merge-sequest-csv.rb

#! /usr/bin/env ruby
# Copyright (c) 2009 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 MergeSequestCsv < ProteomaticScript
    def run()
        
        ls_AllHeader = nil
        ls_AllHeaderPath = nil
        if @output[:mergedResults]
            @input[:sequestResults].each do |ls_Path|
                File::open(ls_Path, 'r') do |f|
                    ls_ThisHeader = f.readline.strip + "\n" + f.readline.strip
                    ls_AllHeader ||= ls_ThisHeader
                    ls_AllHeaderPath ||= ls_Path
                    if (ls_AllHeader != ls_ThisHeader)
                        puts "Error: first two lines must be identical in all input files!"
                        puts "#{File::basename(ls_AllHeaderPath)}: [#{ls_AllHeader}]"
                        puts "#{File::basename(ls_Path)}: [#{ls_ThisHeader}]"
                        exit 1
                    end
                end
            end
            File::open(@output[:mergedResults], 'w') do |lk_Out|
                lk_Out.puts ls_AllHeader
                @input[:sequestResults].each do |ls_Path|
                    ls_Basename = File::basename(ls_Path).sub('.csv', '')
                    File::open(ls_Path, 'r') do |f|
                        ls_ThisHeader = f.readline + f.readline
                        f.each_line do |line|
                            lineArray = line.parse_csv()
                            if (!lineArray[0] && (lineArray[1] && (!lineArray[1].empty?)))
                                scanId = ls_Basename + '.' + lineArray[1]
                                lineArray[1] = scanId
                            end
                            lk_Out.puts lineArray.to_csv()
                        end
                    end
                end
            end
        end
    end
end


script = MergeSequestCsv.new()