spec/trimmer_spec.rb in lederhosen-1.6.2 vs spec/trimmer_spec.rb in lederhosen-1.7.0

@@ -1,16 +1,52 @@
 require 'spec_helper'
 
 describe Lederhosen::Trimmer do
 
-  describe Lederhosen::Trimmer::PairedTrimmer do
+  describe Lederhosen::Trimmer::PairedTrimmer
 
+  describe Lederhosen::Trimmer::ProbabilityTrimmer do
+    let :sequence_trimmer do
+      # default cutoff should be 0.005
+      Lederhosen::Trimmer::ProbabilityTrimmer.new :seq_tech => :illumina
+    end
+
+    it 'can be created' do
+      sequence_trimmer.should_not be_nil
+    end
+
+    it 'trims records as expected'
+
   end
 
+  describe Lederhosen::Trimmer::HuangTrimmer do
+
+    let :sequence_trimmer do
+      Lederhosen::Trimmer::HuangTrimmer.new(:offset => 64, :min => 20)
+    end
+
+    it 'trims records as expected' do
+
+      trimmed_sizes = File.readlines('spec/data/trimmed_sizes.txt').map &:to_i
+
+      File.open('spec/data/example.fastq') do |handle|
+        records = Dna.new handle
+        records.each do |record|
+          trimmed_record = sequence_trimmer.trim_seq record
+          trimmed_record.size.should == trimmed_sizes.shift
+        end
+      end
+    end
+
+  end
+
   describe Lederhosen::Trimmer::QSEQTrimmer do
 
-    let(:qseq_trimmer) { Lederhosen::Trimmer::QSEQTrimmer.new 'spec/data/ILT_L_9_B_001_1.txt.gz', 'spec/data/ILT_L_9_B_001_3.txt.gz' }
+    let :qseq_trimmer do
+      Lederhosen::Trimmer::QSEQTrimmer.new 'spec/data/ILT_L_9_B_001_1.txt.gz',
+                                           'spec/data/ILT_L_9_B_001_3.txt.gz'
+    end
 
     it 'can be initialized' do
       qseq_trimmer.should_not be_nil
     end
 
@@ -25,10 +61,12 @@
     end
   end
 
   describe Lederhosen::Trimmer::InterleavedTrimmer do
 
-    let(:interleaved_trimmer) { Lederhosen::Trimmer::InterleavedTrimmer.new 'spec/data/example.fastq' }
+    let :interleaved_trimmer do
+      Lederhosen::Trimmer::InterleavedTrimmer.new 'spec/data/example.fastq'
+    end
 
     it 'can be initialized' do
       interleaved_trimmer.should_not be_nil
     end