filter-psm-by-fpr.rb

#! /usr/bin/env ruby
# Copyright (c) 2007-2008 Michael Specht
# 
# This file is part of Proteomatic.
# 
# Proteomatic is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# Proteomatic is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#     
# You should have received a copy of the GNU General Public License
# along with Proteomatic.  If not, see <http://www.gnu.org/licenses/>.

require './include/ruby/proteomatic'
require './include/ruby/evaluate-omssa-helper'
require './include/ruby/ext/fastercsv'
require './include/ruby/misc'
require 'set'
require 'yaml'

# requires target/decoy PSM, strips target_ and decoy_, discards all decoy hits

class FilterPsmByFpr < ProteomaticScript
    def run()
        # first check whether all headers are equal, because in the end they will be merged
        ls_Header = nil
        lk_HeaderMap = nil
        @input[:omssaResults].each do |ls_Path|
            File.open(ls_Path, 'r') do |lk_In|
                # skip header
                ls_Header = lk_In.readline
                lk_ThisHeaderMap = mapCsvHeader(ls_Header)
                if (lk_HeaderMap)
                    if (lk_HeaderMap != lk_ThisHeaderMap)
                        puts "Error: The header lines of all input files are not identical (#{ls_Path} is different, for example)."
                        exit 1
                    end
                end
                lk_HeaderMap = lk_ThisHeaderMap
            end
        end

        lk_Result = Hash.new
        lk_Result = cropPsm(@input[:omssaResults], @param[:targetFpr] / 100.0, @param[:scoreThresholdScope] == 'global', @param[:targetPrefix], @param[:decoyPrefix], @param[:decoyAmount], @param[:fprCalculation] == 'd_t')
        
        puts 'Warning: No PSM remaining.' if (lk_Result[:scoreThresholds].empty?)
        
        ls_Header = ''
        File.open(@input[:omssaResults].first, 'r') { |lk_File| ls_Header = lk_File.readline.strip }

        if @output[:croppedPsm]
            File.open(@output[:croppedPsm], 'w') do |lk_Out|
                ls_Header += ', scoreThresholdType, targetFpr, actualFpr, scoreThreshold'
                lk_Out.puts(ls_Header)
                @input[:omssaResults].each do |ls_Path|
                    File.open(ls_Path, 'r') do |lk_In|
                        lk_In.readline
                        lk_In.each do |ls_Line|
                            lk_Line = ls_Line.parse_csv()
                            ls_Spot = '(global)'
                            unless @param[:scoreThresholdScope] == 'global'
                                ls_Scan = lk_Line[1]
                                lk_ScanParts = ls_Scan.split('.')
                                ls_Spot = lk_ScanParts.slice(0, lk_ScanParts.size - 3).join('.')
                            end
                            next unless lk_Result[:actualFpr][ls_Spot]
                            lf_E = BigDecimal.new(lk_Line[lk_HeaderMap['evalue']])
                            ls_DefLine = lk_Line[lk_HeaderMap['defline']]
                            # is it a decoy match? skip it!
                            next if ls_DefLine.index(@param[:decoyPrefix]) == 0
                            # is the score too bad? skip it!
                            next if lf_E > lk_Result[:scoreThresholds][ls_Spot]

                            unless @param[:beStrict] && (lk_Result[:actualFpr][ls_Spot] > @param[:targetFpr] / 100.0)
                                lk_Out.print ls_Line.sub(@param[:targetPrefix], '').strip
                                lk_Out.print ", fpr, #{@param[:targetFpr] / 100.0}, #{lk_Result[:actualFpr][ls_Spot]}, #{lk_Result[:scoreThresholds][ls_Spot]}"
                                lk_Out.puts
                            end
                        end
                    end
                end
            end
        end
    end
end

script = FilterPsmByFpr.new