mspire 0.4.9 → 0.5.0

data/specs/bin/filter_and_validate__multiple_vals_helper.yaml

@@ -1,199 +0,0 @@
---- 
-pephits_precision: 
-- validator: decoy
-  value: 0.992932862190813
-- validator: badAAEst
-  value: 0.178006237270664
-- validator: badAAEst
-  value: -0.0247654296463379 
-- validator: badAA
-  value: 0.301413862599215
-- validator: bias
-  value: 0.19471183136347
-- validator: bias
-  value: -4.79308077902868
-- validator: bias
-  value: 0.402836536134372
-- validator: tmm
-  value: 0.437921755087444
-- validator: tmm
-  value: -0.267185328932326
-- validator: tmm
-  value: -0.155831020815818
-- validator: tmm
-  value: -0.0201924414730414
-- validator: tps
-  value: 0.226148409893993
-pephits: 283
-prothits_precision: 
-- validator: decoy
-  values: 
-    :normal_stdev: 0.00659628206397061
-    :normal: 0.99622641509434
-    :worst: 0.971698113207547
-- validator: badAA
-  values: 
-    :normal_stdev: 0.0305695315962635
-    :normal: 0.334905660377358
-    :worst: 0.0188679245283019
-- validator: badAA
-  values: 
-    :normal_stdev: 0.0
-    :normal: 0.0
-    :worst: 0.0
-- validator: badAA
-  values: 
-    :normal_stdev: 0.0263288499231859
-    :normal: 0.497169811320755
-    :worst: 0.0377358490566038
-- validator: bias
-  values: 
-    :normal_stdev: 0.0329963984643387
-    :normal: 0.355660377358491
-    :worst: 0.0188679245283019
-- validator: bias
-  values: 
-    :normal_stdev: 0.0
-    :normal: 0.0
-    :worst: 0.0
-- validator: bias
-  values: 
-    :normal_stdev: 0.0266832747617573
-    :normal: 0.613207547169811
-    :worst: 0.0943396226415094
-- validator: tmm
-  values: 
-    :normal_stdev: 0.0281442148871296
-    :normal: 0.65377358490566
-    :worst: 0.122641509433962
-- validator: tmm
-  values: 
-    :normal_stdev: 0.0
-    :normal: 0.0
-    :worst: 0.0
-- validator: tmm
-  values: 
-    :normal_stdev: 0.0
-    :normal: 0.0
-    :worst: 0.0
-- validator: tmm
-  values: 
-    :normal_stdev: 0.0
-    :normal: 0.0
-    :worst: 0.0
-- validator: tps
-  values: 
-    :normal_stdev: 0.0317750140353944
-    :normal: 0.402830188679245
-    :worst: 0.0283018867924528
-params: 
-  validators: 
-  - :type: decoy
-    :class: Validator::Decoy
-    :constraint: /^DECOY_/
-    :decoy_on_match: true
-    :correct_wins: true
-  - :calculated_background: 0.127208480565371
-    :type: badAAEst
-    :class: Validator::AAEst
-    :background: 0.001
-    :frequency: 0.0147528119278054
-  - :calculated_background: 0.402826855123675
-    :type: badAAEst
-    :class: Validator::AAEst
-    :background: 0.0
-    :frequency: 0.0463510332199843
-  - :calculated_background: 0.127208480565371
-    :type: badAA
-    :class: Validator::AA
-    :background: 0.001
-    :false_to_total_ratio: 0.180662732637313
-  - :calculated_background: 0.773851590106007
-    :type: bias
-    :class: Validator::Bias
-    :proteins_expected: true
-    :correct_wins: true
-    :background: 0.0
-    :file: /work/john/mspire/specs/../test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-    :false_to_total_ratio: 0.960962324103495
-  - :calculated_background: 0.226148409893993
-    :type: bias
-    :class: Validator::Bias
-    :proteins_expected: false
-    :correct_wins: true
-    :background: 0.0
-    :file: /work/john/mspire/specs/../test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-    :false_to_total_ratio: 0.0390376758965048
-  - :calculated_background: 0.773851590106007
-    :type: bias
-    :class: Validator::Bias
-    :proteins_expected: true
-    :correct_wins: true
-    :background: 0.2
-    :file: /work/john/mspire/specs/../test_files/validator_hits_separate/bias_bioworks_small_HS.fasta
-    :false_to_total_ratio: 0.960962324103495
-  - :calculated_background: 0.359430604982206
-    :type: tmm
-    :soluble_fraction: true
-    :class: Validator::Transmem::Protein
-    :no_include_tm_peps: 0.8
-    :correct_wins: true
-    :background: 0.2
-    :transmem_file: /work/john/mspire/specs/../test_files/bioworks_small.phobius
-    :false_to_total_ratio: 0.283644859813084
-    :min_num_tms: 1
-  - :calculated_background: 0.359430604982206
-    :type: tmm
-    :soluble_fraction: true
-    :class: Validator::Transmem::Protein
-    :no_include_tm_peps: 0.8
-    :correct_wins: true
-    :background: 0.0
-    :transmem_file: /work/john/mspire/specs/../test_files/bioworks_small.phobius
-    :false_to_total_ratio: 0.283644859813084
-    :min_num_tms: 1
-  - :calculated_background: 0.293286219081272
-    :type: tmm
-    :soluble_fraction: true
-    :class: Validator::Transmem::Protein
-    :no_include_tm_peps: false
-    :correct_wins: true
-    :background: 0.0
-    :transmem_file: /work/john/mspire/specs/../test_files/bioworks_small.toppred.out
-    :false_to_total_ratio: 0.253744893327281
-    :min_num_tms: 3
-  - :calculated_background: 0.472924187725632
-    :type: tmm
-    :soluble_fraction: true
-    :class: Validator::Transmem::Protein
-    :no_include_tm_peps: 0.8
-    :correct_wins: true
-    :background: 0.0
-    :transmem_file: /work/john/mspire/specs/../test_files/bioworks_small.toppred.out
-    :false_to_total_ratio: 0.463563704748472
-    :min_num_tms: 1
-  - :type: tps
-    :class: Validator::TruePos
-  ties: true
-  digestion: 
-  - /work/john/mspire/specs/../test_files/bioworks_small.fasta
-  - /work/john/mspire/specs/../test_files/bioworks_small.params
-  prefilter: false
-  output: 
-  - text_table => /work/john/mspire/specs/../test_files/table_output.tmp
-  - yaml => /work/john/mspire/specs/../test_files/filter_and_validate.tmp
-  sequest: 
-    include_deltacnstar: true
-    xcorr1: 0.0
-    ppm: 1000000.0
-    xcorr2: 0.0
-    deltacn: 0.01
-    xcorr3: 0.0
-  top_hit_by: xcorr
-  decoy_on_match: true
-  postfilter: top_per_scan
-  include_ties_in_top_hit_postfilter: false
-  hits_together: true
-  proteins: true
-  include_ties_in_top_hit_prefilter: true
-prothits: 106

data/specs/bin/filter_and_validate_spec.rb

@@ -1,180 +0,0 @@
-require 'yaml'
-
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-require 'spec_id/precision/filter'
-
-describe 'filter_and_validate.rb on small bioworks file' do
-  before(:all) do
-    @progname = 'filter_and_validate.rb'
-
-    @outfile = Tfiles + '/filter_and_validate.tmp'
-
-    # direct call with an array
-    @direct_call = Proc.new {|ar| SpecID::Precision::Filter.new.filter_and_validate_cmdline(ar) }
-    # direct call with a string
-    @direct_call_st = Proc.new {|st| @direct_call.call(st.split(/\s+/)) }
-    @st_to_yaml = Proc.new do |st| 
-      to_call = st + " -o yaml:#{@outfile} "
-      @direct_call.call(to_call.split(/\s+/)) 
-      YAML.load_file(@outfile)
-    end
-
-    @args = ["-1 0.6 -2 0.8 -3 0.9 -d 0.2", (Tfiles + '/bioworks_small.xml ')].join(' ')
-    @interactive_file = Tfiles + '/interactive.tmp'
-    File.open(@interactive_file,'w') do |fh| 
-      string = ["0.6 0.8 0.9 0.2 5000", "dcns:f", "0.6 0.8 dcns:t", "pf:s", "pf:ac", "pf:a"].join("\n")
-      fh.puts string
-    end
-    # uses DECOY_ prefix on two
-    @fake_bioworks_file = Tfiles + '/validator_hits_separate/bioworks_small_HS.xml'
-    @small_bias_fasta_file = Tfiles + '/validator_hits_separate/bias_bioworks_small_HS.fasta'
-    @small_fasta_file = Tfiles + '/bioworks_small.fasta'
-    @params_file = Tfiles + '/bioworks_small.params'
-    @toppred_file = Tfiles + '/bioworks_small.toppred.out'
-    @phobius_file = Tfiles + '/bioworks_small.phobius'
-    @table_output_file = Tfiles + '/table_output.tmp'
-  end
-
-  after(:all) do
-    [@outfile, @interactive_file, @table_output_file].each do |file|
-      File.unlink(file) if File.exist?(file)
-    end
-  end
-
-  # this ensures that the actual commandline version gives usage.
-  it_should_behave_like "a cmdline program"
-
-  it 'filters a file and outputs to table or yaml' do
-    @direct_call_st.call( @args + " -o text_table:#{@outfile}")
-    IO.read(@outfile).should =~ /66/
-    struct = @st_to_yaml.call( @args )
-    struct['pephits'].should == 66
-  end
-
-  it 'responds to --no_deltacnstar' do
-    reply_without = @st_to_yaml.call( @args + " --no_deltacnstar" )
-    reply_without['pephits'].should == 34
-  end
-
-  it 'works with interactive input (includes dcnstar and postfilter)' do
-    @direct_call_st.call( "-o text_table:#{@outfile} -i #{@interactive_file} "  + Tfiles + '/bioworks_small.xml ' )
-    reply = IO.read(@outfile)
-
-    exp = %w(73 40 73 73 33 33)
-    reply.scan(/^peps\s+(\d+)/) do |v|
-      Regexp.last_match[1] == exp.shift
-    end
-  end
-
-  it 'responds to ppm filter' do
-    reply_without = @st_to_yaml.call( @args + " -p 280" )
-    reply_without['pephits'].should == 11
-  end
-
-  it 'responds to --hits_separate' do
-    # this file has two decoy peps that score better than the real peps at
-    # those scans
-        ht_file = Tfiles + '/test_together.tmp.yaml'
-    hs_file = Tfiles + '/test_separate.tmp.yaml'
-    outputs = [ht_file, hs_file].zip(['', ' --hits_separate']).map do |output_file, flag|
-      run_normal = @cmd + " --bias #{@small_bias_fasta_file} --decoy /^DECOY_/ --digestion #{@small_fasta_file},#{@params_file} #{@fake_bioworks_file} -1 0.0 -2 0.0 -3 0.0 -d 0.01 -p 1000000 -o yaml:#{output_file} #{flag}"
-      `#{run_normal}`
-    end
-    structs = [ht_file, hs_file].map do |file| 
-      file.exist_as_a_file?.should be_true
-      struct = YAML.load_file(file)
-      File.unlink file
-      struct
-    end
-
-    comparisons = %w(precision calc_bkg hits_together_param)
-    comps = structs.map do |st|
-      # note that calculated_background may need to be a string if we get our
-      # act together...
-      [ st['pephits_precision'][0]['value'], st['params']['validators'][0][:calculated_background], st['params']['hits_together'] ]
-    end
-    comparisons.zip( *comps ) do |tp, ht, hs|
-      ht.should_not == hs
-    end
-
-  end
-
-  it 'raises error on > 1 decoy validator' do
-    lambda { @st_to_yaml.call( @args + " --decoy /hello/ --decoy path/to/file" ) }.should raise_error(ArgumentError)
-  end
-
-  it 'handles multiple validators of the same kind (except, of course, decoy)' do
-
-    struct = @st_to_yaml.call( "#{@fake_bioworks_file} --proteins  -1 0.0 -2 0.0 -3 0.0 -d 0.01 -p 1000000 --decoy /^DECOY_/ --digestion #{@small_fasta_file},#{@params_file} --bad_aa_est C,0.001 --bad_aa_est E --bad_aa C,0.001 --bias #{@small_bias_fasta_file},true --bias #{@small_bias_fasta_file},false --bias #{@small_bias_fasta_file},true,0.2 --fasta #{@small_fasta_file} --tmm #{@phobius_file},1,true,0.8,0.2 --tmm #{@phobius_file} --tmm #{@toppred_file},3,true,false --tmm #{@toppred_file} --tps #{@small_bias_fasta_file} -o text_table:#{@table_output_file} " )
-    frozen = YAML.load_file( File.dirname(__FILE__) + "/filter_and_validate__multiple_vals_helper.yaml" )
-
-    ## Pephits precision:
-    ordering = frozen['pephits_precision'].map {|v| v['validator'] }
-    vals = frozen['pephits_precision'].map {|v| v['value'] }
-    struct['pephits_precision'].zip(ordering, vals) do |act, vali, val|
-      act['validator'].should == vali
-      act['value'].should == val
-    end
-
-    struct['pephits'].should == frozen['pephits']
-
-    ##### Params:
-    frp = frozen['params']
-    stp = struct['params']
-
-    #puts "frozen validators:"
-    #p frp['validators']
-
-    #puts "seen validators:"
-    #p stp['validators']
-
-    frp['validators'].zip(stp['validators']) do |f,s|
-      if f.is_a? Hash
-        f.keys.each do |k|
-          if k == :file or k == :transmem_file
-            File.basename(f[k]).should == File.basename(s[k].gsub('\\','/'))
-          else
-            s[k].should == f[k]
-            #f[k].should == s[k]
-          end
-        end
-      else
-        f.should == s
-      end
-    end
-
-    %w(ties prefilter top_hit_by decoy_on_match postfilter include_ties_in_top_hit_postfilter hits_together proteins include_ties_in_top_hit_prefilter).each do |k|
-      stp[k].should == frp[k]
-    end
-    
-    ## digestion & output (special)
-    %w(digestion output).each do |k|
-      stp[k].zip(frp[k]).each do |s,f|
-        File.basename( s.gsub('\\', '/') ).should == File.basename(f)
-      end
-    end
-
-    ## Sequest:
-    frp['sequest'].each do |k,v|
-      stp['sequest'][k].should == v
-    end
-
-    ## TODO: Fill in protein level stuff once stabilized
-
-    #struct.should == frozen
-
-    text_table = IO.read(@table_output_file)
-
-    # frozen
-    headings_re = Regexp.new( %w(num decoy badAAEst badAAEst badAA  bias  bias  bias   tmm   tmm   tmm   tmm   tps).join("\\s+") )
-    data_re = Regexp.new( %w(peps 283 0.993 0.178006 -0.024765 0.301 0.195 -4.793 0.403 0.438 -0.267 -0.156 -0.020 0.226).join("\\s+") )
-    prot_re = Regexp.new( %w(106 0.972 0.018868   0.0 0.038 0.019   0.0 0.094 0.123   0.0   0.0   0.0 0.028).join("\\s+") )
-    text_table.should =~ headings_re
-    text_table.should =~ data_re
-    text_table.should =~ prot_re
-  end
-
-end
-
-

data/specs/bin/ms_to_lmat_spec.rb

@@ -1,34 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-
-describe 'ms_to_lmat.rb' do
-
-  before(:all) do
-    @progname = 'ms_to_lmat.rb'
-    @mzxml = Tfiles + "/opd1/twenty_scans.mzXML"
-    @ans_lmata = Tfiles + "/opd1/twenty_scans_answ.lmata"
-    @ans_lmat = Tfiles + "/opd1/twenty_scans_answ.lmat"
-  end
-
-  it_should_behave_like "a cmdline program"
-
-  it 'creates the correct lmata (ascii) file' do
-    cmd = "#{@cmd} #{@mzxml} --ascii"   
-    `#{cmd}`
-    newfile = @mzxml.sub(".mzXML", ".lmata")
-    newfile.exist_as_a_file?.should be_true
-    IO.read(newfile).should == IO.read(@ans_lmata)
-    File.unlink(newfile)
-  end
-
-
-  it 'creates the correct lmat (binary) file' do
-    cmd = "#{@cmd} #{@mzxml}"   
-    `#{cmd}`
-    newfile = @mzxml.sub(".mzXML", ".lmat")
-    newfile.exist_as_a_file?.should be_true
-    IO.read(newfile).should == IO.read(@ans_lmat)
-    File.unlink(newfile)
-  end
-end
-

data/specs/bin/prob_validate_spec.rb

@@ -1,86 +0,0 @@
-require 'yaml'
-
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-require 'spec_id/precision/prob'
-
-describe 'filter_and_validate.rb on small bioworks file' do
-  before(:all) do
-    @progname = 'prob_validate.rb'
-
-    @outfile = Tfiles + '/prob_and_validate.tmp'
-
-    # direct call with an array
-    @direct_call = Proc.new {|ar| SpecID::Precision::Prob.new.precision_vs_num_hits_cmdline(ar) }
-    # direct call with a string
-    @direct_call_st = Proc.new {|st| @direct_call.call(st.split(/\s+/)) }
-    @st_to_yaml = Proc.new do |st| 
-      to_call = st + " -o yaml:#{@outfile} "
-      @direct_call.call(to_call.split(/\s+/)) 
-      YAML.load_file(@outfile)
-    end
-
-    file = Tfiles + '/opd1/000_020_3prots-prot.mod_initprob.xml'
-    @args = [file].join(' ')
-    # uses DECOY_ prefix on two
-    @fake_bioworks_file = Tfiles + '/validator_hits_separate/bioworks_small_HS.xml'
-    @small_bias_fasta_file = Tfiles + '/validator_hits_separate/bias_bioworks_small_HS.fasta'
-    @small_fasta_file = Tfiles + '/bioworks_small.fasta'
-    @params_file = Tfiles + '/bioworks_small.params'
-    @toppred_file = Tfiles + '/bioworks_small.toppred.out'
-    @phobius_file = Tfiles + '/bioworks_small.phobius'
-  end
-
-  after(:all) do 
-    [@outfile].each do |file|
-      File.unlink(file) if File.exist?(file)
-    end
-  end
-
-  ############################ uncomment this::
-  # this ensures that the actual commandline version gives usage.
-  # it_should_behave_like "a cmdline program"
-
-  it 'outputs to yaml' do
-    reply = @st_to_yaml.call( @args )
-    keys = [:probabilities, :params, :pephits, :pephits_precision, :charges, :aaseqs, :count].map {|v| v.to_s }.sort
-    reply.keys.map {|v| v.to_s}.sort.should == keys
-  end
-
-
-  it 'responds to --prob init' do
-    normal = @st_to_yaml.call( @args + " --prob" )
-
- normal[:pephits_precision].first[:values].zip([1.0, 1.0, 0.993333333333333, 0.85]) do |got,exp|
-      got.should be_close(exp, 0.000000000001)
-    end
-    #normal_nsp = @st_to_yaml.call( @args + " --prob nsp" )
-    #normal.should == normal_nsp
-    init = @st_to_yaml.call( @args + " --prob init" )
-
-    init[:pephits_precision].first[:values].should_not == normal[:pephits_precision].first[:values]
-
-
-    init[:pephits_precision].first[:values].zip([1.0, 0.95, 0.963333333333333, 0.8025]) do |got,exp|
-      got.should be_close(exp, 0.000000000001)
-    end
-    with_sort_by = @st_to_yaml.call( @args + " --prob nsp --sort_by_init" )
-    # frozen
-    with_sort_by[:pephits_precision].first[:values].zip([1.0, 0.99, 0.993333333333333, 0.85]) do |got,exp|
-      got.should be_close(exp, 0.000000000001)
-    end
-  end
-
-  it 'works with --to_qvalues flag' do
-    begin
-      normal = @st_to_yaml.call( @args + " --to_qvalues --prob" )
-    rescue RuntimeError
-      # right now the p values in this data set don't lend themselves to
-      # legitimate q-values, so we get a RuntimeError
-      # Need to work this one out
-    end
-  end
-
-end
-
-

data/specs/bin/protein_summary_spec.rb

@@ -1,14 +0,0 @@
-require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
-
-describe 'protein_summary.rb' do
-
-   before(:all) do
-    @progname = 'protein_summary.rb'
-  end
-  it_should_behave_like 'a cmdline program'
-
-  it 'outputs basic protein prophet -prot.xml summary' do
-
-  end
-
-end