lederhosen 0.5.6 → 0.5.7

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "0.5.6"
+  s.version = "0.5.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-09-05"
+  s.date = "2012-09-17"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/tasks/cluster.rb

@@ -16,6 +16,7 @@ module Lederhosen
     method_option :maxaccepts,  :type => :numeric, :default  => 1
     method_option :maxrejects,  :type => :numeric, :default  => 8
     method_option :lib,         :type => :string
+    method_option :libonly,     :type => :boolean, :default  => false
 
     def cluster
       identity   = options[:identity]
@@ -26,6 +27,7 @@ module Lederhosen
       maxrejects = options[:maxrejects]
       wordlen    = options[:wordlen]
       lib        = options[:lib]
+      libonly    = options[:libonly]
 
       ohai "clustering #{input}, saving to #{output}"
 
@@ -45,6 +47,7 @@ module Lederhosen
       ]
 
       cmd << "--lib #{lib}" unless lib.nil?
+      cmd << "--libonly" if libonly == true
 
       cmd = cmd.join(' ')
 

data/lib/lederhosen/version.rb

@@ -2,7 +2,7 @@ module Lederhosen
   module Version
     MAJOR = 0
     MINOR = 5
-    PATCH = 6
+    PATCH = 7
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/spec/cli_spec.rb

@@ -22,6 +22,12 @@ describe Lederhosen::CLI do
     $?.success?.should be_true
   end
 
+  it 'should support libonly clustering (w/ maxaccepts and maxrejects too)' do
+    # clustering reads against themselves because there is no reference database
+    # included in specs/data
+    `./bin/lederhosen cluster --input=#{$test_dir}/joined.fasta --output=#{$test_dir}/joined.libonly.uc --lib=#{$test_dir}/joined.fasta --libonly --identity 0.95 --maxaccepts 500 --maxrejects 12`
+  end
+
   it 'should sort reads' do
     `./bin/lederhosen sort --input=#{$test_dir}/joined.fasta --output=#{$test_dir}/sorted.fasta`
     $?.success?.should be_true

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 7
+  hash: 5
   prerelease: 
   segments: 
   - 0
   - 5
-  - 6
-  version: 0.5.6
+  - 7
+  version: 0.5.7
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-09-05 00:00:00 Z
+date: 2012-09-17 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :runtime