lederhosen 0.2.7 → 0.2.8

data/Gemfile

@@ -1,6 +1,16 @@
 source :rubygems
-gemspec
+
+gem 'dna'
+gem 'progressbar'
+gem 'thor'
 
 group :test do
   gem 'rspec'
 end
+
+group :development do
+  gem 'rdoc', '~> 3.12'
+  gem 'bundler'
+  gem 'jeweler'
+  gem 'rcov'
+end

data/Rakefile

@@ -0,0 +1,56 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+
+require './lib/lederhosen/version.rb'
+
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  gem.name = "lederhosen"
+  gem.homepage = "http://github.com/audy/lederhosen"
+  gem.license = "MIT"
+  gem.summary = "OTU Clustering"
+  gem.description = "Various tools for OTU clustering"
+  gem.email = "harekrishna@gmail.com"
+  gem.authors = ["Austin G. Davis-Richardson"]
+  gem.version = Lederhosen::Version::STRING
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+
+  version = Lederhosen::Version::STRING
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "test #{version}"
+  rdoc.rdoc_files.include('readme.md')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/lib/lederhosen/version.rb

@@ -0,0 +1,9 @@
+module Lederhosen
+  module Version
+    MAJOR = 0
+    MINOR = 2
+    PATCH = 8
+
+    STRING = [MAJOR, MINOR, PATCH].join('.')
+  end
+end

data/spec/{pipeline_spec.rb → cli_spec.rb}

@@ -1,8 +1,8 @@
 require 'spec_helper'
 
-describe 'the pipeline' do
+describe Lederhosen::CLI do
 
-  it 'should exist' do
+  it 'should have an executable' do
     `./bin/lederhosen`
     $?.success?.should be_true
   end
@@ -41,7 +41,13 @@ describe 'the pipeline' do
     `./bin/lederhosen split --reads=#{$test_dir}/joined.fasta --clusters=#{$test_dir}/clusters.uc --out-dir=#{$test_dir}/split --min-clst-size=1`
   end
 
-  it 'should name clusters given a taxcollector database'
+  it 'should create a fasta file containing representative reads for each cluster' do
+    `./bin/lederhosen rep_reads --clusters=#{$test_dir}/clusters.uc --joined=#{$test_dir}/filtered.fasta --output=#{$test_dir}/representatives.fasta`
+    $?.success?.should be_true
+  end
+
+  # Need a taxcollector database for this one.
+  it 'should identify clusters given a taxcollector database'
 
   it 'should add names to otu abundance matrix given blat output' do
     level = %w{kingdom domain phylum class order genus speces}.choice

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 25
+  hash: 7
   prerelease: 
   segments: 
   - 0
   - 2
-  - 7
-  version: 0.2.7
+  - 8
+  version: 0.2.8
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,11 +15,10 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-08-03 00:00:00 Z
+date: 2012-08-07 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: dna
-  prerelease: false
+  type: :runtime
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -29,11 +28,11 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: thor
+  name: dna
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :runtime
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -43,11 +42,11 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id002
-- !ruby/object:Gem::Dependency 
   name: progressbar
   prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :runtime
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -57,11 +56,68 @@ dependencies:
         segments: 
         - 0
         version: "0"
-  type: :runtime
   version_requirements: *id003
-description: Cluster 16S rRNA amplicon data sequenced by paired-end Illumina into OTUs. Also, quality control data first!
-email: 
-- harekrishna@gmail.com
+  name: thor
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 31
+        segments: 
+        - 3
+        - 12
+        version: "3.12"
+  version_requirements: *id004
+  name: rdoc
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id005
+  name: bundler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id006
+  name: jeweler
+  prerelease: false
+- !ruby/object:Gem::Dependency 
+  type: :development
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  version_requirements: *id007
+  name: rcov
+  prerelease: false
+description: Various tools for OTU clustering
+email: harekrishna@gmail.com
 executables: 
 - lederhosen
 extensions: []
@@ -69,14 +125,11 @@ extensions: []
 extra_rdoc_files: []
 
 files: 
-- .gitignore
 - .rspec
 - .rvmrc
 - Gemfile
+- Rakefile
 - bin/lederhosen
-- examples/hierarchical_clustering.sh
-- examples/pipeline.sh
-- lederhosen.gemspec
 - lib/lederhosen.rb
 - lib/lederhosen/buffer.rb
 - lib/lederhosen/cli.rb
@@ -96,8 +149,11 @@ files:
 - lib/lederhosen/tasks/uc_filter.rb
 - lib/lederhosen/tasks/uc_stats.rb
 - lib/lederhosen/tasks/uniquify.rb
-- lib/version.rb
+- lib/lederhosen/version.rb
+- pipelines/hierarchical_clustering.sh
+- pipelines/pipeline.sh
 - readme.md
+- spec/cli_spec.rb
 - spec/data/ILT_L_9_B_001_1.txt.gz
 - spec/data/ILT_L_9_B_001_3.txt.gz
 - spec/data/ILT_L_9_B_002_1.txt.gz
@@ -106,11 +162,10 @@ files:
 - spec/data/otus.csv
 - spec/helpers_spec.rb
 - spec/misc_spec.rb
-- spec/pipeline_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/audy/lederhosen
-licenses: []
-
+licenses: 
+- MIT
 post_install_message: 
 rdoc_options: []
 
@@ -136,19 +191,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: lederhosen
+rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
-summary: 16S rRNA clustering for paired-end Illumina
-test_files: 
-- spec/data/ILT_L_9_B_001_1.txt.gz
-- spec/data/ILT_L_9_B_001_3.txt.gz
-- spec/data/ILT_L_9_B_002_1.txt.gz
-- spec/data/ILT_L_9_B_002_3.txt.gz
-- spec/data/blat.txt
-- spec/data/otus.csv
-- spec/helpers_spec.rb
-- spec/misc_spec.rb
-- spec/pipeline_spec.rb
-- spec/spec_helper.rb
+summary: OTU Clustering
+test_files: []
+

data/.gitignore

@@ -1 +0,0 @@
-*.swp

data/lederhosen.gemspec

@@ -1,24 +0,0 @@
-# -*- encoding: utf-8 -*-
-
-require File.join(File.dirname(__FILE__), 'lib/version')
-
-Gem::Specification.new do |s|
-  s.name        = 'lederhosen'
-  s.version     = Lederhosen::VERSION
-  s.authors     = ["Austin G. Davis-Richardson"]
-  s.email       = ["harekrishna@gmail.com"]
-  s.homepage    = "http://github.com/audy/lederhosen"
-  s.summary     = '16S rRNA clustering for paired-end Illumina'
-  s.description = 'Cluster 16S rRNA amplicon data sequenced by paired-end Illumina into OTUs. Also, quality control data first!'
-
-  s.rubyforge_project = "lederhosen"
-
-  s.files         = `git ls-files`.split("\n")
-  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
-  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
-  s.require_paths = ["lib"]
-
-  s.add_dependency('dna')
-  s.add_dependency('thor')
-  s.add_dependency('progressbar')
-end

data/lib/version.rb

@@ -1,3 +0,0 @@
-module Lederhosen
-  VERSION = '0.2.7'
-end