specs/sample_enzyme_spec.rb in mspire-0.3.1 vs specs/sample_enzyme_spec.rb in mspire-0.3.9

@@ -31,11 +31,96 @@
   it 'contains duplicates IF there are duplicate tryptic sequences' do
     st = "AAAAKCCCCKDDDDKCCCCK"
     peps = SampleEnzyme.new('trypsin').digest(st, 2)
     peps.select {|aaseq| aaseq == 'CCCCK'}.size.should == 2
   end
-
   
 end
+
+describe SampleEnzyme, 'making enzyme calculations on sequences and aaseqs' do
+
+  before(:each) do
+    @full_KRP = SampleEnzyme.new do |se|
+      se.name = 'trypsin'
+      se.cut = 'KR'
+      se.no_cut = 'P'
+      se.sense = 'C'
+    end
+    @just_KR = SampleEnzyme.new do |se|
+      se.name = 'trypsin'
+      se.cut = 'KR'
+      se.no_cut = ''
+      se.sense = 'C'
+    end
+  end
+
+  it 'calculates the number of tolerant termini' do
+    exp = [{
+      # full KR/P
+      'K.EPTIDR.E' => 2,
+      'K.PEPTIDR.E' => 1,
+      'F.EEPTIDR.E' => 1,
+      'F.PEPTIDW.R' => 0,
+    },
+    {
+      # just KR
+      'K.EPTIDR.E' => 2,
+      'K.PEPTIDR.E' => 2,
+      'F.EEPTIDR.E' => 1,
+      'F.PEPTIDW.R' => 0,
+    }
+    ]
+    scall = Sequest::PepXML::SearchHit
+    sample_enzyme_ar = [@full_KRP, @just_KR]
+    sample_enzyme_ar.zip(exp) do |sample_enzyme,hash|
+      hash.each do |seq, val|
+        sample_enzyme.num_tol_term(seq).should == val
+      end
+    end
+  end
+
+  it 'calculates number of missed cleavages' do
+    exp = [{
+    "EPTIDR" => 0,
+    "PEPTIDR" => 0,
+    "EEPTIDR" => 0,
+    "PEPTIDW" => 0,
+    "PERPTIDW" => 0,
+    "PEPKPTIDW" => 0,
+    "PEPKTIDW" => 1,
+    "RTTIDR" => 1,
+    "RTTIKK" => 2,
+    "PKEPRTIDW" => 2,
+    "PKEPRTIDKP" => 2,
+    "PKEPRAALKPEERPTIDKW" => 3,
+    },
+    {
+    "EPTIDR" => 0,
+    "PEPTIDR" => 0,
+    "EEPTIDR" => 0,
+    "PEPTIDW" => 0,
+    "PERPTIDW" => 1,
+    "PEPKPTIDW" => 1,
+    "PEPKTIDW" => 1,
+    "RTTIDR" => 1,
+    "RTTIKK" => 2,
+    "PKEPRTIDW" => 2,
+    "PKEPRTIDKP" => 3,
+    "PKEPRAALKPEERPTIDKW" => 5,
+    }
+    ]
+
+    sample_enzyme_ar = [@full_KRP, @just_KR]
+    sample_enzyme_ar.zip(exp) do |sample_enzyme, hash|
+      hash.each do |aaseq, val|
+        #first, middle, last = SpecID::Pep.split_sequence(seq)
+        # note that we are only using the middle section!
+        sample_enzyme.num_missed_cleavages(aaseq).should == val
+      end
+    end
+  end
+
+end
+