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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 # Hard-Coded argument order and number of arguments
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6 #
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7 actual_output_path_string=ARGV[0]
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8 use_nss=ARGV[1]
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9 use_nrs=ARGV[2]
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10 use_nse=ARGV[3]
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11 use_nsi=ARGV[4]
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12 use_nsm=ARGV[5]
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13 minprob=ARGV[6]
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14 minprob_val=ARGV[7]
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15
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16 wd= Dir.pwd
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17 original_input_files=ARGV.drop(7)
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18 # End hard coded args #
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19
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20 cmd=""
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21
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22 output_substitution_cmds=""
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23
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24 input_files=original_input_files.collect do |input|
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25
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26 # We append ".pep.xml" to the input file name because interprophet can't handle anything else
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27 # In order for this to work properly we need to create a symbolic link our working directory
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28 #
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29 original_input_path=Pathname.new("#{input}")
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30 actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
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31
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32 cmd << "ln -s #{input} #{actual_input_path_string};"
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33 output_substitution_cmds << "ruby -pi -e \"gsub('#{actual_input_path_string}', '#{input}.pep.xml')\" interprophet_output.pep.xml;"
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34 actual_input_path_string
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35 end
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36
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37 interprophet_path=%x[which interprophet.rb]
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38 cmd << interprophet_path.chomp
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39
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40 cmd << " --no-nss" unless use_nss=="blank"
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41 cmd << " --no-nrs" unless use_nrs=="blank"
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42 cmd << " --no-nse" unless use_nse=="blank"
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43 cmd << " --no-nsi" unless use_nsi=="blank"
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44 cmd << " --no-nsm" unless use_nsm=="blank"
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45
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46
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47 input_files.each { |input|
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48 cmd << " #{input}"
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49 }
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50
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51
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52 cmd << " -o interprophet_output.pep.xml -r"
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53
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54 cmd << ";#{output_substitution_cmds}"
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55
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56 %x[#{cmd}]
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57
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