scaffolder-tools 0.1.2 → 0.1.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/.rspec +1 -1
- data/.travis.yml +4 -0
- data/Gemfile +1 -3
- data/README.rdoc +6 -4
- data/Rakefile +3 -2
- data/VERSION +1 -1
- data/features/error_checking.feature +137 -0
- data/features/sequence.feature +30 -73
- data/features/step_definitions/scaffolder-tools.rb +5 -1
- data/features/validate.feature +12 -78
- data/lib/scaffolder/tool/sequence.rb +10 -8
- data/lib/scaffolder/tool_index.rb +0 -7
- data/man/scaffolder-format.7.ronn +127 -0
- data/man/scaffolder-sequence.1.ronn +3 -5
- data/scaffolder-tools.gemspec +16 -30
- data/spec/scaffolder/binary_helper_spec.rb +1 -1
- data/spec/scaffolder/tool/help_spec.rb +64 -74
- data/spec/scaffolder/tool/sequence_spec.rb +55 -16
- data/spec/scaffolder/tool/validate_spec.rb +5 -5
- data/spec/scaffolder/tool_index_spec.rb +1 -1
- data/spec/scaffolder/tool_spec.rb +12 -21
- data/spec/spec_helper.rb +15 -9
- data/spec/support/exit_code_matcher.rb +2 -2
- metadata +120 -214
@@ -1,4 +1,4 @@
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require
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require 'spec_helper'
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describe Scaffolder::Tool::Sequence do
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@@ -11,29 +11,68 @@ describe Scaffolder::Tool::Sequence do
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described_class.description.should == desc
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end
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describe "
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describe "command line argument" do
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before
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before do
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cntg = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
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@scf_file, @seq_file = generate_scaffold_files([cntg])
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end
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subject do
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Bio::FastaFormat.new(
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StringIO.new(
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described_class.new(
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MockSettings.new(
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@scf_file.path,
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@seq_file.path,
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settings)).execute).string)
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end
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-
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@sequence_file = File.new("sequence",'w').path
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describe "empty" do
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-
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-
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-
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let(:settings) do
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{}
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end
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it "should set the fasta definition" do
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subject.definition.should == ""
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end
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it "should return the expected sequence" do
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subject.seq.should == 'ATGC'
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end
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tool = described_class.new(settings)
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@output = StringIO.new(tool.execute)
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end
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-
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-
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describe "--definition" do
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let(:settings) do
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{:definition => 'name'}
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end
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it "should set the fasta definition" do
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subject.definition.should == "name"
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end
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it "should return the expected sequence" do
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subject.seq.should == 'ATGC'
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end
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end
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-
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-
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describe "--with-sequence-digest" do
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let(:settings) do
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{:"with-sequence-digest" => true}
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end
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it "should set the fasta definition" do
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header = "[sha1=627a3d8eb465be91696114803b3410ca92f59cc7]"
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subject.definition.should == header
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end
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it "should return the expected sequence" do
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subject.seq.should == 'ATGC'
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end
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end
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end
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@@ -1,4 +1,4 @@
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require
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require 'spec_helper'
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describe Scaffolder::Tool::Validate do
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@@ -63,7 +63,7 @@ describe Scaffolder::Tool::Validate do
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end
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subject do
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described_class.new(
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described_class.new(MockSettings.new)
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end
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it "should return an empty array when scaffold is valid" do
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@@ -87,7 +87,7 @@ describe Scaffolder::Tool::Validate do
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describe "scaffold validation with no overlapping inserts" do
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subject do
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validate = described_class.new(
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validate = described_class.new(MockSettings.new)
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validate.stubs(:errors).returns([])
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validate
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end
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@@ -105,7 +105,7 @@ describe Scaffolder::Tool::Validate do
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describe "returning errors using the errors method" do
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subject do
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validate = described_class.new(
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validate = described_class.new(MockSettings.new)
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sequence = stub(:source => :seq1)
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validate.stubs(:errors).returns([sequence])
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@@ -133,7 +133,7 @@ describe Scaffolder::Tool::Validate do
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describe "the attributes of the error data" do
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subject do
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validate = described_class.new(
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validate = described_class.new(MockSettings.new)
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@err = {:open => 1,:close => 2,:source => 'some_insert'}
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sequence = stub(:source => 'seq1')
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@@ -1,26 +1,26 @@
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require
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require 'spec_helper'
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describe Scaffolder::Tool do
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describe "initialisation with attributes" do
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before(:each) do
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@settings =
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@settings = MockSettings.new(:fake_scf,:fake_seq)
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end
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subject do
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Scaffolder::Tool.new(@settings)
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end
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its(:scaffold_file){ should == @settings.
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its(:sequence_file){ should == @settings.
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its(:scaffold_file){ should == @settings.scaf_file }
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its(:sequence_file){ should == @settings.seq_file }
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its(:settings){ should == @settings }
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end
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describe "the run method" do
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before(:all) do
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@settings =
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@settings = MockSettings.new
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end
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before(:each) do
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@@ -88,28 +88,28 @@ describe Scaffolder::Tool do
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end
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it "should raise an error if the sequence file is missing" do
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settings =
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settings = MockSettings.new(@scaffold_file,@missing_file)
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tool = Scaffolder::Tool.new(settings)
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lambda{ tool.scaffold }.should raise_error(ArgumentError,
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"Sequence file not found: #{@missing_file}")
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end
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it "should raise an error if the sequence file is empty" do
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settings =
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settings = MockSettings.new(@scaffold_file,@empty_file)
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tool = Scaffolder::Tool.new(settings)
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lambda{ tool.scaffold }.should raise_error(ArgumentError,
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"Sequence file is empty: #{@empty_file}")
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end
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it "should raise an error if the scaffold file is missing" do
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settings =
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settings = MockSettings.new(@missing_file,@sequence_file)
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tool = Scaffolder::Tool.new(settings)
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lambda{ tool.scaffold }.should raise_error(ArgumentError,
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"Scaffold file not found: #{@missing_file}")
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end
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it "should raise an error if the scaffold file is empty" do
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settings =
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settings = MockSettings.new(@empty_file,@sequence_file)
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tool = Scaffolder::Tool.new(settings)
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lambda{ tool.scaffold }.should raise_error(ArgumentError,
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"Scaffold file is empty: #{@empty_file}")
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describe "creating the scaffold with the scaffold method" do
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before(:each) do
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@scaffold_file = File.new('scaffold','w').path
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@sequence_file = File.new('sequence','w').path
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write_scaffold_file(entries,@scaffold_file)
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write_sequence_file(entries,@sequence_file)
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end
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after(:each) do
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File.delete @scaffold_file, @sequence_file
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contig = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
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@scf_file, @seq_file = generate_scaffold_files([contig])
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end
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subject do
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Scaffolder::Tool.new(
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mock_command_line_settings(@scaffold_file,@sequence_file))
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Scaffolder::Tool.new(MockSettings.new(@scf_file.path,@seq_file.path))
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end
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it "should produce the expected sequence scaffold" do
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data/spec/spec_helper.rb
CHANGED
@@ -4,7 +4,6 @@ $LOAD_PATH.unshift(File.dirname(__FILE__))
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require 'tempfile'
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require 'ostruct'
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require 'hashie'
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require 'rspec'
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require 'fakefs/safe'
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require 'mocha'
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RSpec.configure do |config|
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config.mock_with :mocha
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include Scaffolder::Test
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include Scaffolder::Test::Helpers
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def tool_subclasses
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end
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end
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settings = mock
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class MockSettings
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settings.stubs(:scaffold_file).returns(scaf_file)
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attr :scaf_file
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attr :seq_file
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def initialize(scaf_file = nil, seq_file = nil, command_args = {})
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@scaf_file, @seq_file, = scaf_file, seq_file
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@args = command_args
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end
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def rest
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[scaf_file,seq_file]
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end
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def [](arg)
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@args[arg]
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end
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settings
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end
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end
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metadata
CHANGED
@@ -1,267 +1,178 @@
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--- !ruby/object:Gem::Specification
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--- !ruby/object:Gem::Specification
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name: scaffolder-tools
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version: !ruby/object:Gem::Version
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prerelease:
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segments:
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- 0
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- 1
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- 2
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version: 0.1.2
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version: !ruby/object:Gem::Version
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version: 0.1.3
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prerelease:
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platform: ruby
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authors:
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authors:
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- Michael Barton
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autorequire:
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bindir: bin
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cert_chain: []
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requirement: &id001 !ruby/object:Gem::Requirement
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date: 2011-08-13 00:00:00.000000000Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: configliere
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requirement: &2173650600 !ruby/object:Gem::Requirement
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none: false
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requirements:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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segments:
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- 0
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- 1
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version: "0.1"
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- !ruby/object:Gem::Version
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version: '0.1'
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type: :runtime
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name: configliere
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prerelease: false
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version_requirements: *
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- !ruby/object:Gem::Dependency
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-
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version_requirements: *2173650600
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &2173650020 !ruby/object:Gem::Requirement
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none: false
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requirements:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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-
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segments:
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-
- 1
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-
- 4
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version: "1.4"
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- !ruby/object:Gem::Version
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version: '1.4'
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type: :runtime
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name: bio
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prerelease: false
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version_requirements: *
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- !ruby/object:Gem::Dependency
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-
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version_requirements: *2173650020
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- !ruby/object:Gem::Dependency
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name: scaffolder
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requirement: &2173649540 !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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requirements:
|
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- - ~>
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-
- !ruby/object:Gem::Version
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-
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segments:
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-
- 0
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-
- 4
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version: "0.4"
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- !ruby/object:Gem::Version
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version: '0.4'
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type: :runtime
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name: scaffolder
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prerelease: false
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version_requirements: *
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- !ruby/object:Gem::Dependency
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-
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version_requirements: *2173649540
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- !ruby/object:Gem::Dependency
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name: ronn
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requirement: &2173649060 !ruby/object:Gem::Requirement
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none: false
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-
requirements:
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requirements:
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- - ~>
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-
- !ruby/object:Gem::Version
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-
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segments:
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-
- 0
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-
- 7
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version: "0.7"
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- !ruby/object:Gem::Version
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version: '0.7'
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type: :runtime
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name: ronn
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prerelease: false
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version_requirements: *
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- !ruby/object:Gem::Dependency
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requirement: &id005 !ruby/object:Gem::Requirement
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none: false
|
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requirements:
|
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-
- - ~>
|
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- !ruby/object:Gem::Version
|
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hash: 15
|
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segments:
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-
- 1
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-
- 0
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version: "1.0"
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type: :development
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version: '1.0'
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requirement: &id009 !ruby/object:Gem::Requirement
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version: '2.4'
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type: :development
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name: cucumber
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version: '0.10'
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type: :development
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name: fakefs
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requirement: &2173646340 !ruby/object:Gem::Requirement
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segments:
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version: '0.2'
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version: '0.2'
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name: mocha
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requirements:
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version: "0.4"
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version: '0.9'
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type: :development
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name: hashie
|
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name: yard
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requirement: &2173644660 !ruby/object:Gem::Requirement
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version: "0.6"
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name: yard
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version_requirements: *2173644660
|
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|
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name: scaffolder-test-helpers
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requirement: &2173644100 !ruby/object:Gem::Requirement
|
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version: '0.4'
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type: :development
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name: scaffolder-test-helpers
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prerelease: false
|
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version_requirements: *
|
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version_requirements: *2173644100
|
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|
description: Binary to use with scaffolder genome scaffolds
|
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|
-
email: mail@
|
249
|
-
executables:
|
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+
email: mail@next.gs
|
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+
executables:
|
250
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|
- scaffolder
|
251
161
|
extensions: []
|
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|
-
|
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|
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extra_rdoc_files:
|
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extra_rdoc_files:
|
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163
|
- LICENSE.txt
|
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164
|
- README.rdoc
|
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|
-
files:
|
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files:
|
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- .document
|
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- .rspec
|
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- .travis.yml
|
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- Gemfile
|
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- LICENSE.txt
|
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171
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- README.rdoc
|
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|
- Rakefile
|
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|
- VERSION
|
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174
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- bin/scaffolder
|
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- features/error_checking.feature
|
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176
|
- features/help.feature
|
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|
- features/sequence.feature
|
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|
- features/step_definitions/scaffolder-tools.rb
|
@@ -273,6 +184,7 @@ files:
|
|
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|
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|
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- lib/scaffolder/tool/validate.rb
|
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|
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+
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|
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|
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|
277
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|
- man/scaffolder-sequence.1.ronn
|
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190
|
- man/scaffolder-validate.1.ronn
|
@@ -285,41 +197,35 @@ files:
|
|
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197
|
- spec/scaffolder/tool_spec.rb
|
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|
- spec/spec_helper.rb
|
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199
|
- spec/support/exit_code_matcher.rb
|
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|
-
|
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|
-
|
290
|
-
licenses:
|
200
|
+
homepage: http://next.gs
|
201
|
+
licenses:
|
291
202
|
- MIT
|
292
203
|
post_install_message:
|
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204
|
rdoc_options: []
|
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|
-
|
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|
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require_paths:
|
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|
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require_paths:
|
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|
- lib
|
297
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required_ruby_version: !ruby/object:Gem::Requirement
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required_ruby_version: !ruby/object:Gem::Requirement
|
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|
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|
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- -
|
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|
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segments:
|
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requirements:
|
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|
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|
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|
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|
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version: '0'
|
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|
+
segments:
|
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|
- 0
|
305
|
-
|
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|
-
required_rubygems_version: !ruby/object:Gem::Requirement
|
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|
+
hash: 2501104196888492226
|
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|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
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none: false
|
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requirements:
|
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- -
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
+
version: '0'
|
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|
requirements: []
|
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|
-
|
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223
|
rubyforge_project:
|
318
|
-
rubygems_version: 1.
|
224
|
+
rubygems_version: 1.8.6
|
319
225
|
signing_key:
|
320
226
|
specification_version: 3
|
321
227
|
summary: Tools for manipulating genome scaffolds
|
322
|
-
test_files:
|
228
|
+
test_files:
|
323
229
|
- spec/scaffolder/binary_helper_spec.rb
|
324
230
|
- spec/scaffolder/tool/help_spec.rb
|
325
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|
- spec/scaffolder/tool/sequence_spec.rb
|