assembly_pipe 0.0.0

data/test/helper.rb

@@ -0,0 +1,19 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'minitest/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'assembly_pipe'
+
+class MiniTest::Unit::TestCase
+end
+
+MiniTest::Unit.autorun

data/test/test_assembly_pipe.rb

@@ -0,0 +1,38 @@
+require 'helper'
+
+class TestLogFile < MiniTest::Unit::TestCase
+  def setup
+    @file = AssemblyPipe::VelvetOptimiser::LogFile.open("test/data/test_logfile.txt")
+  end
+  
+  def test_open
+    assert_equal AssemblyPipe::VelvetOptimiser::LogFile, @file.class
+  end
+
+  def test_date
+    assert_equal "06/24", @file.date.strftime("%m/%d") 
+  end
+
+  def test_velveth_runs
+    assert_equal 1, @file.velveth_runs.first["Assembly id"]
+    assert_equal 25, @file.velveth_runs.first["Velvet hash value"]
+    assert_equal 1150179650, @file.velveth_runs.first["Roadmap file size"]
+    assert_equal 20, @file.velveth_runs.count
+  end
+
+  def test_vanilla_velvetg_runs
+    assert_equal 3057, @file.vanilla_velvetg_runs.first['Assembly score']
+    assert_equal 30018, @file.vanilla_velvetg_runs.first['length of longest contig']
+    assert_equal 8787270, @file.vanilla_velvetg_runs.to_a.last['Total bases in contigs']
+  end
+
+  def test_final_assembly
+    assert_equal 3, @file.final_assembly['Assembly id']
+    assert_equal 28278189, @file.final_assembly['Assembly score']
+    assert_equal 28278189, @file.final_assembly['Total bases in contigs > 1k']
+  end
+
+  def test_summary_table
+    File.open("test/test.txt", 'w'){|f| f.puts @file.summary_table }
+  end
+end

metadata

@@ -0,0 +1,127 @@
+--- !ruby/object:Gem::Specification 
+name: assembly_pipe
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.0
+platform: ruby
+authors: 
+- robsyme
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-07-07 00:00:00 +08:00
+default_executable: assembly_pipe
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: minitest
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: yard
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 0.6.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.6.2
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+description: A sketch that may not see the light of day assembly pipeline and report generation
+email: rob.syme@gmail.com
+executables: 
+- assembly_pipe
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- assembly_pipe.gemspec
+- bin/assembly_pipe
+- lib/assembly_pipe.rb
+- lib/queue/word_analyzer.rb
+- test/data/test_logfile.txt
+- test/helper.rb
+- test/test_assembly_pipe.rb
+has_rdoc: true
+homepage: http://github.com/robsyme/assembly_pipe
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -149426781813587154
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.5.0
+signing_key: 
+specification_version: 3
+summary: Generating reports from genome assemblies
+test_files: []
+