data.tar.gz: '068f555ffaabe14d92b472c0ad3e7638f4358d9a1fabfd6b0cd73e0283b0b5eb5cc2f5df38d95597d9bb1c0de3f3a933783a1a2063c1881a12cd54100d09e6a1'

data/.gitignore

@@ -3,7 +3,6 @@
 .bundle
 .config
 .yardoc
-Gemfile.lock
 InstalledFiles
 _yardoc
 coverage

data/Gemfile.lock

@@ -0,0 +1,21 @@
+PATH
+  remote: .
+  specs:
+    sequence_logo (1.3.3)
+      bioinform (~> 0.3.1)
+      rmagick (>= 3.2.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    bioinform (0.3.1)
+    rmagick (4.1.2)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  sequence_logo!
+
+BUNDLED WITH
+   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/docker/Dockerfile-rmagick-alpine

@@ -0,0 +1,14 @@
+FROM ruby:alpine
+RUN apk add --virtual .builddeps --update  alpine-sdk curl gzip tar && \
+    curl -o ImageMagick-6.9.10-14.tar.gz "http://mirror.checkdomain.de/imagemagick/ImageMagick-6.9.10-14.tar.gz" && \
+    tar -zxf ImageMagick-6.9.10-14.tar.gz && \
+    apk add --update libgcc libgomp libjpeg-turbo-dev libpng-dev && \
+    cd ImageMagick-6.9.10-14 && \
+    ./configure && \
+    make && \
+    make install && \
+    gem install rmagick --no-document && \
+    apk del .builddeps && \
+    cd / && \
+    rm -rf ImageMagick-6.9.10-14.tar.gz ImageMagick-6.9.10-14 && \
+    rm -rf /var/cache/apk/*

data/docker/Dockerfile-rmagick-slim

@@ -0,0 +1,8 @@
+FROM ruby:slim
+RUN apt-get update && \
+    apt-get install -y ruby build-essential imagemagick libmagickcore-dev libmagickwand-dev pkg-config && \
+    gem install rmagick && \
+    apt-get purge -y build-essential libmagickcore-dev libmagickwand-dev pkg-config && \
+    apt-get autoremove -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*

data/docker/Dockerfile-sequence_logo

@@ -0,0 +1,7 @@
+FROM vorontsovie/rmagick:alpine
+ARG SEQLOGO_VERSION=1.3.2
+RUN gem install sequence_logo -v "$SEQLOGO_VERSION"
+WORKDIR /data
+ENTRYPOINT ["sequence_logo"]
+CMD ["--help"]
+# docker run --rm --mount type=bind,src=$(pwd),dst=/data sequence_logo motif.pcm

data/lib/sequence_logo/canvas_factory.rb

@@ -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/exec/glue_logos.rb

@@ -30,19 +30,19 @@ def make_logo_alignment(aligned_motifs, options)
   alignment
 end
 
-def readlines_from_file_or_stdin(argv, options = {})
+def readlines_from_file_or_stdin(argv, from_stdin: , **options)
   default_options = { source_not_given_msg: 'Specify input data',
                       both_sources_given_msg: 'Specify either file with data or data itself in stdin, not both'}
   options = default_options.merge(options)
-  raise options[:both_sources_given_msg]  if !argv.empty? && !$stdin.tty?
-  if !argv.empty?
-    lines = File.readlines(argv.first)
-  elsif !$stdin.tty?
-    lines = $stdin.readlines
+  raise ArgumentError, options[:both_sources_given_msg]  if from_stdin && !argv.empty?
+  raise ArgumentError, options[:source_not_given_msg]  if !from_stdin && argv.empty?
+  if from_stdin || argv == ['-']
+    $stdin.readlines
+  elsif argv.length == 1
+    File.readlines(argv.first)
   else
-    raise ArgumentError, options[:source_not_given_msg]
+    raise ArgumentError, 'alignment should either be in stdin or in file, specified by arglist'
   end
-  lines
 end
 
 def direct_output_filename(output_file)
@@ -64,7 +64,7 @@ begin
   Usage:
     glue_logos <output file> <alignment infos file>
       or
-    <alignment infos file> | glue_logos <output file>
+    <alignment infos file> | glue_logos <output file> --from-stdin
 
   Alignment infos has the following format (tab separated)
   if motif names not specified - filenames are used as labels:
@@ -78,7 +78,7 @@ begin
   total_orientation = :direct
   default_options = { x_unit: 30, y_unit: 60, logo_shift: 300, scheme: 'nucl_simpa',
                       icd_mode: :discrete, threshold_lines: false,
-                      text_size: 24, background_color: 'white' }
+                      text_size: 24, background_color: 'white', from_stdin: false }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -101,13 +101,18 @@ begin
         options[:background_fill] = Magick::SolidFill.new(v)
       end
     end
+
+    parser.on('--from-stdin') do 
+      options[:from_stdin] = true
+    end
   end
   options = cli.parse_options!(argv)
 
   output_file = argv.shift
   raise ArgumentError, 'Specify output file'  unless output_file
 
-  alignment_lines = readlines_from_file_or_stdin(argv,  source_not_given_msg: 'Specify alignment infos',
+  alignment_lines = readlines_from_file_or_stdin(argv,  from_stdin: options[:from_stdin],
+                                                        source_not_given_msg: 'Specify alignment infos',
                                                         both_sources_given_msg: 'You can specify alignment infos either from file or from stdin. Don\'t use both sources simultaneously')
   alignment = make_logo_alignment(load_alignment_infos(alignment_lines), options)
 

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -16,9 +16,9 @@ def in_necessary_orientations(objects_to_render, orientation, logo_folder)
   end.flatten
 end
 
-def arglist_augmented_with_stdin(argv)
+def arglist_augmented_with_stdin(argv, from_stdin:)
   result = argv
-  result += $stdin.read.shellsplit  unless $stdin.tty?
+  result += $stdin.read.shellsplit  if from_stdin
   result
 end
 
@@ -35,7 +35,7 @@ begin
   Usage:
     sequence_logo [options] <motif file>...
       or
-    ls pcm_folder/*.pcm | sequence_logo [options]
+    ls pcm_folder/*.pcm | sequence_logo --from-stdin [options]
       or
     sequence_logo --sequence <sequence>...
       or
@@ -47,7 +47,7 @@ begin
   default_options = { x_unit: 30, y_unit: 60, scheme: 'nucl_simpa',
                       orientation: :direct, icd_mode: :discrete, threshold_lines: true,
                       logo_folder: '.', background_color: 'white',
-                      from_dinucleotide: false }
+                      from_dinucleotide: false, from_stdin: false }
   cli = SequenceLogo::CLI.new(default_options)
   cli.instance_eval do
     parser.banner = doc
@@ -73,6 +73,13 @@ begin
         options[:background_fill] = Magick::SolidFill.new(v)
       end
     end
+    parser.on('--from-stdin') {
+      options[:from_stdin] = true
+    }
+
+    parser.on('--output-file FILE', 'Resulting image name') {|fn|
+      options[:output_file] = fn
+    }
 
     parser.on('--dinucleotide'){ options[:from_dinucleotide] = true }
   end
@@ -90,7 +97,7 @@ begin
 
   objects_to_render = []
   if options[:sequence]
-    sequences = arglist_augmented_with_stdin(argv)
+    sequences = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one sequence'  if sequences.empty?
 
     sequences.each do |sequence|
@@ -98,7 +105,7 @@ begin
                             name: File.join(logo_folder, sequence)}
     end
   elsif options[:sequence_w_snp]
-    sequences = arglist_augmented_with_stdin(argv)
+    sequences = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one sequence'  if sequences.empty?
 
     sequences.each do |sequence_w_snp|
@@ -106,7 +113,7 @@ begin
                             name: File.join(logo_folder, sequence_w_snp.gsub(/[\[\]\/]/, '_'))}
     end
   else
-    filenames = arglist_augmented_with_stdin(argv)
+    filenames = arglist_augmented_with_stdin(argv, from_stdin: options[:from_stdin])
     raise ArgumentError, 'Specify at least one motif file'  if filenames.empty?
 
     filenames.each do |filename|
@@ -123,8 +130,16 @@ begin
     end
   end
 
+  if options[:output_file]
+    if objects_to_render.size == 1
+      objects_to_render.first[:name] = options[:output_file].sub(/.png$/i, '') # force name
+    else
+      raise 'When output file is specified, the only one logo can be rendered'
+    end
+  end
+
   in_necessary_orientations(objects_to_render, options[:orientation], logo_folder).each do |infos|
-    filename = File.join(logo_folder, infos[:filename])
+    filename = File.absolute_path(infos[:filename], logo_folder)
     infos[:renderable].render(canvas_factory).write("PNG:#{filename}")
   end
 rescue => err

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.2.2"
+  VERSION = "1.3.3"
 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 +1,29 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.2.2
+  version: 1.3.3
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-22 00:00:00.000000000 Z
+date: 2020-08-20 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 +42,7 @@ 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
@@ -51,12 +51,16 @@ extra_rdoc_files: []
 files:
 - ".gitignore"
 - Gemfile
+- Gemfile.lock
 - LICENSE
 - README.md
 - Rakefile
 - TODO.txt
 - bin/glue_logos
 - bin/sequence_logo
+- docker/Dockerfile-rmagick-alpine
+- docker/Dockerfile-rmagick-slim
+- docker/Dockerfile-sequence_logo
 - lib/sequence_logo.rb
 - lib/sequence_logo/alignment.rb
 - lib/sequence_logo/assets/nucl_simpa/a.png
@@ -117,8 +121,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: Tool for drawing sequence logos of motifs