sequence_spec.rb in scaffolder-tools-0.1.3

- old
+ new

@@ -1,6 +1,6 @@
-require File.expand_path(File.join(File.dirname(__FILE__),'..','..','spec_helper'))
+require 'spec_helper'
 
 describe Scaffolder::Tool::Sequence do
 
   it "should inherit from Scaffolder::Tool" do
     described_class.superclass.should == Scaffolder::Tool
@@ -9,32 +9,71 @@
   it "should return the description of the tool" do
     desc = "Generate the fasta output for the scaffold"
     described_class.description.should == desc
   end
 
-  describe "execution when correctly instantiated" do
+  describe "command line argument" do
 
-    before(:each) do
-      entries = [{:name => 'seq1', :nucleotides => 'ATGC'}]
+    before do
+      cntg = Sequence.new(:name => 'seq1', :sequence => 'ATGC')
+      @scf_file, @seq_file = generate_scaffold_files([cntg])
+    end
 
-      @scaffold_file = File.new("scaffold",'w').path
-      @sequence_file = File.new("sequence",'w').path
+    subject do
+      Bio::FastaFormat.new(
+        StringIO.new(
+          described_class.new(
+            MockSettings.new(
+              @scf_file.path,
+              @seq_file.path,
+              settings)).execute).string)
+    end
 
-      write_scaffold_file(entries,@scaffold_file)
-      write_sequence_file(entries,@sequence_file)
-      settings = mock_command_line_settings(@scaffold_file,@sequence_file,{
-        :definition => nil,:no => nil})
+    describe "empty" do
 
-      tool = described_class.new(settings)
-      @output = StringIO.new(tool.execute)
+      let(:settings) do
+        {}
+      end
+
+      it "should set the fasta definition" do
+        subject.definition.should == ""
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
+
     end
 
-    after(:each) do
-      File.delete @scaffold_file, @sequence_file
+    describe "--definition" do
+
+      let(:settings) do
+        {:definition => 'name'}
+      end
+
+      it "should set the fasta definition" do
+        subject.definition.should == "name"
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
+
     end
 
-    it "should return the expected sequence" do
-      Bio::FlatFile.auto(@output).first.seq.should == 'ATGC'
+    describe "--with-sequence-digest" do
+      let(:settings) do
+        {:"with-sequence-digest" => true}
+      end
+
+      it "should set the fasta definition" do
+        header = "[sha1=627a3d8eb465be91696114803b3410ca92f59cc7]"
+        subject.definition.should == header
+      end
+
+      it "should return the expected sequence" do
+        subject.seq.should == 'ATGC'
+      end
     end
 
   end
 
 end