lederhosen 2.0.5 → 2.0.6

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "2.0.5"
+  s.version = "2.0.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2013-01-27"
+  s.date = "2013-02-27"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]
@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
     "lib/lederhosen/tasks/version.rb",
     "lib/lederhosen/uc_parser.rb",
     "lib/lederhosen/version.rb",
+    "logo.png",
     "readme.md",
     "scripts/illumina_pipeline/.gitignore",
     "scripts/illumina_pipeline/Makefile",

data/lib/lederhosen/tasks/otu_table.rb

@@ -39,7 +39,11 @@ module Lederhosen
             if taxonomy == 'unclassified_reads'
               'unclassified_reads'
             else
-              parse_taxonomy(taxonomy)[level]
+              if level == 'original'
+                taxonomy
+              else
+                parse_taxonomy(taxonomy)[level]
+              end
             end
           sample_cluster_count[input_file][tax] += count
         end

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 2
     MINOR = 0
     CODENAME = 'Schnittlauchbrot' # changes for minor versions
-    PATCH = 5
+    PATCH = 6
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -1,4 +1,4 @@
-<img src="http://d.pr/i/26Js+#.png" align="right">
+<img src="https://raw.github.com/audy/lederhosen/master/logo.png" align="right">
 
 # Lederhosen
 
@@ -51,6 +51,10 @@ using paired and non-paired end short reads such as those produced by Illumina (
     `sudo gem install lederhosen`
 4. Check installation by typing `lederhosen`. You should see some help text.
 
+### Need Help?
+
+Bug me: [@heyaudy](http://twitter.com/heyaudy) (twitter)
+
 ## Tasks
 
 Lederhosen is invoked by typing `lederhosen [TASK]`

metadata

@@ -1,108 +1,104 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: lederhosen
-version: !ruby/object:Gem::Version 
-  hash: 5
+version: !ruby/object:Gem::Version
+  version: 2.0.6
   prerelease: 
-  segments: 
-  - 2
-  - 0
-  - 5
-  version: 2.0.5
 platform: ruby
-authors: 
+authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-01-27 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+date: 2013-02-27 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: dna
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  name: dna
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 47
-        segments: 
-        - 0
-        - 12
-        - 0
+    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
         version: 0.12.0
   type: :runtime
-  name: progressbar
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 95
-        segments: 
-        - 0
-        - 16
-        - 0
+    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
         version: 0.16.0
   type: :runtime
-  name: thor
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  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
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 31
-        segments: 
-        - 3
-        - 12
-        version: "3.12"
+      - !ruby/object:Gem::Version
+        version: '3.12'
   type: :development
-  name: rdoc
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  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
     none: false
-    requirements: 
-    - - "="
-      - !ruby/object:Gem::Version 
-        hash: 63
-        segments: 
-        - 1
-        - 8
-        - 4
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
-  name: jeweler
-  version_requirements: *id005
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 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
@@ -124,6 +120,7 @@ files:
 - lib/lederhosen/tasks/version.rb
 - lib/lederhosen/uc_parser.rb
 - lib/lederhosen/version.rb
+- logo.png
 - readme.md
 - scripts/illumina_pipeline/.gitignore
 - scripts/illumina_pipeline/Makefile
@@ -138,37 +135,31 @@ 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 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: -902984509893215788
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: OTU Clustering
 test_files: []
-