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1 require 'pathname'
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2
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3 $VERBOSE=nil
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4
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5 peptide_prophet_path=%x[which peptide_prophet.rb]
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6
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7 actual_output_path_string=ARGV.shift
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8
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9 # Second argument is the original input file name ... we'll change this below
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10 original_input_file=ARGV[0]
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11
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12 # Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input
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13 # name because peptide prophet can't handle anything else
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14
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15 wd= Dir.pwd
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16
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17 original_input_path=Pathname.new("#{original_input_file}")
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18 actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
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19 full_tmp_output_path_string="#{wd}/peptide_prophet_output.pep.xml"
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20
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21 cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
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22
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23 cmd << peptide_prophet_path.chomp
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24
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25
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26 ARGV[0]="#{actual_input_path_string}"
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27
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28 ARGV.each { |a|
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29 cmd << " #{a}"
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30 }
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31
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32 cmd << " -o peptide_prophet_output.pep.xml"
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33
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34 # Finally we need to fix up the output file so any references to the temporary working file are changed to refs to the original input file
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35 cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml"
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36 cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml"
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37
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38 %x[#{cmd}]
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