Class: SpecID::Filter

Inherits:
Object
  • Object
show all
Defined in:
lib/spec_id/filter.rb

Constant Summary collapse

NUM_PROT_FPPR_ITERATIONS = 
10

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.run_from_argv(argv) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 156

def self.run_from_argv(argv)
  obj = self.new
  obj.run_from_argv(argv)
end

Instance Method Details

#calculate_pep_fppr(pephits_ar, methods, args, false_pephits_ar = nil) ⇒ Object

methods should be passed in like this ‘cysteine’ for cysteine_fppr all methods should return [number_false, fppr] returns a hash (by method) for each set of pephits if :dcy is given as a method, then expects the false pephits array



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# File 'lib/spec_id/filter.rb', line 575

def calculate_pep_fppr(pephits_ar, methods, args, false_pephits_ar=nil)
  cnt = 0
  pephits_ar.map do |ph|
    hash = {}
    methods.each do |mth|
      case mth
      when :dcy
        hash[mth.to_sym] = send("#{mth}_fppr".to_sym, ph, false_pephits_ar[cnt])  
      when :cys
        hash[mth.to_sym] = send("#{mth}_fppr".to_sym, ph, *(args[:cys]) )
      when :tps
        hash[mth.to_sym] = send("#{mth}_fppr".to_sym, ph, (args[:tps]) )
      else
        hash[mth.to_sym] = send("#{mth}_fppr".to_sym, ph)  
      end
    end
    cnt += 1
    hash
  end
end

#combined_score(filter_args) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 709

def combined_score(filter_args)
  (x1, x2, x3, deltacn, ppm) = filter_args
  combined_score = x1 + x2 + x3 + 20.0*deltacn + 4000.0*(1.0/ppm)
end

#cys_fppr(pephits, cys_bg_freq, cys_containing_freq) ⇒ Object

returns [#FP, FPPR]



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# File 'lib/spec_id/filter.rb', line 562

def cys_fppr(pephits, cys_bg_freq, cys_containing_freq)
  (total_num_false, cys_fprate, fraction_of_expected) = fraction_false_by_cysteines(pephits, cys_bg_freq, cys_containing_freq)
  [total_num_false, cys_fprate]
end

#dcy_fppr(pephits, false_pephits) ⇒ Object

returns [#FP, FPPR]



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# File 'lib/spec_id/filter.rb', line 552

def dcy_fppr(pephits, false_pephits)
  fps = false_pephits.size
  [fps, fps.to_f/pephits.size]
end

#file_to_prefiltered_spec_id(file, opt) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 757

def file_to_prefiltered_spec_id(file, opt)
  spec_id = nil
  marshal_file = file + ".prefiltered.msh"
  if File.exist?(marshal_file)
    File.open(marshal_file) do |fh|
      spec_id = Marshal.load(fh)
    end
  else
    spec_id = SpecID.new(file)
    spec_id.passed_in_filename = file
    spec_id.top_peps_prefilter!
    ## marshal it!
    if opt.marshal
      File.open(marshal_file, "w") do |fh|
        Marshal.dump(spec_id,fh)
      end
    end
  end
  spec_id
end

#filter_legend(fppr_methods) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 494

def filter_legend(fppr_methods)
  lines = []
  lines << "Note: protein FPPR values are probably optimistic"
  lines << "[this implementation assumes an equal likelihood that a false peptide"
  lines << " comes from a protein with more hits as one with less (which is probably"
  lines << " not the case)]"
  lines << "* = deltacn_star = peptides with deltacn > 1.0 (no sibling hits)"
  if fppr_methods.size > 0
    lines << "Following are methods for determining false identification rate:"
    lines << ['dcy=decoy', 'cys=cysteine', 'tps=known_true_positives'].join(" ")
    ## when tmm is implemented:
    #lines << ['dcy=decoy', 'cys=cysteine', 'tmm=transmembrane', 'tps=known_true_positives'].join(" ")
  end
  lines.join("\n")
end

#filter_params_string(filter_args, fppr_methods) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 678

def filter_params_string(filter_args, fppr_methods)
  (x1, x2, x3, deltacn, ppm) = filter_args
  st = []
  st << "=========================================================================="
  st << " xcorr(1,2,3) >= #{x1},#{x2},#{x3} || deltacn >= #{deltacn} || ppm <= #{ppm} "
  st << ''
  st.join("\n")
  #st = []
  #st << ["xcorr(1,2,3) >= #{x1},#{x2},#{x3}", "deltacn >= #{deltacn}", "ppm <= #{ppm}"].join("\t")
  #st
end

#filter_round(spec_ids, filter_args, args) ⇒ Object

fpr is a SpecID obj that is the false positives cysteines holds an aafreqs object or nil



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# File 'lib/spec_id/filter.rb', line 598

def filter_round(spec_ids, filter_args, args)

  # push fpr on the end for the calculations
  ## FILTER the NORMAL spec_id objects
  little_tables = []
  spec_ids.each_with_index do |spec_id, i|
    normal_results = filter_spec_id(spec_id, filter_args, args)

    ## FILTER the FALSE objects (if given)
    false_results = 
      if args[:dcy]
        little_args_hash = args.dup
        false_results = filter_spec_id(args[:dcy][i], filter_args, little_args_hash)
      end

    ## HOW TO CALCULATE FPPR FOR EVERYTHING:
    # pephits     Fpephits C/Tpephits  TPpephits
    # uniqaa      Funiqaa  C/Tuniqaa   TPuniqaa
    # prothits    ProtFPR(Fpephits, prothits)   ProtFPR(C/Tpephits, prothits)   ProtFPR(total-TPpephits, prothits)
    # OccProthits ProtFPR(Funiqaa, OccProthits) ProtFPR(C/Tuniqaa, OccProthits) ProtFPR(total-TPuniqaa, OccProthits)
    # C/T = cystein or Transmembrane method

    ## set up false results array
    if args[:dcy]
      fr_ar = [false_results[:pephits], false_results[:aaseq]]
    else
      fr_ar = nil
    end
    (pephits_fppr_results, aaseq_fppr_results) = calculate_pep_fppr([normal_results[:pephits], normal_results[:aaseq]], @fppr_methods, args, fr_ar)

    ## NORMAL prothits
    ## update prothits peptides
    updated_proteins = SpecID.passing_proteins(normal_results[:pephits], :update)
    pep_cnt_arr = updated_proteins.map {|v| v.peps.size }

    ## update occams prothits
    if args[:occams_razor]
      updated_occams_protein_triplets = SpecID::occams_razor(updated_proteins, true)
      occams_pep_cnt_arr = updated_occams_protein_triplets.map {|v| v[1].size }
      occams_prots = updated_occams_protein_triplets.map {|v| v[0] }
      normal_results[:occams_razor] = occams_prots
    end

    ## note that the original prot.peps arrays are obliterated by this.
    ## we would need to re-update if someone wanted these

    prothits_fppr_results = {}
    occams_results = {}
    @fppr_methods.each do |mth|
      prothits_fppr_results[mth] = protein_fppr(pep_cnt_arr, pephits_fppr_results[mth].first.ceil.to_i, NUM_PROT_FPPR_ITERATIONS)
      occams_results[mth] = protein_fppr(occams_pep_cnt_arr, aaseq_fppr_results[mth].first.ceil.to_i, NUM_PROT_FPPR_ITERATIONS) if args[:occams_razor]
    end

    fppr_results = {
      :pephits => pephits_fppr_results,
      :aaseq => aaseq_fppr_results,
      :prothits => prothits_fppr_results,
    }
    fppr_results[:occams_razor] = occams_results if args[:occams_razor]

    ## CHANGE ALL RESULTS INTO PERCENTAGES:
    fppr_results.each do |bk,hash|
      hash.each do |k,val|
        hash[k][1] = 100.0 * val[1] 
      end
    end
    little_tables[i] = to_table( spec_id, args, normal_results, fppr_results, @groups_reporting, @fppr_methods, @cat_labels)
  end

  out filter_params_string(filter_args, @fppr_methods)
  little_tables.each do |tbl|
    out tbl.to_formatted_string(nil, '  ')
    out "-----------------------------------------------\n"
  end
  #big_table(spec_ids, filter_args, args, normal_results, groups_reporting, fppr_results, cat_labels)
  
end

#filter_spec_id(spec_id, filter_args, args) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 537

def filter_spec_id(spec_id, filter_args, args)
  results_hash = {}
  # that second argument is to update protein peptides
  pephits = spec_id.filter_sequest(filter_args)

  results_hash[:prothits] = SpecID.passing_proteins(pephits, :no_update)
  results_hash[:pephits] = pephits
  results_hash[:dcn_cnt] = pephits.select{|v| v.deltacn > 1.0}.size
  # be aware that this is a hash keyed by aaseq and values of arrays of
  # peptides sharing the same aaseq!
  results_hash[:aaseq] = pephits.hash_by(:aaseq)
  results_hash
end

#fppr_by_cysteines(ac_num_with_cys, exp_num_with_cys, total_peptides, mean_fraction_true_cys = nil, std_fraction_true_cys = nil) ⇒ Object

(actual # with cys, expected # with cys, total#peptides, mean_fraction_of_cysteines_true, std) PepHit© = Peptide containing cysteine

 # Total PepHit(C)                   # Observed Bad Pep (C)
 ------------------ proportional_to  ---------------------- 
 # Total PepHit                      # Total Bad PepHit (X)
returns the fppr and the total number false



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# File 'lib/spec_id/filter.rb', line 378

def fppr_by_cysteines(ac_num_with_cys, exp_num_with_cys, total_peptides, mean_fraction_true_cys=nil, std_fraction_true_cys=nil) 

  # the number of bona fide BAD cysteine hits
  # (some of the cysteine hits (~5%) are true positives)

  ac_num_with_cys -= exp_num_with_cys * mean_fraction_true_cys if mean_fraction_true_cys
  if ac_num_with_cys < 0.0 ; ac_num_with_cys = 0.0 end
  total_number_false = (ac_num_with_cys * total_peptides).to_f/exp_num_with_cys
  fppr = total_number_false / total_peptides
  [fppr, total_number_false]
end

#fraction_false_by_cysteines(pephits, cys_bg_freq, cys_containing_freq) ⇒ Object

returns [total_number_false, fppr, fraction_expected] also takes a hash of pephits keyed on :aaseq



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# File 'lib/spec_id/filter.rb', line 464

def fraction_false_by_cysteines(pephits, cys_bg_freq, cys_containing_freq)
  (ac, exp) = SpecID::AAFreqs.new.actual_and_expected_number_containing_cysteines(pephits, cys_bg_freq)
  fraction_of_expected = ac.to_f/exp

  (cys_fprate, total_num_false) = fppr_by_cysteines(ac, exp, pephits.size, cys_containing_freq)
  [total_num_false, cys_fprate, fraction_of_expected]
end

#fraction_false_by_true_pos(pephits, true_pos_aaseqs_ar) ⇒ Object

returns [total_number_false, fppr] pephits can be an array or a hash of peptides keyed on :aaseq



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# File 'lib/spec_id/filter.rb', line 515

def fraction_false_by_true_pos(pephits, true_pos_aaseqs_ar)
  if pephits.is_a? Hash
    seqs = pephits.keys
  else
    seqs = pephits.map do |v|
      v.aaseq
    end
  end
  real_tps = 0
  real_fps = 0
  # could also do with partition
  seqs.each do |pep_aaseq|
    if true_pos_aaseqs_ar.any? {|prot_aaseq| prot_aaseq.include? pep_aaseq}
      real_tps += 1
    else
      real_fps += 1
    end
  end
  real_fppr = real_fps.to_f/pephits.size
  [real_fps, real_fppr]
end

#get_cys_freq(arg) ⇒ Object

takes a fasta file or a string ( to be cast as a float )



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# File 'lib/spec_id/filter.rb', line 301

def get_cys_freq(arg)
  if File.exist? arg
    SpecID::AAFreqs.new(arg).aafreqs[:C]
  else
    arg.to_f
  end
end

#get_options(argv) ⇒ Object

if good arguments, returns [files_array, options] else prints an error argument and returns nil



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# File 'lib/spec_id/filter.rb', line 316

def get_options(argv)
  dup_argv = argv.dup

  opt = OpenStruct.new
  opt.x1 = 1.0
  opt.x2 = 1.5
  opt.x3 = 2.0
  opt.c = 0.1
  opt.ppm = 1000.0
  opt.false = false

  opts = OptionParser.new do |op|
    op.banner = "usage: #{File.basename(__FILE__)} [OPTS] <bioworks.xml | bioworks.srg>"
    op.separator("prints number of peptides/proteins ID'd at given thresholds")
    op.separator "only top hit (by xcorr) per scan+charge is considered"

    #op.separator("** 'dcn*' is the number of peptides with deltacn == 1.1")
    #op.separator("   (these are peptides who are the only hit with xcorr > 0)")
    op.separator ""
    op.on("-1", "--xcorr1 N", Float, "xcorr for +1 charge  d: #{opt.x1}") {|v| opt.x1 = v}
    op.on("-2", "--xcorr2 N", Float, "xcorr for +2 charge  d: #{opt.x2}") {|v| opt.x2 = v}
    op.on("-3", "--xcorr3 N", Float, "xcorr for +3 charge  d: #{opt.x3}") {|v| opt.x3 = v}
    op.on("-c", "--deltacn N", Float, ">= deltacn  d: #{opt.c}") {|v| opt.c = v} 
    op.on("-p", "--ppm N", Float,     "<= ppm               d: #{opt.ppm}") {|v| opt.ppm = v} 
    op.separator "                                     if bioworks.xml, = 10^6deltamass/mass"
    op.on("-i", "--interactive", "interactive filtering") {|v| opt.i = v} 
    op.on("-f", "--false a,b,c", Array, "prot prefixes or filenames of decoys") {|v| opt.false = v} 
    op.separator("                                     last given will apply to remaining files")
    op.on("-y", "--cys <fasta_file|freq,[bkg]>", Array, "report fpr by expected cysteine freq") do |v| 
      v[0] = get_cys_freq(v[0])
      opt.cys = v
    end
    op.separator("                                     freq = freq of cysteine as amino acid")
    op.separator("                                     [bkg] = freq of cys containing peps  d: 0.0")
    op.on("--filters_file <file>", "(no -i) file with list of interactive input") {|v| opt.filters_file = v}
    op.on("-t", "--tps <fasta>", "fasta file containing true hits") {|v| opt.tps = v }
    #op.on("--tmm <toppred.out>", "toppred.out file with transmembr. topology") {|v| opt.tps = v }
    op.on("--yaml", "spits out yaml-ized data") {|v| opt.tabulate = v }
    op.on("--combined_score", "shows the combined score") {|v| opt.combined_score = v }
    op.on("--marshal", "will write marshaled data or read existing") {|v| opt.marshal = v }
    op.on("--log <file>", "also writes all output to file") {|v| opt.log = v }
    op.on("--protein_summary", "writes passing proteins to .summary.html files") {|v| opt.protein_summary = v }
    op.on("-z", "--occams_razor", "will show minimal set of proteins") {|v| opt.occams_razor = v }
  end

  opts.parse!(dup_argv)

  if dup_argv.size < 1
    puts opts
    return nil
  end

  [dup_argv, opt]
end

#interactive_help ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 778

def interactive_help
  string = []
  string << "********************************************************"
  string << "INTERACTIVE FILTERING HELP:"
  string << "enter: <x1> <x2> <x3> <dcn> <ppm>"
  string << "or   : x1:<x1> x2:<x2> x3:<x3> dcn:<dcn> ppm:<ppm>"
  string << "or   : dcn:<dcn>"
  string << "or   : <x1> <x2> ppm:<ppm>"
  string << "etc..."
  string << "<enter> to (re)run current values"
  string << "'q' to quit"
  string << "********************************************************"
  string.join("\n")
end

#out(string) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 293

def out(string)
  puts string
  if @logfh
    @logfh.puts string
  end
end

#prep_reply(reply, base) ⇒ Object

assumes its already chomped updates the 5 globals



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# File 'lib/spec_id/filter.rb', line 716

def prep_reply(reply, base)
  if reply == 'q' ; exit ; end
  if reply =~ /^\s*$/
    base
  elsif reply
    arr = reply.split(/\s+/)
    to_change = []
    to_change_hash = {}
    arr.each do |it|
      if it.include? ':'
        (k,v) = it.split(':')
        to_change_hash[k] = v
      else
        to_change << it
      end
    end
    to_change.each_with_index do |tc,i|
      begin
        base[i] = tc.to_f
      rescue NoMethodError
        out "BAD ARG: #{tc}"
        return false
      end
    end
    to_change_hash.each do |k,v|
      case k
      when 'x1' ; base[0] = v
      when 'x2' ; base[1] = v
      when 'x3' ; base[2] = v
      when 'dcn' ; base[3] = v
      when 'ppm' ; base[4] = v
      else
        out "BAD ARG: #{k}:#{v}"
      end
    end
    base.map {|v| v.to_f }
  else
    false
  end
end

#protein_fppr(num_peps_per_protein, number_false_peptides, num_iterations = 10) ⇒ Object

num_peps_per_protein is an array of the number of peptides per protein hit (these are the true hits) assumes that the number follows a gaussian distribution (binomial distributions tend toward gaussians, I believe, at large N) returns [mean_num_wrong, mean_fppr, stdev_num_wrong, stdev_fppr] fppr



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# File 'lib/spec_id/filter.rb', line 395

def protein_fppr( num_peps_per_protein, number_false_peptides, num_iterations=10)

  ## Check for more false peptides than peptides in our proteins:
  total_protein_peps = 0
  contained = num_peps_per_protein.each do |num|
    total_protein_peps += num
  end
  ## All peptides will be wrong every time!
  ## which means all proteins will be wrong every time!
  if number_false_peptides >= total_protein_peps
    # [all proteins wrong, fppr=1.0
    return [num_peps_per_protein.size, 1.0, 0.0, 0.0]
  end


  num_prots = num_peps_per_protein.size
  sample = VecD.new(num_iterations)
  # indexed by peptide_number, pointing to a protein's peptide_count
  # we shuffle the indices and then walk along until we are finished
  # then we count how many proteins still have peptides

  # we create an array to hold the peptide number for each protein, then we
  # can reference the same entity when subtracting the peptides in the
  # algorithm
  cont_pep_num_per_prot_ars = (0...num_iterations).map do |i|
    total_protein_peps = 0
    contained = num_peps_per_protein.map do |num|
      [num]
    end
  end

  cont_num_by_pep_index_ars = cont_pep_num_per_prot_ars.map do |ar|
    index_count = 0
    pc_ar = []
    ar.each do |contained_num|
      contained_num.first.times do
        pc_ar[index_count] = contained_num
        index_count += 1
      end
    end
    pc_ar
  end

  indices = (0...(cont_num_by_pep_index_ars.first.size)).map {|x| x }
   

  (0...num_iterations).each do |i|
    num_false = 0
    indices.shuffle!
    pc = cont_num_by_pep_index_ars[i]
    number_false_peptides.times do |shuffle_index|
      #big_i = indices[shuffle_index]
      pc[indices[shuffle_index]][0] -= 1
    end
    cont_pep_num_per_prot_ars[i].each do |contained_pep_count|
      if contained_pep_count.first == 0
        num_false += 1
      end
    end
    sample[i] = num_false
  end
  (mean_num_wrong, stdev) = sample.sample_stats
  mean_fppr = mean_num_wrong / num_prots
  stdev_fppr = stdev / num_prots
  [mean_num_wrong, mean_fppr, stdev, stdev_fppr]
end

#report_cysteines ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 472

def report_cysteines
  #### UNDERWAY:::
  cys_tps = pep_nums[i] - total_num_false

  puts "CYSTEINE FPR: "
  puts "  (# peps containing >= 1 cysteines)"
  puts "              actual: #{ac}"
  puts "fraction of expected: #{short(fraction_of_expected)}"
  puts "     expected # FP's: " + short(total_num_false)
  puts "      estimated  FPR: " + short( 100.0*cys_fprate ) + " % "

  puts "combined_score = x1 + x2 + x3 + 20.0*deltacn + 4000.0*(1.0/ppm)"
  puts "Combined Score & FPR"
  puts "#{combined_score}\t#{cys_fprate}"
  puts "Combined Score & fraction of expected"
  #puts "#{combined_score} #{fraction_of_expected}"
  to_write_cys_find = ["WRITE_CYS_FIND:", combined_score, fraction_of_expected]
  puts to_write_cys_find.join("\t") if WRITE_CYS_FIND
  puts(['TABULATE:', combined_score, pep_tps, pep_fpr, cys_tps, cys_fprate, '', x1, x2, x3, deltacn, ppm].join("\t")) if opt.tabulate

end

#run_from_argv(argv) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 161

def run_from_argv(argv)
  reply = get_options(argv) 
  return unless reply
  files, opt = reply

  #files = ARGV.map {|file| file }
  #ARGV.clear

  $stderr.puts "reading files (can take a minute or two for large files)..." if $VERBOSE
  spec_ids = files.map do |file|
    spec_id = file_to_prefiltered_spec_id(file, opt)
    spec_id
  end

  ## the options hash
  hash = {} 
  if opt.cys
    if opt.cys[1]
      opt.cys[1] = opt.cys[1].to_f
    else
      opt.cys[1] = 0.0
    end
    hash[:cys] = opt.cys
  end


  hash[:tps] = 
    if opt.tps
      Fasta.new.read_file(opt.tps).prots.map do |prot|
        prot.aaseq.chomp
      end
    end

  hash[:dcy] = 
    if opt.false
      new_spec_ids = []
      prefixes_or_files = SpecID.extend_args(opt.false, files.size)
      false_spec_ids = spec_ids.zip(prefixes_or_files).map do |spec_id, prefix_or_file|
        if File.exist? prefix_or_file
          new_spec_ids << spec_id
          file_to_prefiltered_spec_id(prefix_or_file, opt)
        else 
          (tps, fps) = spec_id.classify_by_prefix(:peps, prefix_or_file)
          fps_specid = spec_id.class.new
          tps_specid = spec_id.class.new

          fps_specid.peps = fps
          tps_specid.peps = tps
          new_spec_ids << tps_specid
          fps_specid
        end
      end
      spec_ids = new_spec_ids
      false_spec_ids 
    end

  defaults = {
    :dcy => nil, # { spec_id => false_spec_id }
    :cys => nil, # [cys_background_freq, cys_containing_freq]
    :tps => nil,
    :tmm => nil,
    :occams_razor => opt.occams_razor,
  }
  args = defaults.merge hash


  base_args = [opt.x1, opt.x2, opt.x3, opt.c, opt.ppm]

  #################################################### <-- 
  @fppr_methods = [:tmm, :tps, :cys, :dcy].select do |x|
    args[x]
  end
  @groups_reporting = [:pephits, :aaseq, :prothits]
  @groups_reporting.push( :occams_razor ) if args[:occams_razor]

  @cat_labels = {
    :pephits => 'pep_hits', 
    :prothits => 'prot_hits',
    :aaseq => 'uniq_aa_hits',
    :occams_razor => 'occams_prot_hits',
  }
  #################################################### <-- 

  if opt.log
    @logfh = File.open(opt.log, 'w')
  else
    @logfh = nil
  end
  #########################################
  # PRINT FILTER LEGEND
  out filter_legend(@fppr_methods)
  #########################################

  if opt.filters_file
    lines = IO.readlines(opt.filters_file)
    lines.each do |line|
      line.chomp!
      answer = prep_reply(line, base_args)
      next if answer == false
      base_args = answer
      filter_round(spec_ids, base_args, args)
    end
  elsif opt.i
    ## CLEAR ARGV (since otherwise, gets reads it!)
    ARGV.clear
    out interactive_help
    reply = "nil"
    loop do
      b = base_args
      out "#{b[0]} #{b[1]} #{b[2]} dcn:#{b[3]} ppm:#{b[4]}"
      loop do
        reply = gets.chomp
        answer = prep_reply(reply, base_args)
        if answer == false
          out interactive_help
        else
          base_args = answer
          filter_round(spec_ids, base_args, args)
          break
        end
      end
    end
  else
    filter_round(spec_ids, base_args, args)
  end

  if opt.log
    @logfh.close
  end

end

#short(num) ⇒ Object

prints shortened number for display



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# File 'lib/spec_id/filter.rb', line 310

def short(num)
  sprintf( "%.3f",num)
end

#tmm_fppr(pephits) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 557

def tmm_fppr(pephits)
  abort "NEED TO IMPLEMENT"
end

#to_table(spec_id, args, normal_results, fppr_results, groups_reporting, fppr_methods, cat_labels) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 690

def to_table(spec_id, args, normal_results, fppr_results, groups_reporting, fppr_methods, cat_labels)
  #table is in the form: { column heading => [ values ] }
  
  title = spec_id.passed_in_filename
  col_labels = ['num', *(fppr_methods.map{|v| "#{v}%" })]

  row_labels = groups_reporting.map {|grp| cat_labels[grp]}
  dt = groups_reporting.map do |grp|
    line = [normal_results[grp].size]
    fppr_methods.each do |mth|
      line << fppr_results[grp][mth][1]
    end
    line
  end

  Table.new(dt, row_labels, col_labels, title)
  #puts(['TABULATE:', combined_score, pep_tps, pep_fppr, real_tps, real_fppr, '', x1, x2, x3, deltacn, ppm].join("\t")) if opt.tabulate
end

#tps_fppr(pephits, true_pos_aaseqs_ar) ⇒ Object 



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# File 'lib/spec_id/filter.rb', line 567

def tps_fppr(pephits, true_pos_aaseqs_ar)
  fraction_false_by_true_pos(pephits, true_pos_aaseqs_ar)
end