transrate 1.0.0 → 1.0.1

data/test/test_comp_metrics.rb

@@ -38,7 +38,7 @@ class Tester
   end
 end
 
-class TestCompMetrics2 < Test::Unit::TestCase
+class TestCompMetrics2 < MiniTest::Test
 
 
   context "ComparativeMetrics" do
@@ -122,7 +122,7 @@ class TestCompMetrics2 < Test::Unit::TestCase
           reference = Transrate::Assembly.new(target)
           comp = Transrate::ComparativeMetrics.new(assembly, reference, 1)
           comp.get_reference_hits crbblast
-          assert_raise Transrate::TransrateError do
+          assert_raises Transrate::TransrateError do
             comp.per_query_contig_reference_coverage
           end
         end

data/test/test_contig.rb

@@ -2,7 +2,7 @@ require 'helper'
 require 'bio'
 require 'benchmark'
 
-class TestContig < Test::Unit::TestCase
+class TestContig < MiniTest::Test
 
   context "Contig" do
 

data/test/test_contig_metrics.rb

@@ -1,6 +1,6 @@
 require 'helper'
 
-class TestContigMetrics < Test::Unit::TestCase
+class TestContigMetrics < MiniTest::Test
 
   context "transrate" do
 

data/test/test_inline.rb

@@ -3,7 +3,7 @@
 require 'helper'
 require 'bio'
 
-class TestInline < Test::Unit::TestCase
+class TestInline < MiniTest::Test
 
   context 'transrate' do
 

data/test/test_optimiser.rb

@@ -1,26 +1,26 @@
 require 'helper'
 require 'tmpdir'
 
-class TestOptimiser < Test::Unit::TestCase
+class TestOptimiser < MiniTest::Test
 
   context "Optimiser" do
 
-    setup do
-      @reference = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
-      left = File.join(File.dirname(__FILE__), "data", "sorghum_100.1.fastq")
-      right = File.join(File.dirname(__FILE__), "data", "sorghum_100.2.fastq")
-      @assembly = Transrate::Assembly.new @reference
-      @readmetrics = Transrate::ReadMetrics.new @assembly
-
-      @readmetrics.run(left, right)
-    end
-
     should "get optimal score" do
-      optimiser = Transrate::ScoreOptimiser.new(@assembly, @readmetrics)
-      assert_in_delta 0.1507, optimiser.raw_score.round(4), 0.005
-      optimal, cutoff = optimiser.optimal_score
-      assert_in_delta 0.4529, optimal.round(4), 0.05
-      assert_in_delta 0.5638, cutoff.round(4), 0.04
+      Dir.mktmpdir do |tmpdir|
+        Dir.chdir tmpdir do
+          @reference = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
+          left = File.join(File.dirname(__FILE__), "data", "sorghum_100.1.fastq")
+          right = File.join(File.dirname(__FILE__), "data", "sorghum_100.2.fastq")
+          @assembly = Transrate::Assembly.new @reference
+          @readmetrics = Transrate::ReadMetrics.new @assembly
+          @readmetrics.run(left, right)
+          optimiser = Transrate::ScoreOptimiser.new(@assembly, @readmetrics)
+          assert_in_delta 0.1507, optimiser.raw_score.round(4), 0.005
+          optimal, cutoff = optimiser.optimal_score
+          assert_in_delta 0.4529, optimal.round(4), 0.05
+          assert_in_delta 0.5638, cutoff.round(4), 0.04
+        end
+      end
     end
 
   end

data/test/test_read_metrics.rb

@@ -1,7 +1,7 @@
 require 'helper'
 require 'tmpdir'
 
-class TestReadMetrics < Test::Unit::TestCase
+class TestReadMetrics < MiniTest::Test
 
   context "ReadMetrics" do
 

data/test/test_salmon.rb

@@ -1,7 +1,7 @@
 require 'helper'
 require 'tmpdir'
 
-class TestSalmon < Test::Unit::TestCase
+class TestSalmon < MiniTest::Test
 
   context "Salmon" do
 

data/test/test_snap.rb

@@ -1,7 +1,7 @@
 require 'helper'
 require 'tmpdir'
 
-class TestSnap < Test::Unit::TestCase
+class TestSnap < MiniTest::Test
 
   context "Snap" do
 

data/test/test_transrate.rb

@@ -2,7 +2,7 @@
 
 require 'helper'
 
-class TestTransrate < Test::Unit::TestCase
+class TestTransrate < MiniTest::Test
 
   context "transrate" do
 

data/test/test_transrater.rb

@@ -3,7 +3,7 @@
 require 'helper'
 require 'tmpdir'
 
-class TestTransrater < Test::Unit::TestCase
+class TestTransrater < MiniTest::Test
 
   context "transrater" do
 
@@ -20,7 +20,7 @@ class TestTransrater < Test::Unit::TestCase
     end
 
     should "raise error when assembly input is nil" do
-      assert_raise Transrate::TransrateError do
+      assert_raises Transrate::TransrateError do
         rater = Transrate::Transrater.new(nil, @reference)
       end
     end

data/test/vagrant/centos_6.5_64/Vagrantfile

@@ -0,0 +1,122 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "chef/centos-6.5"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { mysql_password: "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end

data/test/vagrant/debian_7.4_64/Vagrantfile

@@ -0,0 +1,126 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "chef/debian-7.4"
+
+  # Provision the virtual machine with a local script, provision.sh,
+  # in the same directory as the Vagrantfile
+  config.vm.provision "shell", path: "provision.sh"	
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { mysql_password: "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end

data/test/vagrant/debian_7.4_64/provision.sh

@@ -0,0 +1,28 @@
+su vagrant
+
+# Setup
+sudo apt-get update -y
+sudo apt-get install -y curl build-essential git zlib1g zlib1g-dev cmake
+
+# Install a multi-user RVM install with the latest ruby
+sudo gpg --keyserver hkp://keys.gnupg.net --recv-keys D39DC0E3
+\curl -sSL https://get.rvm.io | bash -s stable --ruby
+source /usr/local/rvm/scripts/rvm
+
+# Add user to RVM group
+sudo usermod -a -G rvm vagrant
+
+# Install transrate
+git clone https://github.com/Blahah/transrate.git
+cd transrate
+sudo chmod -R 777 .
+
+# Install transrate-tools
+cd ..
+git clone https://github.com/Blahah/transrate-tools.git
+
+# Install dependencies
+gem install bundler rake
+bundle install
+bundle exec rake compile
+bundle exec bin/transrate --install-deps

data/test/vagrant/fedora_20_64/Vagrantfile

@@ -0,0 +1,122 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "box-cutter/fedora20"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { mysql_password: "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end