assemblotron 0.0.2

data/test/helper.rb

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+require 'simplecov'
+require 'coveralls'
+
+SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
+  SimpleCov::Formatter::HTMLFormatter,
+  Coveralls::SimpleCov::Formatter
+]
+SimpleCov.start
+
+require 'minitest/autorun'
+begin; require 'turn/autorun'; rescue LoadError; end
+require 'shoulda-context'
+require 'assemblotron'
+
+Turn.config.format = :pretty
+Turn.config.trace = 1

data/test/test_installer.rb

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+require 'helper'
+
+class TestInstaller < Test::Unit::TestCase
+
+  context 'Installer' do
+
+    setup do
+      @c = Assemblotron::Controller.new
+      @c.init_settings
+    end
+
+    should 'expect a YAML set of download sources for an assembler' do
+
+      assert_equal 1, 2
+    end
+
+    should 'download the appropriate version for the host system' do
+      assert_equal 1, 2
+    end
+
+    should 'install missing assemblers and make them available in PATH' do
+      assert_equal 1, 2
+    end
+
+  end # context
+
+end # TestInstaller

data/test/test_sample.rb

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+require 'helper'
+
+class TestSample < Test::Unit::TestCase
+
+  context 'Sample' do
+
+    setup do
+      datadir = File.join(File.dirname(__FILE__), 'data')
+      datadir = File.absolute_path datadir
+      l = File.join(datadir, 'thousand_reads_l.fq') 
+      r = File.join(datadir, 'thousand_reads_r.fq')
+      @sample = Assemblotron::Sample.new(l, r)
+    end
+
+    should 'subsample the specified number of reads' do
+      ns = [50, 100, 200, 500]
+      ns.each do |n|
+        l, r = @sample.subsample n
+        actual_n_l = `wc -l #{l}`.to_i / 4
+        actual_n_r = `wc -l #{r}`.to_i / 4
+        assert_equal n, actual_n_l, "left read subsample size should be #{n}"
+        assert_equal n, actual_n_r, "right read subsample size should be #{n}"
+      end
+    end
+
+  end # context
+
+end # TestSample

data/test/test_soap_denovo_trans.rb

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+require 'helper'
+
+class TestSoapDenovoTrans < Test::Unit::TestCase
+
+  context "SoapDenovoTrans constructor" do
+
+    setup do
+      @c = Assemblotron::Controller.new
+      @c.init_settings
+      @t = Biopsy::Target.new
+      @t.load_by_name 'soap_denovo_trans'
+      @s = SoapDenovoTrans.new
+      @params = { 
+        :readformat => 'fastq',
+        :insertsize => '200',
+        :l => 'l.fq',
+        :r => 'r.fq',
+        :path => 'SOAPdenovo-Trans',
+        :memory => 12,
+        :threads => 8,
+        :out => 1,
+      }
+    end
+
+    should "construct a valid command" do
+      params = {
+        :K => 1,
+        :d => 2,
+        :M => 9,
+        :F => true,
+        :L => 200,
+        :u => false,
+        :e => 6,
+        :t => 6
+      }
+      @params.merge! params
+      expected = "SOAPdenovo-Trans all -s soapdt.config"
+      expected += " -a 12 -o 1 -p 8 -K 1 -d 2 -F -M 9 -L 200"
+      expected += " -e 6 -t 6 -G 50"
+      assert_equal expected, @s.construct_command(@params)
+    end
+
+    should "automatically include defaults" do
+      expected = "SOAPdenovo-Trans all -s soapdt.config"
+      expected += " -a 12 -o 1 -p 8 -K 23 -d 0 -F -M 1"
+      expected += " -L 100 -e 2 -t 5 -G 50"
+      assert_equal expected, @s.construct_command(@params)
+    end
+
+  end # SoapDenovoTrans constructor context
+
+end # TestSoapDenovoTrans

metadata

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+--- !ruby/object:Gem::Specification
+name: assemblotron
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- Richard Smith
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.1'
+- !ruby/object:Gem::Dependency
+  name: biopsy
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.1.8
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.1.8
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: transrate
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.0.12
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.0.12
+- !ruby/object:Gem::Dependency
+  name: RubyInline
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: turn
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.7
+description: 
+email: rds45@cam.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- README.md
+- Rakefile
+- lib/assemblotron.rb
+- lib/assemblotron/assemblers/constructors/abyss.rb
+- lib/assemblotron/assemblers/constructors/read_joiner.rb
+- lib/assemblotron/assemblers/constructors/sga.rb
+- lib/assemblotron/assemblers/constructors/soap_denovo_trans.rb
+- lib/assemblotron/assemblers/constructors/velvet_oases.rb
+- lib/assemblotron/assemblers/soap_denovo_trans.rb
+- lib/assemblotron/assemblers/soap_denovo_trans.yml
+- lib/assemblotron/objectives/assembly_score.rb
+- lib/assemblotron/sample.rb
+- lib/assemblotron/system.rb
+- lib/assemblotron/version.rb
+- test/data/subset.thousand_reads_l.fq
+- test/data/subset.thousand_reads_r.fq
+- test/data/thousand_reads_l.fq
+- test/data/thousand_reads_r.fq
+- test/helper.rb
+- test/test_installer.rb
+- test/test_sample.rb
+- test/test_soap_denovo_trans.rb
+homepage: https://github.com/blahah/assemblotron
+licenses: []
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: automatically produce *optimal* assemblies from DNA/RNA sequencing reads
+test_files: []
+has_rdoc: