mspire-mascot-dat 0.0.1

data/spec/mspire/mascot/dat_spec.rb

@@ -0,0 +1,94 @@
+require 'spec_helper'
+
+require 'mspire/mascot/dat'
+
+describe 'dat file can be open for reading with block' do
+  let(:file) { TESTFILES + '/F004129.dat' }
+
+  specify '#open(file)' do
+    Mspire::Mascot::Dat.open(file) do |dat|
+      dat.should be_a(Mspire::Mascot::Dat)
+    end
+  end
+end
+
+describe 'reading a dat file' do
+  before(:each) do
+    @file = TESTFILES + '/F004129.dat'
+    @io = File.open(@file)
+    @dat = Mspire::Mascot::Dat.new(@io)
+  end
+
+  after(:each) do
+    @io.close
+  end
+
+  it 'knows all the sections, with queries grouped' do
+    @dat.sections.should == [:parameters, :masses, :unimod, :enzyme, :header, :summary, :decoy_summary, :peptides, :decoy_peptides, :proteins, :index, :queries]
+  end
+
+  it 'can retrieve queries at random' do
+    @dat.query(1).title.should == '1.2746.2746.2'
+    @dat.query(2).title.should == '1.2745.2745.4'
+  end
+
+  it 'can retrieve every peptide' do
+    start = [ [1,1,'VMLSDADPSLEQYYVNVR'], 
+      [2,1,'MDSSSGSQGNGSFMDQNSLGILNMDNLK'],
+      [2,2,'STGAESSEEXLREAYIMASVEHVNLLK'],
+      [2,3,'LSSPPSTSHTYEGKLLTKPTHTNTDLR'],
+      [2,4,'MDSSSGSQGNGSFMDQNSLGILNMDNLK']]
+
+    last = [2,10,'NGSSVAGTSVLSPSIPLTLVVLPALMIAQK']
+
+    last_pep = nil
+    @dat.each_peptide do |peptide|
+      last_pep = peptide
+      (qnum, pnum, aa) = start.shift
+      if qnum
+        peptide.query_num.should == qnum
+        peptide.peptide_num.should == pnum
+        peptide.seq.should == aa
+      end
+    end
+    (qnum, pnum, aa) = last
+    peptide = last_pep
+    peptide.query_num.should == qnum
+    peptide.peptide_num.should == pnum
+    peptide.seq.should == aa
+
+    # this proves that each_peptide can also return an enumerator if asked
+    cnts = @dat.each_peptide.with_index.map do |peptide,i|
+      peptide.should(be_a(Mspire::Mascot::Dat::Peptide)) && i
+    end
+    cnts.should == (0..10).to_a
+  end
+
+  it 'can retrieve decoy peptides' do
+    ions_score_target = @dat.each_peptide(true, 1).map do |peptide|
+      peptide.should(be_a(Mspire::Mascot::Dat::Peptide))
+      peptide.peptide_num.should == 1
+      peptide.ions_score
+    end
+    ions_score_target.should == [0.22, 4.11] 
+
+    ions_score_decoy = @dat.each_peptide(false, 1).map do |peptide|
+      peptide.should(be_a(Mspire::Mascot::Dat::Peptide))
+      peptide.peptide_num.should == 1
+      peptide.ions_score
+    end
+    ions_score_decoy.should == [3.52, 4.58]
+  end
+
+  it 'can retrieve just the n peptides' do
+    n = 1
+    cnt = 0
+    @dat.each_peptide(true, n) do |peptide|
+      cnt += 1
+      peptide.should(be_a(Mspire::Mascot::Dat::Peptide))
+      peptide.query_num.should == cnt
+      peptide.peptide_num.should == 1
+    end
+  end
+
+end