sequence_logo 1.0.2 → 1.0.3

data/sequence_logo.gemspec

@@ -1,21 +1,21 @@
-# -*- encoding: utf-8 -*-
-require File.expand_path('../lib/sequence_logo/version', __FILE__)
-
-Gem::Specification.new do |gem|
-  gem.authors       = ["Ilya Vorontsov"]
-  gem.email         = ["prijutme4ty@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/)
-}
-  gem.summary       = %q{Tool for drawing sequence logos of motifs}
-  gem.homepage      = ""
-
-  gem.files         = `git ls-files`.split($\)
-  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
-  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
-  gem.name          = "sequence_logo"
-  gem.require_paths = ["lib"]
-  gem.version       = SequenceLogo::VERSION
-  
-  gem.add_dependency('rmagick', '~> 2.13.1')
-end
+# -*- encoding: utf-8 -*-
+require File.expand_path('../lib/sequence_logo/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.authors       = ["Ilya Vorontsov"]
+  gem.email         = ["prijutme4ty@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/)
+}
+  gem.summary       = %q{Tool for drawing sequence logos of motifs}
+  gem.homepage      = ""
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.name          = "sequence_logo"
+  gem.require_paths = ["lib"]
+  gem.version       = SequenceLogo::VERSION
+  
+  gem.add_dependency('rmagick', '~> 2.13.1')
+end

data/test/data/pcm/AHR_si.pcm

@@ -0,0 +1,10 @@
+AHR_si
+40.51343240527031  18.259112547756697  56.41253757072521  38.77363485291994
+10.877470982533044  11.870876719950774  34.66312982331297  96.54723985087516
+21.7165707818416  43.883079837598544  20.706746561638717  67.6523201955933
+2.5465132509466635  1.3171620263517245  145.8637051322628  4.231336967110781
+0.0  150.35847450464382  1.4927836298652875  2.1074592421627525
+3.441039751299748  0.7902972158110341  149.37613720253387  0.3512432070271259
+0.0  3.441039751299748  0.7024864140542533  149.81519121131782
+0.0  0.0  153.95871737667187  0.0
+43.07922333291745  66.87558226865211  16.159862546986584  27.844049228115868

data/test/data/pcm/AIRE_f2.pcm

@@ -0,0 +1,19 @@
+AIRE_f2
+16.428571428571484  10.795918367346953  5.1632653061224625  8.918367346938803
+7.51020408163268  7.51020408163268  5.632653061224489  20.65306122448985
+5.632653061224489  5.632653061224489  8.448979591836776  21.591836734693906
+1.877551020408166  0.0  36.612244897959265  2.8163265306122534
+0.0  0.0  33.79591836734698  7.51020408163268
+13.14285714285717  1.877551020408166  0.938775510204083  25.346938775510242
+15.959183673469415  3.755102040816336  0.938775510204083  20.65306122448985
+15.02040816326536  5.632653061224489  5.632653061224489  15.02040816326536
+14.081632653061265  2.8163265306122534  5.632653061224489  18.775510204081698
+21.591836734693945  3.755102040816336  5.632653061224489  10.326530612244925
+15.959183673469415  1.877551020408166  2.8163265306122534  20.65306122448985
+9.38775510204083  5.632653061224489  2.8163265306122534  23.469387755102094
+0.0  0.938775510204083  36.612244897959265  3.755102040816336
+0.0  0.0  40.36734693877556  0.938775510204083
+9.38775510204083  3.755102040816336  10.326530612244925  17.836734693877606
+2.8163265306122534  7.51020408163268  7.51020408163268  23.469387755102094
+18.77551020408166  0.938775510204083  6.571428571428585  15.02040816326536
+16.663265306122497  11.030612244898006  4.45918367346938  9.153061224489816

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.0.2
-  prerelease: 
+  version: 1.0.3
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-31 00:00:00.000000000 Z
+date: 2013-04-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -22,28 +20,18 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.13.1
-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.\n  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/)\n"
+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
 executables:
-- create_all_logos
-- generate_logo
-- pmflogo
+- glue_logos
+- sequence_logo
 extensions: []
 extra_rdoc_files: []
 files:
@@ -52,17 +40,17 @@ files:
 - LICENSE
 - README.md
 - Rakefile
-- bin/create_all_logos
-- bin/generate_logo
-- bin/pmflogo
+- TODO.txt
+- bin/glue_logos
+- bin/sequence_logo
 - lib/sequence_logo.rb
 - lib/sequence_logo/assets/nucl_simpa/a.png
 - lib/sequence_logo/assets/nucl_simpa/c.png
 - lib/sequence_logo/assets/nucl_simpa/g.png
 - lib/sequence_logo/assets/nucl_simpa/t.png
-- lib/sequence_logo/exec/create_all_logos.rb
-- lib/sequence_logo/exec/generate_logo.rb
-- lib/sequence_logo/exec/pmflogo.rb
+- lib/sequence_logo/cli.rb
+- lib/sequence_logo/exec/glue_logos.rb
+- lib/sequence_logo/exec/sequence_logo.rb
 - lib/sequence_logo/pmflogo_lib.rb
 - lib/sequence_logo/version.rb
 - lib/sequence_logo/ytilib.rb
@@ -73,31 +61,44 @@ files:
 - lib/sequence_logo/ytilib/iupac.rb
 - lib/sequence_logo/ytilib/pm.rb
 - lib/sequence_logo/ytilib/pmsd.rb
+- lib/sequence_logo/ytilib/ppm_support.rb
 - lib/sequence_logo/ytilib/randoom.rb
 - lib/sequence_logo/ytilib/ytilib.rb
 - sequence_logo.gemspec
+- test/data/logo/AHR_si_direct.png
+- test/data/logo/AHR_si_revcomp.png
+- test/data/logo/AIRE_f2_direct.png
+- test/data/logo/AIRE_f2_revcomp.png
+- test/data/pcm/AHR_si.pcm
+- test/data/pcm/AIRE_f2.pcm
 homepage: ''
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Tool for drawing sequence logos of motifs
-test_files: []
+test_files:
+- test/data/logo/AHR_si_direct.png
+- test/data/logo/AHR_si_revcomp.png
+- test/data/logo/AIRE_f2_direct.png
+- test/data/logo/AIRE_f2_revcomp.png
+- test/data/pcm/AHR_si.pcm
+- test/data/pcm/AIRE_f2.pcm
+has_rdoc: 

data/bin/create_all_logos

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'sequence_logo/exec/create_all_logos.rb'

data/bin/generate_logo

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'sequence_logo/exec/generate_logo.rb'

data/bin/pmflogo

@@ -1,3 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'sequence_logo/exec/pmflogo.rb'

data/lib/sequence_logo/exec/create_all_logos.rb

@@ -1,25 +0,0 @@
-require 'sequence_logo'
-require 'fileutils'
-
-motifs_folder = ARGV.shift
-unless motifs_folder && Dir.exist?(motifs_folder)
-  puts('Specified input folder not exists')
-  exit(1)
-end
-
-logo_folder = ARGV.shift
-unless logo_folder
-  puts('Output logo folder must be specified')
-  exit(1)
-end
-
-Dir.mkdir(logo_folder)  unless Dir.exist?(logo_folder)
-
-Dir.glob(File.join(motifs_folder, '*')).to_enum.each do |filename|
-  filename_wo_ext = File.basename(filename, File.extname(filename))
-  direct_output = File.join(logo_folder,"#{filename_wo_ext}_direct.png")
-  revcomp_output = File.join(logo_folder,"#{filename_wo_ext}_revcomp.png")
-
-  draw_logo(filename, direct_output, words_count: 'default', x_unit: 30, y_size: 60, icd_mode: 'discrete', revcomp: 'direct')
-  draw_logo(filename, revcomp_output, words_count: 'default', x_unit: 30, y_size: 60, icd_mode: 'discrete', revcomp: 'revcomp')
-end

data/lib/sequence_logo/exec/generate_logo.rb

@@ -1,18 +0,0 @@
-require 'sequence_logo'
-require 'fileutils'
-
-filename = ARGV.shift
-unless filename && File.exist?(filename)
-  puts 'Existing input file should be specified'
-  exit(1)
-end
-
-logo_dir = ARGV.shift || File.dirname(filename)
-FileUtils.mkdir(logo_dir) unless Dir.exist?(logo_dir)
-
-filename_wo_ext = File.basename(filename, File.extname(filename))
-direct_output = File.join(logo_dir,"#{filename_wo_ext}_direct.png")
-revcomp_output = File.join(logo_dir,"#{filename_wo_ext}_revcomp.png")
-
-draw_logo(filename, direct_output,  x_unit: 30, y_size: 60, revcomp: 'direct')
-draw_logo(filename, revcomp_output, x_unit: 30, y_size: 60, revcomp: 'revcomp')

data/lib/sequence_logo/exec/pmflogo.rb

@@ -1,26 +0,0 @@
-# pmflogo <input_file> <output_logo_filename> [words_count] [x_unit=100] [y_size=200] [icd_mode=discrete|weblogo] [revcomp=no|yes] [scheme=nucl_simpa] [paper_mode=no|yes] [threshold_lines=yes|no]
-# Any optional argument can be set as 'default' e.g.
-#   pmflogo motif.pcm logo.png default 30 60 default yes
-# skipped parameters are also substituted as default (in example above icd_mode is default, and also scheme, paper_mode and threshold_lines)
-
-require 'sequence_logo'
-
-if ARGV.size < 2
-  puts('At least two arguments must be specified, see usage of pmflogo')
-  exit(2)
-end
-
-input_file, output_logo_filename = ARGV.shift(2)
-unless File.exist?(input_file)
-  puts('Specified input file not exists')
-  exit(1)
-end
-
-options = {}
-options[:words_count] = ARGV.shift
-options[:x_unit], options[:y_size] = ARGV.shift(2)
-options[:icd_mode], options[:revcomp], options[:scheme], options[:paper_mode], options[:threshold_lines] = ARGV.shift(5)
-
-options.reject!{|k,v| v.nil?}
-
-draw_logo(input_file, output_logo_filename, options)