mspire 0.4.9 → 0.5.0

data/specs/spec_id_spec.rb

@@ -1,366 +0,0 @@
-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
-  include SpecID
-  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
-  include SpecID
-  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
-  include SpecID
-  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',
-      :sqt => Tfiles + '/small.sqt',
-      :sqg => 'whatever.sqg',
-    }
-    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

@@ -1,33 +0,0 @@
-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
-  
-