scaffolder-test-helpers 0.3.0 → 0.4.0

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

data/lib/scaffolder/test/annotation.rb

@@ -0,0 +1,34 @@
+require 'scaffolder'
+
+module Scaffolder::Test
+  class Annotation
+
+    [:seqname,:start,:end,:strand,:phase,:feature].each do |attribute|
+      define_method(attribute) do |*arg|
+        unless arg.first
+          return @options[attribute]
+        end
+        @options[attribute] = arg.first
+        return self
+      end
+    end
+
+    def initialize(options = Hash.new)
+      defaults = {:seqname => 'record', :start => 1, :end     => 10,
+                  :strand  => '+',      :phase => 1, :feature => 'CDS'}
+      @options = defaults.merge(options)
+    end
+
+    def initialize_copy(source)
+      super
+      @options = @options.dup
+    end
+
+    def to_gff3_record
+      Bio::GFF::GFF3::Record.new(
+        self.seqname, nil, self.feature, self.start,
+        self.end,     nil, self.strand,  self.phase)
+    end
+
+  end
+end

data/lib/scaffolder/test/helpers.rb

@@ -4,6 +4,7 @@ require 'scaffolder'
 
 require 'scaffolder/test/sequence'
 require 'scaffolder/test/unresolved'
+require 'scaffolder/test/annotation'
 
 module Scaffolder::Test
   module Helpers
@@ -28,6 +29,12 @@ module Scaffolder::Test
       file
     end
 
+    def generate_gff3_file(records,file = Tempfile.new("gff"))
+      gff = Bio::GFF::GFF3.new
+      gff.records = records.map{|r| r.to_gff3_record}
+      File.open(file.path,'w'){|out| out.print(gff) }
+      file
+    end
 
   end
 end

data/scaffolder-test-helpers.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{scaffolder-test-helpers}
-  s.version = "0.3.0"
+  s.version = "0.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Michael Barton"]
-  s.date = %q{2011-06-02}
+  s.date = %q{2011-06-07}
   s.description = %q{Useful Helper methods and classes for testing scaffolder.}
   s.email = %q{mail@michaelbarton.me.uk}
   s.extra_rdoc_files = [
@@ -23,10 +23,12 @@ Gem::Specification.new do |s|
     "README.rdoc",
     "Rakefile",
     "VERSION",
+    "lib/scaffolder/test/annotation.rb",
     "lib/scaffolder/test/helpers.rb",
     "lib/scaffolder/test/sequence.rb",
     "lib/scaffolder/test/unresolved.rb",
     "scaffolder-test-helpers.gemspec",
+    "spec/scaffolder/test/annotation_spec.rb",
     "spec/scaffolder/test/helpers_spec.rb",
     "spec/scaffolder/test/sequence_spec.rb",
     "spec/scaffolder/test/unresolved_spec.rb",
@@ -37,7 +39,7 @@ Gem::Specification.new do |s|
   s.require_paths = ["lib"]
   s.rubygems_version = %q{1.3.7}
   s.summary = %q{Methods and classes for testing scaffolder.}
-  s.test_files = ["spec/scaffolder/test/helpers_spec.rb", "spec/scaffolder/test/sequence_spec.rb", "spec/scaffolder/test/unresolved_spec.rb", "spec/spec_helper.rb"]
+  s.test_files = ["spec/scaffolder/test/annotation_spec.rb", "spec/scaffolder/test/helpers_spec.rb", "spec/scaffolder/test/sequence_spec.rb", "spec/scaffolder/test/unresolved_spec.rb", "spec/spec_helper.rb"]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION

data/spec/scaffolder/test/annotation_spec.rb

@@ -0,0 +1,63 @@
+require File.join(File.dirname(__FILE__),'..','..','spec_helper')
+
+describe Scaffolder::Test::Annotation do
+
+  describe "initialization" do
+
+    context "with all parameters" do
+      subject do
+        described_class.new(
+          :seqname => 'c1', :start => 4, :end     => 6,
+          :strand  => '+',  :phase => 1, :feature => 'CDS')
+      end
+
+      its(:seqname){should == 'c1'}
+      its(:start)  {should == 4}
+      its(:end)    {should == 6}
+      its(:strand) {should == '+'}
+      its(:phase)  {should == 1}
+      its(:feature){should == 'CDS'}
+    end
+
+    context "using default parameters" do
+      subject do
+        described_class.new
+      end
+
+      its(:seqname){should == 'record'}
+      its(:start)  {should == 1}
+      its(:end)    {should == 10}
+      its(:strand) {should == '+'}
+      its(:phase)  {should == 1}
+      its(:feature){should == 'CDS'}
+    end
+
+  end
+
+  describe "#to_gff3_record" do
+
+      subject do
+        described_class.new.to_gff3_record
+      end
+
+      it "should generate a Bio::GFF::GFF3::Record" do
+        expected = Bio::GFF::GFF3::Record.new(
+          subject.seqname, nil, subject.feature, subject.start,
+          subject.end,     nil, subject.strand,  subject.phase)
+        subject.should == expected
+      end
+
+  end
+
+  describe "#clone" do
+
+    it "should duplicate the internal options state" do
+      a = described_class.new
+      b = a.clone
+
+      a.instance_variable_get("@options").
+        should_not equal(b.instance_variable_get("@options"))
+    end
+
+  end
+end

data/spec/scaffolder/test/helpers_spec.rb

@@ -2,70 +2,113 @@ require File.join(File.dirname(__FILE__),'..','..','spec_helper')
 
 describe Scaffolder::Test::Helpers, "#generate_scaffold_files method" do
 
-  describe "pass an array with a single sequence" do
+  describe "#generate_scaffold_files" do
 
-    before(:all) do
-      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG')]
-      @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
-    end
+    context "passed an array with a single sequence" do
 
-    it "should create the corresponding scaffold file" do
-      File.exists?(@scaf_file.path).should be_true
-      scaffold = YAML.load(File.read(@scaf_file.path))
-      scaffold.should == [{'sequence' => {'source' => 'c1'}}]
-    end
+      before(:all) do
+        entries = [Sequence.new(:name => 'c1',:sequence => 'ATG')]
+        @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
+      end
+
+      it "should create the corresponding scaffold file" do
+        File.exists?(@scaf_file.path).should be_true
+        scaffold = YAML.load(File.read(@scaf_file.path))
+        scaffold.should == [{'sequence' => {'source' => 'c1'}}]
+      end
+
+      it "should create the corresponding sequence file" do
+        File.exists?(@seq_file.path).should be_true
+        sequence = File.read(@seq_file.path)
+        sequence.should == ">c1\nATG\n"
+      end
 
-    it "should create the corresponding sequence file" do
-      File.exists?(@seq_file.path).should be_true
-      sequence = File.read(@seq_file.path)
-      sequence.should == ">c1\nATG\n"
     end
 
-  end
+    context "passed an array with two sequences" do
 
-  describe "pass an array with two sequences" do
+      before(:all) do
+        entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
+                   Sequence.new(:name => 'c2',:sequence => 'ATG')]
+        @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
+      end
 
-    before(:all) do
-      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
-                 Sequence.new(:name => 'c2',:sequence => 'ATG')]
-      @scaf_file, @seq_file = described_class.generate_scaffold_files(entries)
-    end
+      it "should create the corresponding scaffold file" do
+        File.exists?(@scaf_file.path).should be_true
+        scaffold = YAML.load(File.read(@scaf_file.path))
+        scaffold.should == [{'sequence' => {'source' => 'c1'}},
+          {'sequence' => {'source' => 'c2'}}]
+      end
+
+      it "should create the corresponding sequence file" do
+        File.exists?(@seq_file.path).should be_true
+        sequence = File.read(@seq_file.path)
+        sequence.should == ">c1\nATG\n>c2\nATG\n"
+      end
 
-    it "should create the corresponding scaffold file" do
-      File.exists?(@scaf_file.path).should be_true
-      scaffold = YAML.load(File.read(@scaf_file.path))
-      scaffold.should == [{'sequence' => {'source' => 'c1'}},
-        {'sequence' => {'source' => 'c2'}}]
     end
 
-    it "should create the corresponding sequence file" do
-      File.exists?(@seq_file.path).should be_true
-      sequence = File.read(@seq_file.path)
-      sequence.should == ">c1\nATG\n>c2\nATG\n"
+    context "passed an array with a sequence and an unresolved region" do
+
+      before(:all) do
+        entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
+                   Unresolved.new(:length => 5)]
+        @scaf_file, @seq_file = generate_scaffold_files(entries)
+      end
+
+      it "should create the corresponding scaffold file" do
+        File.exists?(@scaf_file.path).should be_true
+        scaffold = YAML.load(File.read(@scaf_file.path))
+        scaffold.should == [{'sequence' => {'source' => 'c1'}},
+          {'unresolved' => {'length' => 5}}]
+      end
+
+      it "should create the corresponding sequence file" do
+        File.exists?(@seq_file.path).should be_true
+        sequence = File.read(@seq_file.path)
+        sequence.should == ">c1\nATG\n"
+      end
+
     end
 
   end
 
-  describe "pass an array with a sequence and an unresolved region" do
+  describe "#generate_gff3_file" do
 
-    before(:all) do
-      entries = [Sequence.new(:name => 'c1',:sequence => 'ATG'),
-                 Unresolved.new(:length => 5)]
-      @scaf_file, @seq_file = generate_scaffold_files(entries)
+    subject do
+      described_class.generate_gff3_file(records)
     end
 
-    it "should create the corresponding scaffold file" do
-      File.exists?(@scaf_file.path).should be_true
-      scaffold = YAML.load(File.read(@scaf_file.path))
-      scaffold.should == [{'sequence' => {'source' => 'c1'}},
-        {'unresolved' => {'length' => 5}}]
+    context "passed an empty array" do
+
+      let(:records){ [] }
+
+      it "should create a file" do
+        File.exists?(subject.path).should be_true
+      end
+
+      it "should generate an empty gff3 file" do
+        File.read(subject.path).should == "##gff-version 3\n"
+      end
+
     end
 
-    it "should create the corresponding sequence file" do
-      File.exists?(@seq_file.path).should be_true
-      sequence = File.read(@seq_file.path)
-      sequence.should == ">c1\nATG\n"
+    context "passed an array with a single record" do
+
+      let(:records){ [Annotation.new(
+        :seqname => 'c1', :start => 4, :end => 6, :strand => '+',:phase => 1)] }
+
+      it "should create a file" do
+        File.exists?(subject.path).should be_true
+      end
+
+      it "should generate an empty gff3 file" do
+        record = "c1\t.\tCDS\t4\t6\t.\t+\t1\t.\n"
+        File.read(subject.path).should == "##gff-version 3\n" + record
+      end
+
     end
 
   end
+
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: scaffolder-test-helpers
 version: !ruby/object:Gem::Version 
-  hash: 19
+  hash: 15
   prerelease: false
   segments: 
   - 0
-  - 3
+  - 4
   - 0
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors: 
 - Michael Barton
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-02 00:00:00 -04:00
+date: 2011-06-07 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -124,10 +124,12 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
+- lib/scaffolder/test/annotation.rb
 - lib/scaffolder/test/helpers.rb
 - lib/scaffolder/test/sequence.rb
 - lib/scaffolder/test/unresolved.rb
 - scaffolder-test-helpers.gemspec
+- spec/scaffolder/test/annotation_spec.rb
 - spec/scaffolder/test/helpers_spec.rb
 - spec/scaffolder/test/sequence_spec.rb
 - spec/scaffolder/test/unresolved_spec.rb
@@ -167,6 +169,7 @@ signing_key:
 specification_version: 3
 summary: Methods and classes for testing scaffolder.
 test_files: 
+- spec/scaffolder/test/annotation_spec.rb
 - spec/scaffolder/test/helpers_spec.rb
 - spec/scaffolder/test/sequence_spec.rb
 - spec/scaffolder/test/unresolved_spec.rb