filter-psm-by-mass-accuracy.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'

class CropPsmByMassAccuracy < ProteomaticScript
    def run()
        lf_MaxPpm = @param[:maxPpm]
        lk_Result = Hash.new
        
        # 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

        li_HitCount = 0
        li_SelectCount = 0
        if @output[:croppedPsm]
            File.open(@output[:croppedPsm], 'w') do |lk_Out|
                lk_Out.puts(ls_Header)
                @input[:omssaResults].each do |ls_Path|
                    File.open(ls_Path, 'r') do |lk_In|
                        # skip header
                        lk_In.readline
                        lk_In.each do |ls_Line|
                            li_HitCount += 1
                            lk_Line = ls_Line.parse_csv()
                            lf_Mass = lk_Line[lk_HeaderMap['mass']].to_f
                            lf_TheoMass = lk_Line[lk_HeaderMap['theomass']].to_f
                            # is the ppm mass error too bad? skip it!
                            # calculate mass error in ppm
                            lf_ThisPpm = ((lf_Mass - lf_TheoMass).abs / lf_TheoMass) * 1000000.0
                            # skip this PSM if ppm is not good
                            next if lf_ThisPpm > lf_MaxPpm
                            li_SelectCount += 1
                            
                            lk_Out.puts ls_Line
                        end
                    end
                end
            end
        end
        puts "Discarded #{li_HitCount - li_SelectCount} (#{sprintf('%1.1f', (li_HitCount - li_SelectCount).to_f * 100.0 / li_HitCount)}%) of #{li_HitCount} hits."
    end
end

script = CropPsmByMassAccuracy.new