ms-sequest 0.1.2 → 0.2.1

data/spec/ms/sequest/bioworks_spec.rb

@@ -1,153 +0,0 @@
-
-# TODO work on this guy!
-=begin
-
-require File.expand_path( File.dirname(__FILE__) + '/../tap_spec_helper' )
-
-require 'spec_id'
-require 'spec_id/bioworks'
-#require 'benchmark'
-
-describe Bioworks, 'set from an xml file' do
-  # NEED TO DEBUG THIS PROB!
-  it 'can set one with labeled proteins' do
-    file = Tfiles + "/bioworks_with_INV_small.xml"
-    obj = Bioworks.new(file)
-    obj.proteins.size.should == 19
-    file = Tfiles + '/bioworks_small.xml'
-    obj = Bioworks.new(file)
-    obj.proteins.size.should == 106
-  end
-
-  it 'can parse an xml file NOT derived from multi-concensus' do
-    tf_bioworks_single_xml_small = Tfiles + '/bioworks_single_run_small.xml'
-    obj = Bioworks.new(tf_bioworks_single_xml_small)
-    gfn = '5prot_mix_michrom_20fmol_200pmol'
-    origfilename = '5prot_mix_michrom_20fmol_200pmol.RAW'
-    origfilepath = 'C:\Xcalibur\sequest'
-    obj.global_filename.should == gfn
-    obj.origfilename.should == origfilename
-    obj.origfilepath.should == origfilepath
-    obj.proteins.size.should == 7
-    obj.proteins.first.peptides.first.base_name.should ==  gfn
-    obj.proteins.first.peptides.first.file.should ==  "152"
-    obj.proteins.first.peptides.first.charge.should == 2
-    # @TODO: add more tests here
-  end
-
-  it 'can output in excel format (**semi-verified right now)' do
-    tf_bioworks_to_excel = Tfiles + '/tf_bioworks2excel.bioXML'
-    tf_bioworks_to_excel_actual = Tfiles + '/tf_bioworks2excel.txt.actual'
-    tmpfile = Tfiles + "/tf_bioworks_to_excel.tmp"
-    bio = Bioworks.new(tf_bioworks_to_excel)
-    bio.to_excel(tmpfile)
-    tmpfile.exist_as_a_file?.should be_true
-    #File.should exist_as_a_file(tmpfile)
-    exp = _arr_of_arrs(tf_bioworks_to_excel_actual)
-    act = _arr_of_arrs(tmpfile)
-    exp.each_index do |i|
-      break if i == 23 ## this is where the ordering becomes arbitrary between guys with the same scans, but different filenames
-      _assert_equal_pieces(exp[i], act[i], exp[i][0] =~ /\d/)
-    end
-
-    File.unlink tmpfile
-  end
-
-  # prot is boolean if this is a protein line!
-  def _assert_equal_pieces(exp, act, prot)
-    # equal as floats (by delta)
-    exp.each_index do |i|
-      if i == 5  # both proteins and peptides
-        act[i].to_f.should be_close(exp[i].to_f, 0.1)
-      elsif i == 3 && !prot
-        act[i].to_f.should be_close(exp[i].to_f, 0.01)
-      elsif i == 6 && !prot
-        act[i].to_f.should be_close(exp[i].to_f, 0.01)
-      elsif i == 9 && prot
-        ## NEED TO GET THESE BACK (for consistency):
-        #act[i].split(" ")[0].should =~ exp[i].split(" ")[0]
-      else
-        ## NEED TO GET THESE BACK (for consistency):
-        #act[i].should == exp[i]
-      end
-    end
-  end
-
-  # takes a bioworks excel (in txt format) and outputs an arr of arrs
-  def _arr_of_arrs(file)
-    IO.readlines(file).collect do |line|
-      line.chomp!
-      line.split("\t")
-    end
-  end
-
-  it 'can return unique peptides and proteins by sequence+charge (private)' do
-    cnt = 0
-    answer = [%w(2 PEPTIDE), %w(3 PEPTIDE), %w(3 PEPY), %w(2 PEPY)]
-    exp_peps = answer.collect! do |arr|
-      pep = Bioworks::Pep.new
-      pep.charge = arr[0]
-      pep.sequence = arr[1]
-      pep
-    end
-    exp_prots = [[0,2],[1,4,5],[3],[6]].collect do |arr|
-      arr.collect do |num|
-        prot = Bioworks::Prot.new
-        prot.reference = "#{num}"
-        prot
-      end
-    end
-    exp_peps = exp_peps.zip(exp_prots)
-    exp_peps.collect! do |both|
-      both[0].proteins = [both[1]]
-      both[0]
-    end
-
-    peptides = [%w(2 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPTIDE), %w(3 PEPY), %w(3 PEPTIDE), %w(3 PEPTIDE), %w(2 PEPY)].collect do |arr|
-      pep = Bioworks::Pep.new
-      pep.charge = arr[0]
-      pep.sequence = arr[1]
-      pep.proteins = [Bioworks::Prot.new]
-      pep.proteins.first.reference = "#{cnt}"
-      cnt += 1
-      pep
-    end
-    peptides, proteins = Bioworks.new._uniq_peps_by_sequence_charge(peptides)
-    proteins.size.should == peptides.size
-    exp_peps.each_with_index do |pep, i|
-      peptides[i].charge.should == pep.charge
-      peptides[i].sequence.should == pep.sequence
-    end
-
-    exp_prots.each_index do |i|
-      exp_prots[i].each_index do |j|
-        proteins[i][j].reference.should == exp_prots[i][j].reference
-      end
-    end
-  end
-
-end
-
-describe Bioworks::Pep do
-  it 'can be initialized from a hash' do
-    hash = {:sequence => 0, :mass => 1, :deltamass => 2, :charge => 3, :xcorr => 4, :deltacn => 5, :sp => 6, :rsp => 7, :ions => 8, :count => 9, :tic => 10, :proteins => 11, :base_name => 12, :first_scan => 13, :last_scan => 14, :peptide_probability => 15, :file => 16, :_num_proteins => 17, :_first_prot => 18}
-    pep = Bioworks::Pep.new(hash)
-    hash.each do |k,v|
-      pep.send(k).should == v
-    end
-  end
-
-  it 'correctly extracts file information' do
-    pep = Bioworks::Pep.new
-    testing = ['005a, 1131', '005b, 1131 - 1133', '1131', '1131 - 1133']
-    answers = [%w(005a 1131 1131), %w(005b 1131 1133), [nil, '1131', '1131'], [nil, '1131', '1133']]
-    testing.zip(answers) do |ar|
-      ans = pep.class.extract_file_info(ar[0])
-      ans.join(" ").should == ar[1].join(" ") 
-    end
-  end
-
-end
-
-
-=end