macroape 3.3.0 → 3.3.1

data/README.md

@@ -41,14 +41,17 @@ Or install it yourself as:
     require 'macroape'
     background = [1,1,1,1]
     discretization = 10
-    first_pwm_matrix = [[1,2,3,4], [1,2,3,4], [4,1,2,3,], [5,3,2,4], [4,1,2,3], [7,8,9,11]]
-    pwm_first = PWM::SingleMatrix.new(first_pwm_matrix).with_background(background).discrete(discretization)
-    pwm_second = PWM::SingleMatrix.load_pat('another_pwm.pat').with_background(background).discrete(discretization)
-    cmp = PWMCompare::PWMCompare.new(pwm_first, pwm_second)
+    pwm_first = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
+    pwm_second = Bioinform::PWM.new(File.read('first_pwm.pat')).background(background).discrete(discretization)
+    
+    cmp = Macroape::PWMCompare.new(pwm_first, pwm_second)
     first_threshold = pwm_first.threshold(pvalue)
     second_threshold = pwm_second.threshold(pvalue)
+    
     similarity_info = cmp.jaccard(first_threshold, second_threshold)
     puts "Jaccard similarity: #{similarity_info[:similarity]}"
+    
+  For more details look a source code of utilities in lib/exec/ folder
 
 ## Contributing
 

data/lib/macroape/collection.rb

@@ -10,5 +10,13 @@ module Macroape
       @pwms[pwm.name] = pwm
       @infos[pwm.name] = info
     end
+    def ==(other)
+      @rough_discretization == other.rough_discretization && 
+      @precise_discretization == other.precise_discretization && 
+      @background == other.background && 
+      @pvalues == other.pvalues && 
+      @pwms == other.pwms &&
+      @infos == other.infos
+    end
   end
 end

data/lib/macroape/exec/eval_similarity.rb

@@ -28,7 +28,6 @@ Examples:
 
 $:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
-require 'bioinform'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'
   STDERR.puts help_string

data/lib/macroape/exec/find_pvalue.rb

@@ -26,7 +26,6 @@ Examples:
 
 $:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
-require 'bioinform'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'
   STDERR.puts help_string

data/lib/macroape/exec/find_threshold.rb

@@ -22,7 +22,6 @@ Example:
 
 $:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
-require 'bioinform'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'
   STDERR.puts help_string

data/lib/macroape/exec/preprocess_collection.rb

@@ -17,7 +17,6 @@ Example:
 
 $:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
-require 'bioinform'
 require 'yaml'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'

data/lib/macroape/exec/scan_collection.rb

@@ -25,7 +25,6 @@ Example:
 
 $:.unshift File.join(File.dirname(__FILE__),'./../../')
 require 'macroape'
-require 'bioinform'
 require 'yaml'
 
 if ARGV.empty? or ARGV.include? '-h' or ARGV.include? '-help' or ARGV.include? '--help' or ARGV.include? '--h'

data/lib/macroape/version.rb

@@ -1,3 +1,3 @@
 module Macroape
-  VERSION = "3.3.0"
+  VERSION = "3.3.1"
 end

data/macroape.gemspec

@@ -1,19 +1,19 @@
-# -*- encoding: utf-8 -*-
-require File.expand_path('../lib/macroape/version', __FILE__)
-
-Gem::Specification.new do |gem|
-  gem.authors       = ["Ilya Vorontsov"]
-  gem.email         = ["prijutme4ty@gmail.com"]
-  gem.description   = %q{Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure and best alignment between a pair of Position Weight Matrices(PWM), finding thresholds by P-values and inside out and even searching a collection of motifs for the most similar ones. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw}
-  gem.summary       = %q{PWM comparison tool using MACROAPE approach}
-  gem.homepage      = "http://autosome.ru/macroape/"
-
-  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          = "macroape"
-  gem.require_paths = ["lib"]
-  gem.version       = Macroape::VERSION
-  
-  gem.add_dependency('bioinform', '~> 0.1.0')
-end
+# -*- encoding: utf-8 -*-
+require File.expand_path('../lib/macroape/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.authors       = ["Ilya Vorontsov"]
+  gem.email         = ["prijutme4ty@gmail.com"]
+  gem.description   = %q{Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value Estimation. It's a bioinformatic tool for evaluating similarity measure and best alignment between a pair of Position Weight Matrices(PWM), finding thresholds by P-values and inside out and even searching a collection of motifs for the most similar ones. Used approach and application described in manual at https://docs.google.com/document/pub?id=1_jsxhMNzMzy4d2d_byAd3n6Szg5gEcqG_Sf7w9tEqWw}
+  gem.summary       = %q{PWM comparison tool using MACROAPE approach}
+  gem.homepage      = "http://autosome.ru/macroape/"
+
+  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          = "macroape"
+  gem.require_paths = ["lib"]
+  gem.version       = Macroape::VERSION
+  
+  gem.add_dependency('bioinform', '>= 0.1.1')
+end

data/test/preprocess_collection_test.rb

@@ -1,9 +1,11 @@
 require 'test_helper'
+require 'yaml'
+require 'macroape'
 
 class TestPreprocessCollection < Test::Unit::TestCase
   def test_multipvalue_preproceessing
-    system(Helpers.exec_cmd('preprocess_collection','./test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent'))
-    assert_equal File.read('test/data/test_collection.yaml'), File.read('test/data/test_collection.yaml.tmp')
+    system(Helpers.exec_cmd('preprocess_collection','test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent'))
+    assert_equal YAML.load_file('test/data/test_collection.yaml'), YAML.load_file('test/data/test_collection.yaml.tmp')
     File.delete 'test/data/test_collection.yaml.tmp'
   end
 end

data/test/scan_collection_test.rb

@@ -2,16 +2,16 @@ require 'test_helper'
 
 class TestScanCollection < Test::Unit::TestCase
   def test_scan_default_cutoff
-    assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt'), 
-                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --silent'), &:read)
+    assert_equal File.read('test/data/KLF4_f2_scan_results_default_cutoff.txt').gsub("\r\n", "\n"),
+                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --silent'), &:read).gsub("\r\n","\n")
   end
   def test_scan_and_output_all_results
-    assert_equal File.read('test/data/KLF4_f2_scan_results_all.txt'), 
-                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent'), &:read)
+    assert_equal File.read('test/data/KLF4_f2_scan_results_all.txt').gsub("\r\n", "\n"),
+                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --all --silent'), &:read).gsub("\r\n","\n")
       
   end
   def test_scan_precise_mode
-    assert_equal File.read('test/data/KLF4_f2_scan_results_precise_mode.txt'),
-                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent'), &:read)
+    assert_equal File.read('test/data/KLF4_f2_scan_results_precise_mode.txt').gsub("\r\n","\n"),
+                 IO.popen(Helpers.exec_cmd('scan_collection','test/data/KLF4_f2.pat test/data/test_collection.yaml --precise --all --silent'), &:read).gsub("\r\n", "\n")
   end
 end

data/test/test_helper.rb

@@ -1,3 +1,5 @@
+$LOAD_PATH.unshift File.dirname(__FILE__) + '/../lib'
+$LOAD_PATH.unshift File.dirname(__FILE__)
 require 'test/unit'
  
 module Helpers

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: macroape
 version: !ruby/object:Gem::Version
-  version: 3.3.0
+  version: 3.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,24 +9,24 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-20 00:00:00.000000000 Z
+date: 2012-06-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bioinform
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.1
 description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
   Estimation. It's a bioinformatic tool for evaluating similarity measure and best
   alignment between a pair of Position Weight Matrices(PWM), finding thresholds by