mspire 0.3.1 → 0.3.9

data/specs/spec_id/sequest_spec.rb

@@ -0,0 +1,38 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'spec_id'
+require 'spec_id/sequest'
+require 'set'
+
+class MockPepHit
+  attr_accessor :first_scan, :xcorr, :idd
+  def initialize(*args)
+    (@first_scan, @xcorr, @idd) = args
+  end
+end
+
+describe Sequest, ": with small mock set" do
+  before(:each) do
+    index = 0
+    hits = [[0, 5.0, 0], [0, 4.0, 1], [0, 3.0, 2], 
+      [1, 5.0, 3], [1, 4.0, 4],
+      [2, 5.5, 5], 
+      [3, 5.5, 6], [3, 5.5, 7], [3, 4.0, 8], [3, 2.4, 9], [3, 2.4, 10]
+    ].map do |hit|
+      MockPepHit.new(*hit)
+    end
+    @peps = hits.sort_by {rand}
+  end
+
+  it 'returns "other" hits' do
+    included = [2, 8, 9, 10]
+    first_index = 2
+    last_index = 10
+    reply = Sequest.other_hits(@peps, first_index,last_index,:first_scan, [:xcorr, {:down => :xcorr}])
+    reply.map {|hit| hit.idd }.to_set.should == included.to_set
+
+    # same, but optimized
+    reply = Sequest.other_hits_sorted_by_xcorr(@peps, first_index,last_index,:first_scan)
+    reply.map {|hit| hit.idd }.to_set.should == included.to_set
+  end
+
+end

data/specs/spec_id/sqt_spec.rb

@@ -1,5 +1,6 @@
 require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
 
+require 'spec_id/sqt'
 require 'spec_id/srf'
 
 SpecHelperHeaderHash = {
@@ -80,7 +81,7 @@ describe 'converting a large srf to sqt' do
     end
     it 'converts without bothering with the database' do
       @srf.to_sqt(@output)
-      @output.should exist
+      @output.exist_as_a_file?.should be_true
       lines = File.readlines(@output)
       lines.size.should == 80910
       header_lines = lines.grep(/^H/)
@@ -104,13 +105,13 @@ describe 'converting a large srf to sqt' do
       my_error_string.should include(wacky_path)
       @srf.header.db_filename = @original_db_filename
       $stderr = STDERR
-      @output.should exist
+      @output.exist_as_a_file?.should be_true
       IO.readlines(@output).size.should == 80910
       del(@output)
     end
     it 'can get db info with correct path' do
       @srf.to_sqt(@output, :db_info => true, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest')
-      @output.should exist
+      @output.exist_as_a_file?.should be_true
       lines = IO.readlines(@output)
       has_md5 = lines.any? do |line|
         line =~ /DBMD5Sum\s+202b1d95e91f2da30191174a7f13a04e/
@@ -136,3 +137,110 @@ describe 'converting a large srf to sqt' do
     end
   end
 end
+
+HeaderHash = {}
+header_doublets = [
+  %w(SQTGenerator	mspire),
+  %w(SQTGeneratorVersion	0.3.1),
+  %w(Database	C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta),
+  %w(FragmentMasses	AVG),
+  %w(PrecursorMasses	AVG),
+  ['StartTime', ''],
+  ['Alg-MSModel', 'LCQ Deca XP'],
+  %w(DBLocusCount	4237),
+  %w(Alg-FragMassTol	1.0000),
+  %w(Alg-PreMassTol	25.0000),
+  ['Alg-IonSeries', '0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0'],
+  %w(Alg-PreMassUnits	ppm),
+  ['Alg-Enzyme', 'Trypsin(KR/P) (2)'],
+
+  ['Comment', ['ultra small file created for testing', 'Created from Bioworks .srf file']],
+  ['DynamicMod', ['M*=+15.99940', 'STY#=+79.97990']],
+  ['StaticMod', []],
+].each do |double|
+  HeaderHash[double[0]] = double[1]
+end
+
+TestSpectra = {
+  :first => { :first_scan=>2, :last_scan=>2, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>390.92919921875, :total_intensity=>2653.90307617188, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[]},
+  :last => { :first_scan=>27, :last_scan=>27, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>393.008056640625, :total_intensity=>2896.16967773438, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[] },
+  :seventeenth => {:first_scan=>23, :last_scan=>23, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>1022.10571289062, :total_intensity=>3637.86059570312, :lowest_sp=>0.0, :num_matched_peptides=>41},
+  :first_match_17 => { :rxcorr=>1, :rsp=>5, :mh=>1022.11662242, :deltacn_orig=>0.0, :xcorr=>0.725152492523193, :sp=>73.9527359008789, :ions_matched=>6, :ions_total=>24, :sequence=>"-.MGT#TTM*GVK.L", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>0.0672458708286285, :aaseq => 'MGTTTMGVK' },
+  :last_match_17 => {:rxcorr=>10, :rsp=>16, :mh=>1022.09807242, :deltacn_orig=>0.398330867290497, :xcorr=>0.436301857233047, :sp=>49.735767364502, :ions_matched=>5, :ions_total=>21, :sequence=>"-.MRT#TSFAK.V", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>1.1, :aaseq => 'MRTTSFAK'},
+  :last_match_17_last_loci => {:reference =>'gi|16129390|ref|NP_415948.1|', :first_entry =>'gi|16129390|ref|NP_415948.1|', :locus =>'gi|16129390|ref|NP_415948.1|', :description => 'Fake description' }
+}
+
+
+describe SQT, ": reading a small sqt file" do
+  before(:each) do
+    file = Tfiles + '/small.sqt'
+    file.exist_as_a_file?.should be_true
+    @sqt = SQT.new(file)
+  end
+
+  it 'can access header entries like a hash' do
+    header = @sqt.header
+    HeaderHash.each do |k,v|
+      header[k].should == v
+    end
+  end
+
+  it 'can access header entries with methods' do
+    header = @sqt.header
+    # for example:
+    header.database.should == HeaderHash['Database']
+    # all working:
+    HeaderHash.each do |k,v|
+      header.send(SQT::Header::KeysToAtts[k]).should == v
+    end
+
+  end
+
+  it 'has spectra, matches, and loci' do
+    svt = @sqt.spectra[16]
+    reply = {:first => @sqt.spectra.first, :last => @sqt.spectra.last, :seventeenth => svt, :first_match_17 => svt.matches.first, :last_match_17 => svt.matches.last, :last_match_17_last_loci => svt.matches.last.loci.last}
+    [:first, :last, :seventeenth, :first_match_17, :last_match_17, :last_match_17_last_loci].each do |key|
+      TestSpectra[key].each do |k,v|
+        if v.is_a? Float
+          reply[key].send(k).should be_close(v, 0.0000000001)
+        else
+          reply[key].send(k).should == v
+        end
+      end
+    end
+    @sqt.spectra[16].matches.first.loci.size.should == 1
+    @sqt.spectra[16].matches.last.loci.size.should == 1
+  end
+
+end
+
+describe SQTGroup, ': acting as a SpecID on large files' do
+  spec_large do 
+    before(:each) do
+      file1 = Tfiles_l + '/opd1_2runs_2mods/sequest/020.sqt'
+      file2 = Tfiles_l + '/opd1_2runs_2mods/sequest/040.sqt'
+      file1.exist_as_a_file?.should be_true
+      file2.exist_as_a_file?.should be_true
+      @sqg = SQTGroup.new([file1, file2])
+    end
+
+    it 'has peptide hits' do
+      peps = @sqg.peps
+      peps.size.should == 38512  # frozen
+      # first hit in 020
+      peps.first.sequence.should == 'R.Y#RLGGS#T#K.K'
+      peps.first.base_name.should == '020'
+      # last hit in 040
+      peps.last.sequence.should == 'K.NQTNNRFK.T'
+      peps.last.base_name.should == '040'
+    end
+
+    it 'has prots' do
+      ## FROZEN:
+      @sqg.prots.size.should == 3994
+      sorted = @sqg.prots.sort_by {|v| v.reference }
+      sorted.first.reference.should == 'gi|16127996|ref|NP_414543.1|'
+      sorted.first.peps.size.should == 33
+    end
+  end
+end

data/specs/spec_id_spec.rb

@@ -219,6 +219,8 @@ describe SpecID, 'class methods' do
       :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

data/specs/transmem/phobius_spec.rb

@@ -1,3 +1,5 @@
+require 'yaml'
+
 require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
 
 # contains shared behavior that we need.
@@ -73,7 +75,7 @@ end
 
 describe "a phobius parser", :shared => true do
   it 'parses a phobius file into a hash structure' do
-    @file_to_hash.should exist
+    @file_to_hash.exist_as_a_file?.should be_true
     hash = @class.default_index(@file_to_hash)
     hash.should == @structure_to_create
   end

data/specs/transmem/toppred_spec.rb

@@ -19,7 +19,7 @@ end
 
 describe "a toppred parser", :shared => true do
   it 'parses a toppred file into a hash structure' do
-    @file_to_hash.should exist
+    @file_to_hash.exist_as_a_file?.should be_true
     hash = @class.default_index(@file_to_hash)
     hash.should == @structure_to_create
   end

data/specs/validator/aa_est_spec.rb

@@ -0,0 +1,66 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require File.expand_path( File.dirname(__FILE__) + '/../validator_helper' )
+
+
+require 'validator/aa_est'
+require 'spec_id'
+require 'spec_id/digestor'
+
+klass = Validator::AAEst
+
+describe klass, "using frequency estimates" do
+  before(:each) do
+    @small_fasta = Tfiles + '/small.fasta'
+    @sequest_params = Tfiles + '/bioworks32.params'
+    #         C/D      C/D    J     (7)
+    @seqs = %w(ABCDEFGC CCDCCC JJJJJ XYZ WXXXYZ TXXXXXYZ ZZXIIPTYZ ZZXTYZZ ZZZZ YYYYYTL)
+    @peps =  @seqs.map {|n| v = SpecID::GenericPep.new; v.aaseq = n ; v }
+    val = klass.new('C')
+    val.frequency = 0.11
+    @validator = val
+  end
+  #C: 0.0157714433456144
+  #D: 0.0526145691939758
+
+  it_should_behave_like 'a validator'
+
+  it 'calculates false_to_total_ratio correctly' do
+    obj = klass.new('C', :frequency => 0.0157714433456144)
+    obj.set_false_to_total_ratio(@peps)
+    exp = 0.949318337979434 / @seqs.size
+    obj.false_to_total_ratio.should be_close(exp, 0.0001)  # freeze for consistency
+  end
+
+  it 'calculates fttr each time fresh' do
+    myar = @peps.map
+    obj = klass.new('C', :frequency => 0.0157714433456144)
+    obj.pephit_precision(myar)
+    fttr1 = obj.false_to_total_ratio
+    obj.pephit_precision(myar)
+    fttr2 = obj.false_to_total_ratio
+    fttr1.should == fttr2
+    myar.pop
+    obj.pephit_precision(myar)
+    fttr3 = obj.false_to_total_ratio
+    fttr3.should_not == fttr1
+  end
+
+  it 'gives consistent precision of peptides given fastafile and aa (even negative)' do
+    aa = 'C'
+    val = klass.new(aa).set_frequency(Fasta.new(@small_fasta).prots)
+    # I checked this answer out by hand and it is correct
+    val.pephit_precision(@peps).should be_close(-1.10677, 0.001)
+  end
+
+  it 'gives same precision done at once or incrementally' do
+    obj = klass.new('C', :frequency => 0.0157714433456144)
+
+    all_at_once = obj.pephit_precision(@peps)
+
+    precisions = @peps.map do |pep|
+      obj.increment_pephits_precision(pep)
+    end
+    precisions.last.should == all_at_once
+  end
+end
+

data/specs/validator/aa_spec.rb

@@ -10,60 +10,7 @@ klass = Validator::AA
 
 class MyAA < Validator::AA ; def initialize ; end ; end
 
-describe klass, "using frequency estimates" do
-  before(:each) do
-    @small_fasta = Tfiles + '/small.fasta'
-    @sequest_params = Tfiles + '/bioworks32.params'
-    #         C/D      C/D    J     (7)
-    @seqs = %w(ABCDEFGC CCDCCC JJJJJ XYZ WXXXYZ TXXXXXYZ ZZXIIPTYZ ZZXTYZZ ZZZZ YYYYYTL)
-    @peps =  @seqs.map {|n| v = SpecID::GenericPep.new; v.aaseq = n ; v }
-    val = klass.new('C')
-    val.frequency = 0.11
-    @validator = val
-  end
-  #C: 0.0157714433456144
-  #D: 0.0526145691939758
-
-  it_should_behave_like 'a validator'
-
-  it 'calculates precision from actual and expected correctly' do
-    MyAA.new.pephit_precision_from_actual_and_expected(5, 10, 100).should == 0.5
-    (0..10).each do |actual|
-      precision = MyAA.new.pephit_precision_from_actual_and_expected(actual, 10, 100)
-      answer = 1.0 - (actual.to_f/10.0)
-      precision.should be_close(answer, 0.00000001)
-      #0 -> 1
-      #1 -> 0.9
-      #2 -> 0.8
-    end
-  end
-
-  it 'calculates precision (with background) reasonably and consistently' do
-    (0..10).each do |bkg|
-      precision = MyAA.new.pephit_precision_from_actual_and_expected(5, 10, 100, bkg.to_f/100)
-      answer = 0.5 + bkg.to_f/10
-      answer = 1.0 if answer > 1.0 
-      precision.should == answer
-    end
-  end
-
-  it 'calculates at_least_one correctly' do
-    aa = 'C'
-    freq = 0.0157714433456144  ## from @small_fasta
-    (actual, expected) = MyAA.new.at_least_one(aa, freq, @seqs)
-    actual.should == 2
-    expected.should be_close(0.949318337979434, 0.0001)  # freeze for consistency
-  end
-
-  it 'gives consistent precision of peptides given fastafile and aa (even negative)' do
-    aa = 'C'
-    val = klass.new(aa).set_frequency(Fasta.new(@small_fasta))
-    # I checked this answer out by hand and it is correct
-    val.pephit_precision(@peps).should be_close(-1.10677, 0.001)
-  end
-end
-
-describe klass, "using empirical digestion data" do
+describe klass, "using digestion data" do
 
   before(:each) do
     @small_fasta = Tfiles + '/small.fasta'
@@ -88,20 +35,6 @@ describe klass, "using empirical digestion data" do
     # correct)
     val.false_to_total_ratio.should be_close(0.177629264861062, 0.0000000000001)
   end
-
-  it 'can validate with theoretical digestion or frequency estimate' do
-    aa = 'C'
-    val = klass.new(aa)
-    val.false_to_total_ratio = 0.177629264861062
-    answ = val.pephit_precision(@peps)
-    # frozen
-    answ.should be_close(-0.125940594059407, 0.0000000001)
-
-    val.frequency = 0.0157714433456144  ## from @small_fasta
-    val.false_to_total_ratio = nil
-    answ = val.pephit_precision(@peps)
-    answ.should be_close(-1.10677485094924, 0.0000000001)
-  end
 end
 
 

data/specs/validator/background_spec.rb

@@ -1,3 +1,5 @@
+require 'yaml'
+
 require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
 
 require 'validator/background'

data/specs/validator/bias_spec.rb

@@ -57,6 +57,7 @@ describe klass, "on small mock set" do
 
     @fasta_obj = FastaHelper::FastaObj
     @validator = klass.new(@fasta_obj)
+    @validator.false_to_total_ratio = 0.22  # arbitrary
   end
 
   it_should_behave_like 'a validator'
@@ -76,7 +77,7 @@ describe klass, "on small mock set" do
     # cw=t,e=t; cw=t,e=f; cw=f,e=t; cw=f,e=f
     [true, false].each do |correct_wins|
       [true, false].each do |fasta_expected|
-        val = klass.new(@fasta_obj, :proteins_expected => fasta_expected, :correct_wins => correct_wins)
+        val = klass.new(@fasta_obj, :proteins_expected => fasta_expected, :correct_wins => correct_wins, :false_to_total_ratio => 1.0)
         tp, fp = answ.shift
         exp = calc_precision(tp, fp)
         val.pephit_precision(@peps).should == exp
@@ -93,32 +94,7 @@ describe klass, "on small mock set" do
     background = 0.24
     [true, false].each do |correct_wins|
       [true, false].each do |fasta_expected|
-        val = klass.new(@fasta_obj, :proteins_expected => fasta_expected, :correct_wins => correct_wins, :background => background)
-        peps_size = @peps.size
-        exp_tp, exp_fp = answ.shift
-        exp = calc_precision(exp_tp, exp_fp)
-        val.pephit_precision(@peps).should_not == exp
-        actual_precision = val.pephit_precision(@peps)
-        act_tp, act_fp = val.partition(@peps)
-        act_tp.size.should == exp_tp
-        act_fp.size.should == exp_fp
-        exp_fp_correctd = exp_fp.to_f - (peps_size.to_f * background)
-        expected_precision = calc_precision(peps_size.to_f - exp_fp_correctd, exp_fp_correctd)
-        # internally, the num of false hits is controlled so as not to bottom
-        # out below zero, here we control the precision (same effect)
-        expected_precision = 1.0 if expected_precision > 1.0
-        actual_precision.should == expected_precision
-      end
-    end
-  end
-
-  it 'correctly incorporates background' do
-    answ = [[3,4], [6,1], [1,6], [4,3]]
-    # cw=t,e=t; cw=t,e=f; cw=f,e=t; cw=f,e=f
-    background = 0.24
-    [true, false].each do |correct_wins|
-      [true, false].each do |fasta_expected|
-        val = klass.new(@fasta_obj, :proteins_expected => fasta_expected, :correct_wins => correct_wins, :background => background)
+        val = klass.new(@fasta_obj, :proteins_expected => fasta_expected, :correct_wins => correct_wins, :background => background, :false_to_total_ratio => 1.0)
         peps_size = @peps.size
         exp_tp, exp_fp = answ.shift
         exp = calc_precision(exp_tp, exp_fp)

data/specs/validator/decoy_spec.rb

@@ -23,7 +23,7 @@ describe klass, 'reporting precision on peptides from cat prots' do
     peps[4].prots = [prots[5]]            # FP
     peps[5].prots = [prots[4]]            # FP
     @peps = peps
-    @validator = klass.new(/FAKE/)
+    @validator = klass.new(:constraint => /FAKE/)
   end
 
   it_should_behave_like 'a validator'
@@ -39,7 +39,7 @@ describe klass, 'reporting precision on peptides from cat prots' do
 
     [true, false].each do |incorrect_on_match|
       [true, false].each do |correct_wins|
-        val = klass.new(protein_matches.shift, incorrect_on_match, correct_wins)
+        val = klass.new(:constraint => protein_matches.shift, :decoy_on_match => incorrect_on_match, :correct_wins => correct_wins)
         answ = val.pephit_precision(@peps)
         exp = ValidatorHelper::Decoy.precision_from_partition_array(answ_arr.shift)
         answ.should == exp

data/specs/validator/transmem_spec.rb

@@ -34,6 +34,7 @@ describe klass, "on small mock set" do
     @peps[7].prots = [@prots[8], @prots[9]] # nil pep
 
     @validator = klass.new(@toppred_file)
+    @validator.false_to_total_ratio = 1.0
   end
 
   it_should_behave_like 'a validator'
@@ -80,7 +81,7 @@ describe klass, "on small mock set" do
   end
 
   it 'can calculate precision incrementally' do
-    val = klass.new(@toppred_file, :min_num_tms => 2)
+    val = klass.new(@toppred_file, :min_num_tms => 2, :false_to_total_ratio => 1.0)
     # usually we'd update the false_to_total_ratio, but not bothering for test
     # here we HAVE to set the status hash before hand... (we could redo this
     # section)