Mercurial > repos > iracooke > protk
comparison peptide_prophet_wrapper.rb @ 2:418f42b34049 draft
Reuploading
| author | iracooke |
|---|---|
| date | Mon, 23 Jul 2012 00:20:58 -0400 |
| parents | a929e27eb203 |
| children |
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| 1:deaedec14cc8 | 2:418f42b34049 |
|---|---|
| 1 require 'pathname' | |
| 2 | |
| 3 $VERBOSE=nil | |
| 4 | |
| 5 peptide_prophet_path=%x[which peptide_prophet.rb] | |
| 6 | |
| 7 actual_output_path_string=ARGV.shift | |
| 8 | |
| 9 # Second argument is the original input file name ... we'll change this below | |
| 10 original_input_file=ARGV[0] | |
| 11 | |
| 12 # Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input | |
| 13 # name because peptide prophet can't handle anything else | |
| 14 | |
| 15 wd= Dir.pwd | |
| 16 | |
| 17 original_input_path=Pathname.new("#{original_input_file}") | |
| 18 actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml" | |
| 19 full_tmp_output_path_string="#{wd}/peptide_prophet_output.pep.xml" | |
| 20 | |
| 21 cmd = "ln -s #{original_input_file} #{actual_input_path_string};" | |
| 22 | |
| 23 cmd << peptide_prophet_path.chomp | |
| 24 | |
| 25 | |
| 26 ARGV[0]="#{actual_input_path_string}" | |
| 27 | |
| 28 ARGV.each { |a| | |
| 29 cmd << " #{a}" | |
| 30 } | |
| 31 | |
| 32 cmd << " -o peptide_prophet_output.pep.xml" | |
| 33 | |
| 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 | |
| 35 cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml" | |
| 36 cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml" | |
| 37 | |
| 38 %x[#{cmd}] |