acnfp-trans-counter 0.1.0 → 0.2.0

data/Gemfile

@@ -6,7 +6,7 @@ source "http://rubygems.org"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "bio", ">=1.4.1"
+  gem "bio", ">=1.4"
   gem "thor", ">=0.14.6"
   gem "shoulda", ">= 0"
   gem "bundler", "~> 1.0.0"

data/Gemfile.lock

@@ -1,14 +1,14 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio (1.4.1.5000)
+    bio (1.4.2)
     git (1.2.5)
     jeweler (1.5.2)
       bundler (~> 1.0.0)
       git (>= 1.2.5)
       rake
-    rake (0.8.7)
-    rcov (0.9.9)
+    rake (0.9.2)
+    rcov (0.9.10)
     shoulda (2.11.3)
     thor (0.14.6)
 
@@ -16,7 +16,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  bio (>= 1.4.1)
+  bio (>= 1.4)
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
   rcov

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/acnfp-trans-counter.gemspec

@@ -4,15 +4,14 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{acnfp-trans-counter}
-  s.version = "0.1.0"
+  s.name = "acnfp-trans-counter"
+  s.version = "0.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Robert Syme"]
-  s.date = %q{2011-04-04}
-  s.default_executable = %q{acnfp-trans-counter}
-  s.description = %q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
-  s.email = %q{rob.syme@gmail.com}
+  s.date = "2011-09-15"
+  s.description = "A quick and dirty tool for analysis of transition and transversion frequency aross and alignment"
+  s.email = "rob.syme@gmail.com"
   s.executables = ["acnfp-trans-counter"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -32,11 +31,11 @@ Gem::Specification.new do |s|
     "test/helper.rb",
     "test/test_acnfp-trans-counter.rb"
   ]
-  s.homepage = %q{http://github.com/robsyme/acnfp-trans-counter}
+  s.homepage = "http://github.com/robsyme/acnfp-trans-counter"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.5.0}
-  s.summary = %q{A quick and dirty tool for analysis of transition and transversion frequency aross and alignment}
+  s.rubygems_version = "1.8.10"
+  s.summary = "A quick and dirty tool for analysis of transition and transversion frequency aross and alignment"
   s.test_files = [
     "test/helper.rb",
     "test/test_acnfp-trans-counter.rb"
@@ -46,7 +45,7 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_development_dependency(%q<bio>, [">= 1.4"])
       s.add_development_dependency(%q<thor>, [">= 0.14.6"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
@@ -55,7 +54,7 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
       s.add_runtime_dependency(%q<thor>, [">= 0.14.6"])
     else
-      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<bio>, [">= 1.4"])
       s.add_dependency(%q<thor>, [">= 0.14.6"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
@@ -65,7 +64,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<thor>, [">= 0.14.6"])
     end
   else
-    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<bio>, [">= 1.4"])
     s.add_dependency(%q<thor>, [">= 0.14.6"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])

data/bin/acnfp-trans-counter

@@ -12,13 +12,17 @@ class AcnfpTransCounter < Thor
       transition_count = 0
       transversion_count = 0
       indel_count = 0
+      informative_count = 0
       
       alignment = Bio::Alignment::OriginalAlignment.new([a,b])
       alignment.each_site do |site|
-        next if site[0] == site[1]
         next if site.has_gap?
-        next if site.include? "N"
 
+        if site[0] == site[1] or site.include? "N"
+          informative_count += 1
+          next
+        end
+        
         case site.sort.map{|char| char.upcase}
         when %w{C T}, %w{A G}
           transition_count += 1
@@ -37,8 +41,8 @@ class AcnfpTransCounter < Thor
 
       puts "Transversions: %d (%.2f%%)" % [transversion_count, 100 * transversion_count / mutation_count]
       puts "Transitions:   %d (%.2f%%)" % [transition_count, 100 * transition_count / mutation_count]
-
       puts "Transversions / Transitions: %.2f" % [transversion_count.to_f / transition_count]
+      puts "Non-indel sites: %d" % informative_count
       puts
     end
   end

metadata

@@ -1,116 +1,114 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: acnfp-trans-counter
-version: !ruby/object:Gem::Version 
+version: !ruby/object:Gem::Version
+  version: 0.2.0
   prerelease: 
-  version: 0.1.0
 platform: ruby
-authors: 
+authors:
 - Robert Syme
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-04-04 00:00:00 +08:00
-default_executable: acnfp-trans-counter
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2011-09-15 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bio
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &27025480 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 1.4.1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :development
   prerelease: false
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
+  version_requirements: *27025480
+- !ruby/object:Gem::Dependency
   name: thor
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &27025000 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.14.6
   type: :development
   prerelease: false
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
+  version_requirements: *27025000
+- !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &27024380 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
+  version_requirements: *27024380
+- !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &27023740 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
+      - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
+  version_requirements: *27023740
+- !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &26946160 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
+      - !ruby/object:Gem::Version
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
+  version_requirements: *26946160
+- !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &26945680 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
+  version_requirements: *26945680
+- !ruby/object:Gem::Dependency
   name: bio
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &26945200 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
+  version_requirements: *26945200
+- !ruby/object:Gem::Dependency
   name: thor
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  requirement: &26944680 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *id008
-description: A quick and dirty tool for analysis of transition and transversion frequency aross and alignment
+  version_requirements: *26944680
+description: A quick and dirty tool for analysis of transition and transversion frequency
+  aross and alignment
 email: rob.syme@gmail.com
-executables: 
+executables:
 - acnfp-trans-counter
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
-files: 
+files:
 - .document
 - Gemfile
 - Gemfile.lock
@@ -123,37 +121,35 @@ files:
 - lib/acnfp-trans-counter.rb
 - test/helper.rb
 - test/test_acnfp-trans-counter.rb
-has_rdoc: true
 homepage: http://github.com/robsyme/acnfp-trans-counter
-licenses: 
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 492392011685652161
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -3079593327036305129
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.5.0
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: A quick and dirty tool for analysis of transition and transversion frequency aross and alignment
-test_files: 
+summary: A quick and dirty tool for analysis of transition and transversion frequency
+  aross and alignment
+test_files:
 - test/helper.rb
 - test/test_acnfp-trans-counter.rb