Mercurial > repos > iracooke > tpp_prophets

comparison peptide_prophet_wrapper.rb @ 2:25261529840c

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author iracooke
date Mon, 04 Mar 2013 17:11:46 -0500
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children a67a5d30bb80
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1:49d15d40117d 2:25261529840c
1 require 'pathname'
2
3 $VERBOSE=nil
4
5 actual_output_path_string=ARGV.shift
6
7 # Second argument is the original input file name ... we'll change this below
8 original_input_file=ARGV[0]
9
10 # Before doing anything we append create a link to the input file in our working dir with ".pep.xml" appended to the input
11 # name because peptide prophet can't handle anything else
12
13 wd= Dir.pwd
14
15 original_input_path=Pathname.new("#{original_input_file}")
16 actual_input_path_string="#{wd}/#{original_input_path.basename}.pep.xml"
17 full_tmp_output_path_string="#{wd}/peptide_prophet_output.pep.xml"
18
19 cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
20
21 cmd << "rvm 1.9.3@protk-1.1.9 do peptide_prophet.rb"
22
23
24 ARGV[0]="#{actual_input_path_string}"
25
26 ARGV.each { |a|
27 cmd << " #{a}"
28 }
29
30 cmd << " -o peptide_prophet_output.pep.xml"
31
32 # 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
33 cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml"
34 cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml"
35
36 %x[#{cmd}]