lederhosen 2.0.4 → 2.0.5

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "2.0.4"
+  s.version = "2.0.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2013-01-25"
+  s.date = "2013-01-27"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/tasks/separate_unclassified.rb

@@ -21,15 +21,18 @@ module Lederhosen
       unclassifieds = Set.new
       handle = File.open(uc_file)
       uc = UCParser.new(handle)
+      total_reads = 0
 
       if not strict
         uc.each do |result|
           unclassifieds << result.query if result.miss?
+          total_reads += 1
         end
 
       elsif strict
 
         uc.each_slice(2) do |left, right|
+          total_reads += 2
           if left.miss? || right.miss? # at least one is a miss
             unclassifieds << left.query
             unclassifieds << right.query
@@ -48,6 +51,7 @@ module Lederhosen
       end
 
       ohai "found #{unclassifieds.size} unclassified #{'(strict pairing)' if strict} reads."
+      ohai "unclassified: #{'%0.2f' % (100*unclassifieds.size/total_reads.to_f)} %"
 
       handle.close
 

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 2
     MINOR = 0
     CODENAME = 'Schnittlauchbrot' # changes for minor versions
-    PATCH = 4
+    PATCH = 5
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

metadata

@@ -1,104 +1,108 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: lederhosen
-version: !ruby/object:Gem::Version
-  version: 2.0.4
+version: !ruby/object:Gem::Version 
+  hash: 5
   prerelease: 
+  segments: 
+  - 2
+  - 0
+  - 5
+  version: 2.0.5
 platform: ruby
-authors:
+authors: 
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-25 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: dna
-  requirement: !ruby/object:Gem::Requirement
+
+date: 2013-01-27 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
   type: :runtime
+  name: dna
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: progressbar
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 47
+        segments: 
+        - 0
+        - 12
+        - 0
         version: 0.12.0
   type: :runtime
+  name: progressbar
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.12.0
-- !ruby/object:Gem::Dependency
-  name: thor
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 95
+        segments: 
+        - 0
+        - 16
+        - 0
         version: 0.16.0
   type: :runtime
+  name: thor
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.16.0
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
   type: :development
+  name: rdoc
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - "="
+      - !ruby/object:Gem::Version 
+        hash: 63
+        segments: 
+        - 1
+        - 8
+        - 4
         version: 1.8.4
   type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+  name: jeweler
+  version_requirements: *id005
 description: Various tools for OTU clustering
 email: harekrishna@gmail.com
-executables:
+executables: 
 - lederhosen
 extensions: []
-extra_rdoc_files:
+
+extra_rdoc_files: 
 - LICENSE.txt
-files:
+files: 
 - .rspec
 - Gemfile
 - LICENSE.txt
@@ -134,31 +138,37 @@ files:
 - spec/spec_helper.rb
 - spec/uc_parser_spec.rb
 homepage: http://audy.github.com/lederhosen
-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
-      version: '0'
-      segments:
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
       - 0
-      hash: -4055931160934268209
-required_rubygems_version: !ruby/object:Gem::Requirement
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 requirements: []
+
 rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: OTU Clustering
 test_files: []
+