scaffolder-test-helpers 0.2.2 → 0.3.0

data/Rakefile

@@ -25,6 +25,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{Useful Helper methods and classes for testing scaffolder.}
   gem.email = "mail@michaelbarton.me.uk"
   gem.authors = ["Michael Barton"]
+  gem.test_files = Dir['spec/**/*.rb']
 end
 Jeweler::RubygemsDotOrgTasks.new
 

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.3.0

data/lib/scaffolder/test/sequence.rb

@@ -22,16 +22,43 @@ module Scaffolder::Test
       end
     end
 
+    def inserts(arg = nil)
+      return @options[:inserts] if arg.nil?
+      @options[:inserts] ||= Array.new
+      if arg.instance_of?(Array)
+       arg.each {|a| @options[:inserts] << a}
+      else
+        @options[:inserts] << arg
+      end
+      return self
+    end
+
     def to_hash
-      hash = {'source' => name}
-      [:start,:stop,:reverse].each do |attribute|
-        hash[attribute.to_s] = @options[attribute] if @options[attribute]
+      hash = {'source' => name}.merge stringify_keys(@options)
+      if @options[:inserts]
+        hash['inserts'] = Array.new
+        @options[:inserts].each_with_index do |insert,i|
+          hash['inserts'] << {'source' => "insert#{i+1}"}.merge(stringify_keys(insert))
+        end
       end
       {'sequence' => hash}
     end
 
     def to_fasta
-      Bio::Sequence.new(sequence).output(:fasta,:header => name).strip
+      fasta = Bio::Sequence.new(sequence).output(:fasta,:header => name)
+      inserts.each_with_index do |insert,i|
+        fasta << Bio::Sequence.new(insert[:sequence]).output(:fasta,:header => "insert#{i+1}")
+      end if inserts
+      fasta.strip
+    end
+
+    private
+
+    def stringify_keys(hash)
+      [:start,:stop,:reverse,:open,:close].inject(Hash.new) do |stringified,key|
+        stringified[key.to_s] = hash[key] if hash[key]
+        stringified
+      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 = "0.2.2"
+  s.version = "0.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Michael Barton"]
-  s.date = %q{2011-04-05}
+  s.date = %q{2011-06-02}
   s.description = %q{Useful Helper methods and classes for testing scaffolder.}
   s.email = %q{mail@michaelbarton.me.uk}
   s.extra_rdoc_files = [
@@ -37,12 +37,7 @@ 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/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/sequence_spec.rb

@@ -14,6 +14,92 @@ describe Scaffolder::Test::Sequence do
     its(:to_hash) {should == {'sequence' => {'source' => 'contig1'}} }
   end
 
+  describe "with an insert" do
+
+    describe "added as a hash at initialisation" do
+
+      subject do
+        described_class.new(:name => 'contig1',:sequence => 'ATGCCC',:inserts =>[{
+          :open => 3, :close => 4, :sequence => 'TTT'}])
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+
+      its(:to_fasta){should == ">contig1\nATGCCC\n>insert1\nTTT"}
+      its(:to_hash) {should == {'sequence' => {'source' => 'contig1','inserts' => [{
+        'open' => 3, 'close' => 4, 'source' => 'insert1'}]}} }
+
+    end
+
+    describe "added singularly to an existing contig" do
+
+      subject do
+        contig = described_class.new(:name => 'contig1',:sequence => 'ATGCCC')
+        contig.inserts({:open => 3, :close => 4, :sequence => 'TTT'})
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+
+      its(:to_fasta){should == ">contig1\nATGCCC\n>insert1\nTTT"}
+      its(:to_hash) {should == {'sequence' => {'source' => 'contig1','inserts' => [{
+        'open' => 3, 'close' => 4, 'source' => 'insert1'}]}} }
+
+    end
+
+    describe "added singularly to an existing contig" do
+
+      subject do
+        contig = described_class.new(:name => 'contig1',:sequence => 'ATGCCC')
+        contig.inserts({:open => 3, :close => 4, :sequence => 'TTT'})
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+
+      its(:to_fasta){should == ">contig1\nATGCCC\n>insert1\nTTT"}
+      its(:to_hash) {should == {'sequence' => {'source' => 'contig1','inserts' => [{
+        'open' => 3, 'close' => 4, 'source' => 'insert1'}]}} }
+
+    end
+
+    describe "added as an array to an existing contig" do
+
+      subject do
+        contig = described_class.new(:name => 'contig1',:sequence => 'ATGCCC')
+        contig.inserts([{:open => 3, :close => 4, :sequence => 'TTT'}])
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+
+      its(:to_fasta){should == ">contig1\nATGCCC\n>insert1\nTTT"}
+      its(:to_hash) {should == {'sequence' => {'source' => 'contig1','inserts' => [{
+        'open' => 3, 'close' => 4, 'source' => 'insert1'}]}} }
+
+    end
+
+    describe "added to an existing contig with one insert" do
+
+      subject do
+        contig = described_class.new(:name => 'contig1',:sequence => 'ATGCCC',
+          :inserts =>[{:open => 3, :close => 4, :sequence => 'TTT'}])
+        contig.inserts([{:open => 3, :close => 4, :sequence => 'TTT'}])
+      end
+
+      its(:name)    {should == 'contig1'}
+      its(:sequence){should == 'ATGCCC'}
+
+      its(:to_fasta){should == ">contig1\nATGCCC\n>insert1\nTTT\n>insert2\nTTT"}
+      its(:to_hash) {should == {'sequence' => {'source' => 'contig1','inserts' => [
+          {'open' => 3, 'close' => 4, 'source' => 'insert1'},
+          {'open' => 3, 'close' => 4, 'source' => 'insert2'}
+      ]}}}
+
+    end
+  end
+
   [:start,:stop,:reverse].each do |attribute|
 
     describe "instance with #{attribute} attribute" do

metadata

@@ -5,9 +5,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 2
-  - 2
-  version: 0.2.2
+  - 3
+  - 0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Michael Barton
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-05 00:00:00 -04:00
+date: 2011-06-02 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency