mspire 0.2.4 → 0.3.0

data/test/tc_mzxml.rb

@@ -1,88 +0,0 @@
-require 'test/unit'
-require 'spec/mzxml/parser'
-
-class SpecMzXML < Test::Unit::TestCase
-  def initialize(arg)
-    super(arg)
-    @tfiles = File.dirname(__FILE__) + '/tfiles/'
-    @tscans = @tfiles + "opd1/twenty_scans.mzXML"
-    @big_file = "../bioworks2prophet/xml/opd00001_test_set/opd00001_prophprepped/000.mzXML"
-  end
-
-  def test_times_and_spectra
-    #parser = Spec::MzXML::Parser.new
-    #arr = parser.parse_times_and_spectra( @tscans)
-    (times, spectra) = Spec::MzXML::Parser.new.times_and_spectra(@tscans)
-    times = %w(0.440000 5.150000 10.690000 16.400000 22.370000)
-    num_peaks = [992, 814, 796, 849, 813]
-    ind_0_2__3 = [301.430114746094, 22192.0]
-    ind_0_n2__n1 = [1499.09912109375, 111286.0]
-    ind_n1_2__3 = [301.243774414062, 77503.0]
-    ind_n1_n2__n1 = [1499.42016601562, 13.0]
-    assert_equal_pair(ind_0_2__3, spectra[0][2..3])
-    assert_equal_pair(ind_0_n2__n1, spectra[0][-2..-1])
-    assert_equal_pair(ind_n1_2__3, spectra[-1][2..3])
-    assert_equal_pair(ind_n1_n2__n1, spectra[-1][-2..-1])
-   
-    num_peaks.each_with_index do |n,i|
-      assert_equal(n, spectra[i].size/2)
-    end
-    times.each_with_index do |t,i|
-      assert_equal(t, times[i])
-    end
-    
-  end
-
-  def test_basic_info
-    hash = Spec::MzXML::Parser.new.basic_info(@tscans)
-    assert_equal({:scan_count=>[20, 5, 15], :start_time=>0.44, :end_time=>27.05, :start_mz=>300.0, :end_mz=>1500.0, :ms_level=>1}, hash, "basic info the same")
-  end
-
-  def assert_equal_pair(exp, pair)
-    assert_in_delta(exp[0], pair[0], 0.000000001)
-    assert_in_delta(exp[1], pair[1], 0.000000001)
-  end
-
-  def test_file_to_mzxml
-    if has_t2x?
-      sr_raw = @tfiles + 'smallraw.RAW'
-      sr_noext = @tfiles + 'smallraw'
-      sr_mzxml = @tfiles + 'smallraw.mzXML'
-      klass = Spec::MzXML
-      # given raw
-      file = klass.file_to_mzxml(sr_raw)
-      file_to_mzxml_assert(file)
-      # given mzXML 
-      file = klass.file_to_mzxml(sr_mzxml)
-      file_to_mzxml_assert(file)
-      File.unlink(sr_mzxml)
-      # given basename (and no mzXML)
-      file = klass.file_to_mzxml(sr_noext)
-      file_to_mzxml_assert(file)
-      # given basename (and mzXML)
-      file = klass.file_to_mzxml(sr_noext)
-      file_to_mzxml_assert(file)
-      File.unlink(sr_mzxml)
-    else
-      puts "SKIPPING tests requiring 't2x' to convert RAW to mzXML"
-      puts "(look in the archive folder of the gem for t2x binary for linux)"
-    end
-  end
-    
-
-  def file_to_mzxml_assert(file)
-    assert(file, "file is not nil")
-    assert(File.exist?(file), "file #{file} exists")
-    assert_match(/\.mzXML$/, file, "file ends in mzXML")
-  end
-
-  # returns true if 't2x' matches 'Usage'
-  def has_t2x?
-    reply = ''
-    eval(%q{reply = `t2x`})
-    reply.include? 't2x'
-  end
-
-end
-
-

data/test/tc_mzxml_to_lmat.rb

@@ -1,36 +0,0 @@
-
-require 'test/unit'
-
-
-class TestMzXML2LMat < Test::Unit::TestCase
-  ROOT_DIR = File.join(File.dirname(__FILE__), '..')
-
-  def initialize(arg)
-    super(arg)
-    @tfiles = File.dirname(File.expand_path(__FILE__)) + '/tfiles/'
-    @mzxml = @tfiles + "opd1/twenty_scans.mzXML"
-    @mzxml_big = @tfiles + "yeast_gly_mzXML/000.mzXML"
-    @cmd = "ruby -I #{File.join(ROOT_DIR, 'lib')} -S #{File.join(ROOT_DIR, 'bin', 'mzxml_to_lmat.rb')} "
-    @ans_lmata = @tfiles + "opd1/twenty_scans_answ.lmata"
-    @ans_lmat = @tfiles + "opd1/twenty_scans_answ.lmat"
-  end
-
-  def test_basic_ascii
-    cmd = "#{@cmd} #{@mzxml} --ascii"   
-    puts `#{cmd}`
-    newfile = @mzxml.sub(".mzXML", ".lmata")
-    assert(File.exist?(newfile), "#{newfile} exists")
-    assert(IO.read(@ans_lmata), IO.read(newfile))
-    File.unlink(newfile)
-  end
-
-  def test_basic_binary
-    cmd = "#{@cmd} #{@mzxml}"   
-    puts `#{cmd}`
-    newfile = @mzxml.sub(".mzXML", ".lmat")
-    assert(File.exist?(newfile), "#{newfile} exists")
-    assert(IO.read(@ans_lmat), IO.read(newfile))
-    File.unlink(newfile)
-  end
-end
-

data/test/tc_peptide_parent_times.rb

@@ -1,27 +0,0 @@
-
-require 'test/unit'
-
-class PeptideParentTimesTest < Test::Unit::TestCase
-
-  def initialize(arg)
-    super(arg)
-    @tfiles = "tfiles" # relative test file directory
-  end
-
-  def test_blank
-    ## need to finish this guy up:
-    puts "\nSKIPPING: tests for peptide_parent_times"
-  end
-
-  def Xtest_run
-    reply = `ruby ../script/peptide_parent_times.rb 1.00 tfiles/yeast_gly_small-prot.xml tfiles/yeast_gly_small.xml tfiles/020a.mzXML.timeIndex`
-    #puts reply
-    string1 = File.open((@tfiles +'/'+'yeast_gly_small.1.0_1.0_1.0.parentTimes__020a.working')).read
-    assert(string1.size > 20)
-    string2 = File.open((@tfiles +'/'+'yeast_gly_small.1.0_1.0_1.0.parentTimes__020a')).read
-    assert_equal(string1, string2)
-    to_delete = %w(yeast_gly_small.xml.seqchargehash yeast_gly_small-prot.xml.1.0_1.0_1.0.protpep yeast_gly_small.1.0_1.0_1.0.parentTimes__020a)
-    with_dir = to_delete.collect { |f| @tfiles + '/' + f }
-    with_dir.each { |f| File.unlink f }
-  end
-end

data/test/tc_precision.rb

@@ -1,60 +0,0 @@
-
-require 'test/unit'
-require File.dirname(File.expand_path(__FILE__)) + '/load_bin_path'
-
-
-class PrecTest < Test::Unit::TestCase
-  ROOT_DIR = File.join(File.dirname(__FILE__), "..")
-
-  def initialize(arg)
-    super(arg)
-    @tfiles = File.dirname(__FILE__) + '/tfiles/'
-    @tf_bioworks_esmall_xml = @tfiles + "bioworks_with_INV_small.xml" 
-    @tf_bioworks_shuff = @tfiles + "bioworks_with_SHUFF_small.xml"
-    @cmd = "ruby -I#{File.join(ROOT_DIR, "lib")} -S precision.rb "
-    @tf_html = @tfiles + "ppv.html"
-    @tf_png = @tfiles + "ppv.png"
-    @nodelete = false
-  end
-
-  def test_usage
-    assert_match(/Usage:/, `#{@cmd}`)
-  end
-
-  def test_basic_cat
-    output = `#{@cmd} -o #{@tf_html} -f SHUFF_ --prefix #{@tf_bioworks_shuff}`
-    puts output
-    
-    assert_match(/<table.*<\/table>/m, IO.read(@tf_html), "has html table in it")
-    assert_match(/10.*0.3000/m, IO.read(@tf_html), "has values")
-    [@tf_html, @tf_png].each do |file|
-      assert(File.exist?(file), "file #{file} exists")
-      File.unlink(file) unless @nodelete
-    end
-  end
-
-  def test_multiple_files
-    output = `#{@cmd} -o #{@tf_html} -f SHUFF_,INV_ --prefix #{@tf_bioworks_shuff} #{@tf_bioworks_esmall_xml}`
-    assert_match(/<table.*<\/table>/m, IO.read(@tf_html), "has html table in it")
-    assert_match(/1.*1.0000.*1.*1.0000.*0.*0.*15.*0.8667/m, IO.read(@tf_html), "has values")
-    [@tf_html, @tf_png].each do |file|
-      assert(File.exist?(file), "file #{file} exists")
-      File.unlink(file) unless @nodelete
-    end
-  end
-
-  def test_area_under_curve
-    file = @tfiles + 'ppv_area.txt'
-    `#{@cmd} -o #{file} -a -f SHUFF_ --prefix #{@tf_bioworks_shuff}`
-    assert(File.exist?(file), "file #{file} exists")
-    output = IO.read(file)
-    assert_match(/Prec.*7.39206/, output, "consistency check")
-    File.unlink file
-     
-    outfile = File.join(File.dirname(__FILE__), 'other.html')
-    `#{@cmd} -o #{outfile} -f SHUFF_ --prefix #{@tf_bioworks_shuff}`
-    File.unlink outfile
-    File.unlink File.join(File.dirname(__FILE__),'other.png')
-  end
-
-end

data/test/tc_roc.rb

@@ -1,166 +0,0 @@
-
-require 'test/unit'
-
-require 'roc'
-
-class ROCTest < Test::Unit::TestCase
-
-  def initialize(arg)
-    super(arg)
-  end
-
-  def test_area_under_curve
-    x = [1,2,3]
-    y = [2,3,4]
-    _test_auc(6,x,y)
-
-    x = [1,2,3]
-    y = [-2,-3,-4]
-    _test_auc(-6, x, y)
-
-    x = [1,2,3]
-    y = [4,3,2]
-    _test_auc(6, x, y)
-
-    x = [1,2,3]
-    y = [-4,-3,-2]
-    _test_auc(-6, x, y)
-
-    x = [4,5,6]
-    y = [2,1,2]
-    _test_auc(3, x, y)
-
-    x = [4,5,6]
-    y = [-2,-1,-2]
-    _test_auc(-3, x, y)
-  end
-
-  def _test_auc(expected_area,x,y)
-    area = ROC.new.area_under_curve(x,y)
-    assert_equal(expected_area, area)
-  end
-
-  def test_prep_list
-    t = true
-    f = false
-    x,y = ROC.new.prep_list([[0,f],[1,f],[2,f],[3,t],[3,f],[0,f],[4,f],[1,t],[2,t]])
-    assert_equal([1,2,3], x)
-    assert_equal([0,0,1,2,3,4], y)
-  end
-
-  def test_tps_and_ppv
-    tp = %w(1 2 3 4 5 6 6 6 7 8 9 10 10 10 10 11 12 ).collect {|c| c.to_f } # 17 total
-    fp = %w(3.5 4 5 5 5 6 6 6.5 7 8 9 9.5 10 15).collect {|c| c.to_f } # 14 total
-    xe = [1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 16, 17]
-    #       1, 2, 3, 4        5,   6,             7,             8,   9
-    #       10              11                12
-    ye = [1, 1, 1, 4.0/6.0, 0.5, 8.0/(7.0+8.0), 9.0/(9.0+9.0), 0.5, 11.0/(11.0+ 11.0),  15.0/(15.0+13.0), 16.0/(16.0+13.0), 17.0/(17.0+13.0)]
-    _test_tps_and_ppv_method(tp,fp,xe,ye,"complex real-life-like scenario")
-
-    ## leading fp's
-    tp = [1,2,3]
-    fp = [0,0,1,2,3,4]
-    xe = [1,2,3]
-    ye = [1.0/(1+3), 2.0/(2+4), 3.0/(3+5)]
-    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading fps")
-
-    ## leading tp's
-    tp = [-1,2,3]
-    fp = [0,4]
-    xe = [1,2,3]
-    ye = [1.0/(1+0), 2.0/(2+1), 3.0/(3+1)]
-    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading tps")
-
-    ## equal tp's leading
-    tp = [0.0001,0.0001,0.0001,2]
-    fp = [0.01,4.0]
-    xe = [3,4]
-    ye = [3.0/(3+0), 4.0/(4+1)]
-    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal tps leading")
-
-    ## equal arrays with some repeated values
-    tp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
-    fp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
-    xe = [1,2,4,5,6,7]
-    ye = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
-    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal arrays with some repeated values")
-
-  end
-
-  def _test_tps_and_ppv_method(tp,fp,xe,ye,message='')
-    (x,y) = ROC.new.tps_and_ppv(tp,fp)
-    assert_equal(x.size, y.size)
-    assert_equal(xe, x)
-    assert_equal(ye, y, "tps_and_ppv: #{message}")
-  end
-
-end
-
-class DecoyROCTest < ROCTest
-
-  def test_pred_tps_ppv__leading_fps
-    ## leading fp's
-    hits = [1,2,3]
-    decoys = [0,0,1,2,3,4]
-    num_hits_e = [1,2,3]
-    num_fps = [3,4,5]
-    tps_e = make_tps_e(num_fps, num_hits_e)
-    ppv_e = make_ppv_e(tps_e, num_hits_e)
-    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
-  end
-
-  def test_pred_tps_ppv__leading_tps
-    ## leading tp's
-    hits = [-1,2,3]
-    decoys = [0,4]
-    num_hits_e = [1,2,3]
-    num_fps = [0,1,1]
-    tps_e = make_tps_e(num_fps, num_hits_e)
-    ppv_e = make_ppv_e(tps_e, num_hits_e)
-    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
-  end
-
-  def test_pred_tps_ppv__equal_tps_leading
-    hits = [0.0001,0.0001,0.0001,2]
-    decoys = [0.01,4.0]
-    num_hits_e = [3,4]
-    num_fps = [0,1]
-    tps_e = make_tps_e(num_fps, num_hits_e)
-    ppv_e = make_ppv_e(tps_e, num_hits_e)
-    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
-  end
-
-  def test_pred_tps_ppv__equal_arrays_with_some_repeated_values
-    hits = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
-    decoys = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
-    num_hits_e = [1,2,4,5,6,7]
-    num_fps = [1,2,4,5,6,7]
-    tps_e = make_tps_e(num_fps, num_hits_e)
-    ppv_e = make_ppv_e(tps_e, num_hits_e)
-    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
-  end
-
-  def _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
-    answer = DecoyROC.new.pred_and_tps_and_ppv(hits, decoys)
-    expected = [num_hits_e, tps_e, ppv_e]
-    %w(num_hits num_tps ppv).each_with_index do |cat, i|
-      assert_equal(expected[i], answer[i], cat)
-    end
-  end
-
-  def make_tps_e(num_fps, num_hits_e)
-    tps_e = []
-    num_hits_e.each_with_index do |v,i|
-      tps_e[i] = v - num_fps[i]
-    end
-    tps_e
-  end
-
-  def make_ppv_e(tps_e, num_hits_e)
-    ppv_e = []
-    tps_e.each_with_index {|v,i| ppv_e[i] = v.to_f/num_hits_e[i] }
-    ppv_e
-  end
-
-end
-

data/test/tc_sample_enzyme.rb

@@ -1,32 +0,0 @@
-
-require 'test/unit'
-require 'sample_enzyme'
-require 'set'
-
-class Trypsin < Test::Unit::TestCase
-  def test_no_missed_cleavage
-    st = "CRGATKKTAGRPMEK"
-    assert_equal(%w(CR GATK K TAGRPMEK), SampleEnzyme.tryptic(st))
-    st = "CATRP"
-    assert_equal(%w(CATRP), SampleEnzyme.tryptic(st))
-    st = "RCATRP"
-    assert_equal(%w(R CATRP), SampleEnzyme.tryptic(st))
-    st = ""
-    assert_equal([], SampleEnzyme.tryptic(st))
-    st = "R"
-    assert_equal(%w(R), SampleEnzyme.tryptic(st))
-  end
-
-  def test_missed_cleavage
-    st = "CRGATKKTAGRPMEKLLLERTKY"
-    zero = %w(CR GATK K TAGRPMEK LLLER TK Y)
-    assert_equal(zero.to_set, SampleEnzyme.tryptic(st,0).to_set)
-    one = %w(CRGATK GATKK KTAGRPMEK TAGRPMEKLLLER LLLERTK TKY)
-    assert_equal((zero+one).to_set, SampleEnzyme.tryptic(st,1).to_set)
-    two = %w(CRGATKK GATKKTAGRPMEK KTAGRPMEKLLLER TAGRPMEKLLLERTK LLLERTKY)
-    all = zero + one + two
-    assert_equal(all.to_set, SampleEnzyme.tryptic(st,2).to_set)
-  end
-
-
-end

data/test/tc_scan.rb

@@ -1,26 +0,0 @@
-
-require 'test/unit'
-require 'spec/scan'
-
-class ScanTest < Test::Unit::TestCase
-  include Spec
-  def test_add_parent_scan
-    s1 = Scan.new(1,1,0.13)
-    s2 = Scan.new(2,2,0.23)
-    s3 = Scan.new(3,2,0.33)
-    s4 = Scan.new(4,3,0.43)
-    s5 = Scan.new(5,3,0.53)
-    s6 = Scan.new(6,1,0.63)
-    s7 = Scan.new(7,2,0.73)
-    s8 = Scan.new(8,3,0.83)
-    s9 = Scan.new(9,2,0.93)
-    scans = [s1,s2,s3,s4,s5,s6,s7,s8,s9]
-    parents = [nil,s1,s1,s3,s3,nil,s6,s7,s6]
-    Scan.add_parent_scan(scans)
-
-    scans.each_with_index do |scan,i|
-      assert_equal parents[i], scan.parent
-    end
-  end
-
-end