Mercurial > repos > iracooke > tpp_prophets

comparison protein_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 3f0cb90824f1
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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
18 cmd = "ln -s #{original_input_file} #{actual_input_path_string};"
19
20 cmd << "rvm 1.9.3@protk-1.1.9 do protein_prophet.rb"
21
22
23 ARGV[0]="#{actual_input_path_string}"
24
25 ARGV.each { |a|
26
27 cmd << " #{a}"
28 }
29
30 cmd << " -o protein_prophet_results.prot.xml"
31
32 cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}.pep.xml')\" protein_prophet_results.prot.xml"
33
34 %x[#{cmd}]
35