prob_spec.rb in mspire-0.3.9

- old
+ new
@@ -39,73 +39,6 @@
   end
 
 end
 
 
-=begin
-  it 'gets precision with all validators (including probability and decoy)' do
-    ## create some decoy peptides!
-    @spec_id.peps.sort_by {|pep| pep.probability }[100..-1].each_with_index do |pep,i|
-      if i % 3 == 0
-        pep.prots.each {|prot| prot.protein_name = 'DECOY_' + prot.protein_name }
-      end
-    end
-    # check which ones are ACTUALLY normal and decoy
-    (decoy, normal) = @spec_id.peps.partition do |pep|
-      pep.prots.all? {|prot| prot.protein_name =~ /^DECOY_/}
-    end
-    num_decoy = decoy.size
-    num_normal = normal.size
-  end
 
-prob_spec_helper = File.expand_path( File.dirname(__FILE__) + '/prob_spec_helper' )
-
-# this does a minimal test to see if this functions properly
-# (not for accuracy, which is done in validator_spec)
-## WITH FASTA FILE:
-base_dir = Tfiles_l + '/opd1_2runs_2mods/sequest'
-fasta_file = base_dir + '/ecoli_K12_ncbi_20060321.fasta'
-params_file = base_dir + '/ecoli.params'
-bias_file = base_dir + '/ecoli_K12_ncbi_20060321.bias.fasta'
-toppred_file = base_dir + '/ecoli_K12_ncbi_20060321.toppred.xml'
-
-fasta_file.should exist
-
-prob = Validator::Probability.new
-badaa_freq = Validator::AA.new('C', :frequency => 0.0115866200193321)
-badaa_dig = Validator::AA.new('C')
-bias = Validator::Bias.new(Fasta.new(bias_file))
-transmem = Validator::Transmem::Protein.new(toppred_file)
-decoy = Validator::Decoy.new(/^DECOY_/)
-
-turn_on_digestion = true
-if turn_on_digestion
-  # digestion based validators need this set!
-  digested_peps = Digestor.digest(Fasta.new(fasta_file), Sequest::Params.new(params_file))
-  [badaa_dig, bias, transmem].each do |val|
-    val.set_false_to_total_ratio(digested_peps)
-  end
-end
-transmem.transmem_status_hash = transmem.create_transmem_status_hash(@spec_id.peps)
-val_list = [decoy, badaa_freq, badaa_dig, prob, bias, transmem]
-
-opts = { :validators => val_list }
-
-
-hash = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id, opts)
-#puts "OUTPUT: "
-#puts hash.to_yaml
-
-
-# frozen
-e_hash = ProbMSHelper::Answer2
-# hash[:pephits_precision].size.should == e_hash[:pephits_precision].size
-# other data types are tested above, just testing validators
-hash[:pephits_precision].zip( e_hash[:pephits_precision] ) do |val_hash, val_hash_e|
-  val_hash[:values].size.should == num_normal
-  #val_hash[:validator].should == val_hash_e[:validator]
-  val_hash[:values].zip(val_hash_e[:values]) {|v,e| v.should be_close(e, 0.000000001)}
-end
-    end
-end
-
-=end