mspire 0.2.4 → 0.3.0

data/specs/spec_id_spec.rb

@@ -0,0 +1,361 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+
+require 'spec_id'
+require 'spec_id/srf'
+
+# we use this to set the values of generic proteins below
+require 'set_from_hash'
+
+
+describe 'creating a list of proteins from peptides', :shared => true do
+  before(:each) do
+    # EXPECTS @prots and a @meth proc that takes two args, an array of
+    # peptides and the details of the list creation
+
+    hashes = [
+      {:aaseq => 'PEP0', :xcorr => 1.2, :deltacn => 0.1, :ppm => 40, :charge => 2, :prots => [prots[0],prots[1]]},
+      {:aaseq => 'PEP1', :xcorr => 1.3, :deltacn => 0.1, :ppm => 50, :charge => 3, :prots => [prots[1],prots[2]]},
+      {:aaseq => 'PEP2', :xcorr => 1.4, :deltacn => 0.1, :ppm => 50, :charge => 1, :prots => [prots[3]]},
+      {:aaseq => 'PEP3', :xcorr => 1.5, :deltacn => 1.1, :ppm => 20, :charge => 2, :prots => [prots[4]]},
+      {:aaseq => 'PEP4', :xcorr => 1.3, :deltacn => 0.1, :ppm => 20, :charge => 2, :prots => [prots[0]]},
+      {:aaseq => 'PEP5', :xcorr => 1.3, :deltacn => 0.1, :ppm => 40, :charge => 2, :prots => prots[1,2]},
+    ]
+
+    @peps = hashes.map do |hash|
+      SRF::OUT::Pep.new.set_from_hash(hash) 
+    end
+  end
+
+  it 'compiles protein lists from peps not touching peps attr (:no_update)' do
+
+    prts = @meth.call(@peps, :no_update)
+    exp = (0..4).map do |n|
+      "prot_" + n.to_s
+    end
+    refs = prts.map {|v| v.reference }.sort
+    refs.should == exp
+    prts.each do |prt|
+      prt.peps.should == []
+    end
+  end
+
+  it 'compiles protein lists with updated peps attribute (:update)' do
+
+    prts = @meth.call(@peps, :update)
+    prot_0_before = prts.select {|v| v.reference == 'prot_0'}.first
+    protein_match(prts, 'prot_0', %w(PEP0 PEP4))
+    protein_match(prts, 'prot_1', %w(PEP0 PEP1 PEP5))
+    protein_match(prts, 'prot_2', %w(PEP1 PEP5))
+    protein_match(prts, 'prot_3', %w(PEP2))
+    protein_match(prts, 'prot_4', %w(PEP3))
+    srt_ref = prts.map {|v| v.reference}.sort
+    %w(prot_0 prot_1 prot_2 prot_3 prot_4).should == srt_ref  # just the right number of prots
+    prot_0 = prts.select {|v| v.reference == 'prot_0'}.first
+    prot_0_before.__id__.should ==  prot_0.__id__ # proteins are identical
+
+
+    prot_0_before = prts.select {|v| v.reference == 'prot_0'}.first.__id__
+  end
+
+  it 'compiles protein lists of new proteins (:new)' do
+    prts = SpecID.protein_list(@peps, :new)
+    prot_0_before = prts.select {|v| v.reference == 'prot_0'}.first
+    protein_match(prts, 'prot_0', %w(PEP0 PEP4))
+    protein_match(prts, 'prot_1', %w(PEP0 PEP1 PEP5))
+    protein_match(prts, 'prot_2', %w(PEP1 PEP5))
+    protein_match(prts, 'prot_3', %w(PEP2))
+    protein_match(prts, 'prot_4', %w(PEP3))
+    srt_ref = prts.map {|v| v.reference}.sort
+    #assert_equal(%w(prot_0 prot_1 prot_2 prot_3 prot_4), srt_ref, "just the right number of prots")
+    %w(prot_0 prot_1 prot_2 prot_3 prot_4).should == srt_ref # just the right number of prots
+    prot_0 = prts.select {|v| v.reference == 'prot_0'}.first
+    #assert_not_equal(prot_0_before, prot_0.__id__, "proteins are not identical")
+    prot_0_before.should_not == prot_0.__id__ # proteins are not identical
+  end
+
+  # checks that among prts, the protein with ref has peptides with pepseqs
+  # aaseqs
+  def protein_match(prts, ref, pepseqs)
+    prt = prts.select{|v| v.reference == ref }.first
+    sorted_prt_peps_aaseqs = prt.peps.map {|v| v.aaseq }.sort 
+    sorted_pepseqs = pepseqs.sort
+    pepseqs.should == sorted_prt_peps_aaseqs
+  end
+
+end
+
+describe SpecID, 'with generic proteins' do
+  before(:all) do
+    @prots = (0..7).map do |n|
+      SpecID::GenericProt.new.set_from_hash({:reference => "prot_"+n.to_s, :peps => []})
+    end
+    @meth = proc {|peps, kind| SpecID.protein_list(peps, kind) }
+  end
+  it_should_behave_like 'creating a list of proteins from peptides'
+end
+
+describe SpecID, 'with array based proteins' do
+  before(:all) do
+    @prots = (0..7).map do |n|
+      SRF::OUT::Prot.new.set_from_hash({:reference => "prot_"+n.to_s, :peps => []})
+    end
+    @meth = proc {|peps, kind| SpecID.protein_list(peps, kind) }
+  end
+  it_should_behave_like 'creating a list of proteins from peptides'
+end
+
+module Boolean ; end
+class TrueClass ; include Boolean end
+class FalseClass; include Boolean end
+
+describe SpecID, 'being created' do
+  it 'can be from small bioworks.xml' do
+    sp = SpecID.new(Tfiles + '/bioworks_small.xml')
+    sp.prots.size.should == 106
+  end
+
+  it 'can be from small -prot.xml (newer prophet versions)' do
+    prot_xml = Tfiles + '/interact-opd1_mods_small-prot.xml'
+    sp = SpecID.new(prot_xml)
+    sp.is_a?(SpecID).should be_true
+    sp.is_a?(Proph::ProtSummary).should be_true
+    sp.prots.size.should == 20
+    sp.peps.size.should == 31
+    types = {
+      :protein_name => String,
+      :n_indistinguishable_proteins => Integer,
+      :probability => Float,
+      :percent_coverage => Float,
+      :unique_stripped_peptides => Array,
+      :group_sibling_id => String,
+      :total_number_peptides => Integer,
+      :pct_spectrum_ids => Float,
+      :peps => Array,
+    }
+    sp.prots.each do |prot|
+      types.each { |cl,tp| prot.send(cl).is_a?(tp).should be_true }
+    end
+    types = {
+      :aaseq => String,
+      :peptide_sequence => String,
+      :charge => Integer,
+      :initial_probability => Float,
+      :nsp_adjusted_probability => Float,
+      :weight => Float,
+      :is_nondegenerate_evidence => Boolean,  # no Boolean class
+      :n_enzymatic_termini => Integer,
+      :n_sibling_peptides => Float,
+      :n_sibling_peptides_bin => Integer,
+      :n_instances => Integer,
+      :is_contributing_evidence => Boolean,
+      :calc_neutral_pep_mass => Float,
+      :modification_info => Object,
+      :mod_info => Object,
+    }
+    sp.peps.each do |pep|
+      types.each { |cl,tp| pep.send(cl).is_a?(tp).should be_true }
+    end
+    prot_ars = []
+    sp.peps.each do |pep|
+      if pep.prots.size > 1
+        prot_ars << pep.prots
+      end
+    end
+    prot_ars.each do |prt_ar|
+      prt_ar.each do |prt|
+        # the nils because this is a small file and their proteins are not
+        # found
+        ((prt.is_a?(SpecID::Prot) == true) or  prt.nil?).should be_true
+        ((prt.is_a?(Proph::Prot) == true) or prt.nil?).should be_true
+      end
+    end
+    mod_objects = []
+    sp.peps.each do |pep| 
+      if !pep.mod_info.nil? 
+        mod_objects << pep.mod_info
+      end
+    end
+    # frozen
+    mod_objects.size.should == 23
+  end
+
+  spec_large do
+    it 'works on a large file' do
+      file = Tfiles_l + '/opd1_2runs_2mods/prophet/interact-opd1_mods-prot.xml'
+      #file = '/work/john/db_quest/verify_prophet/orbi/prophet_results/orbi_f00-prot.xml'
+      start = Time.now
+      sp = SpecID.new(file)
+      puts "- Took #{Time.now - start} seconds to read"
+      prot_ars = []
+      sp.peps.each do |pep|
+        if pep.prots.size > 1
+          prot_ars << pep.prots
+        end
+      end
+      prot_ars.each do |prt_ar|
+        prt_ar.each do |prt|
+          # the nils because this is a small file and their proteins are not
+          # found
+          prt.is_a?(SpecID::Prot).should be_true
+          prt.is_a?(Proph::Prot).should be_true
+        end
+      end
+
+    end
+  end
+
+  it_should 'can be from -prot.xml (older prophet versions)' do
+    prot_xml = Tfiles + '/4-03-03_small-prot.xml'
+    prot_xml = Tfiles + '/yeast_gly_small-prot.xml'
+  end
+end
+
+describe SpecID, 'class methods' do
+
+  it 'determines filetype (small files)' do
+    files = {
+      :bioworks => Tfiles + "/bioworks_small.xml",
+      :protproph => Tfiles + '/opd1/000_020_3prots-prot.xml',
+      :pepproph => Tfiles + '/opd1_2runs_2mods/interact-opd1_mods__small.xml',
+      :srf => Tfiles + '/head_of_7MIX.srf',
+      :srg => 'whatever.srg',
+    }
+    files.each do |key,val|
+      SpecID.file_type(val).should == key.to_s
+    end
+    ## WOULD BE NICE TO GET THIS WORKING, TOO
+    # assert_equal('protproph', SpecID.file_type(@old_prot_proph))
+  end
+
+  it 'can remove non-standard amino acids' do
+    hash = {"K.PEPTIDE.Z" => "K.PEPTIDE.Z", "K.*M" => "K.M", "aI" => 'I', "YI.&" => "YI.", "EI.!@#\$%^&*(){}[]|\\;:'\"<>,?/EI" => 'EI.EI'}
+    cl = proc {|v| SpecID::Pep.remove_non_amino_acids(v) }
+    hash.each do |k,v|
+      cl.call(k).should == v
+    end
+  end
+
+end
+
+describe SpecID, "determining the minimum set of proteins from pephits" do
+
+  before(:all) do
+    class MyProt ; include SpecID::Prot ; end
+    class MyPep ; include SpecID::Pep ; attr_accessor :xcorr end
+  end
+
+  it 'can do occams razor on small set' do
+    
+    prots = (0..6).to_a.map do |n|
+      prot = MyProt.new
+      prot.reference = "ref_#{n}"
+      prot
+    end
+
+    peps = (0..12).to_a.map {|v| MyPep.new }
+
+    #           0   1   2   3   4   5   6   7   8   9   10  11    12 
+    aaseqs = %w(AAA BBB CCC ABC AAA BBB CCC ABC DDD EEE FFF EEEEE DDD)
+    xcorrs = [1.0, 2.0, 3.0, 4.0, 1.0, 2.0, 3.0, 4.0, 0.5, 0.6, 0.7, 0.8, 0.5]
+
+    peps.zip(aaseqs, xcorrs) do |pep,aaseq,xcorr|
+      pep.aaseq = aaseq
+      pep.xcorr = xcorr
+    end
+
+    prots[0].peps = peps[0,4]
+    prots[1].peps = [peps[2]]  ## should be missing
+
+    test_prots = prots[0,2]
+    answ = SpecID.occams_razor(test_prots)
+    answ.each do |an|
+      an[0].is_a?(SpecID::Prot).should be_true
+    end
+    first = answ.first
+    first[0].should == prots[0]
+    equal_array_content( prots[0].peps, first[1])
+
+    require 'pp'
+    #pp answ
+
+
+    prots[0].peps = peps[0,4]
+    prots[1].peps = [peps[2]]  ## should be missing
+    prots[2].peps = []  ## should be missing
+
+    answ = SpecID.occams_razor(test_prots, true)
+    puts '- NEED MORE tests HERE!' if $specdoc
+    #pp answ
+
+
+    #prots[2].peps = [peps[2]]
+    #prots[2].peps.push( peps[3] ) ## should be there since it has 2
+    #prots[3].peps = [peps[3]] ## should be missing
+  end
+
+  def equal_array_content(exp1, ans, message='')
+    exp1.each do |item|
+      ans.should include(item)
+    end
+  end
+
+
+end
+
+
+require 'fasta'
+
+describe SpecID::Pep, "with a small fasta object" do
+  before(:each) do
+    @prots = []
+
+    aaseq = ('A'..'Z').to_a.join('')
+    header = "prot1"
+    @prots << Fasta::Prot.new(header, aaseq)
+
+    aaseq = ('A'..'Z').to_a.reverse.join('')
+    header = "prot1_reverse"
+    @prots << Fasta::Prot.new(header, aaseq)
+
+    aaseq = ('A'..'Z').to_a.join('')
+    header = "prot1_identical"
+    @prots << Fasta::Prot.new(header, aaseq)
+
+    aaseq = ('A'..'E').to_a.join('')
+    header = "prot1_short"
+    @prots << Fasta::Prot.new(header, aaseq)
+
+    aaseq = ('A'..'E').to_a.reverse.join('')
+    header = "prot1_reverse_short"
+    @prots << Fasta::Prot.new(header, aaseq)
+
+    @fasta = Fasta.new(@prots)
+
+  end
+  it "can find protein groups from a fasta object" do
+    pep_seqs = %w(ABCD DEFG ABCD DEFG EDCB FEDCB XYZ RANDOM AEABA) 
+    arr = SpecID::Pep.protein_groups_by_sequence(pep_seqs, @fasta)
+
+    prots = @prots
+    exp = [[prots[0], prots[2], prots[3]], [prots[0], prots[2]], [prots[0], prots[2], prots[3]], [prots[0],prots[2]], [prots[1], prots[4]], [prots[1]], [prots[0], prots[2]], [], []]
+
+    arr.should == exp
+  end
+end
+
+
+###########################
+# old tests
+###########################
+
+=begin
+def test_classify_by_false_flag
+  file = @tfiles + "bioworks_with_INV_small.xml"
+  sp = SpecID.new(file)
+  assert_equal(19, sp.prots.size)
+  (tp, fp) = sp.classify_by_false_flag(:prots, "INV_", true, true)
+  assert_equal(4, fp.size, "num false pos")
+  assert_equal(15, tp.size, "num true pos")
+end
+
+=end

data/specs/spec_id_xml_spec.rb

@@ -0,0 +1,33 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+
+require 'spec_id_xml'
+
+describe SpecIDXML, 'included with a simple object' do
+  before(:all) do
+    class Bob
+      include SpecIDXML
+      def initialize(first=nil, second=nil)
+        @first = first ; @second = second 
+      end
+    end
+  end
+
+  it 'creates short element xmls using an objects instance variables' do
+    obj = Bob.new(1, 2) 
+    st = obj.short_element_xml_from_instance_vars("bob")
+    # the ordering is arbitrary: "<bob first=\"1\" second=\"2\"/>\n"
+    st.should =~ /second="2"/
+    st.should =~ /first="1"/
+    st.should =~ /^<bob /
+    st.should =~ />$/
+  end
+
+  it 'escapes special characters' do
+    obj = Bob.new
+    obj.escape_special_chars("&><\"'").should == "&amp;&gt;&lt;&quot;&apos;"
+    obj.escape_special_chars("PE&PT>I<D\"E'").should == "PE&amp;PT&gt;I&lt;D&quot;E&apos;"
+  end
+
+end
+  
+