pcm2pwm.rb in bioinform-0.2.0

- old
+ new
@@ -1,47 +1,53 @@
 require_relative '../../bioinform'
-require 'docopt'
+require 'optparse'
 require 'shellwords'
 
 module Bioinform
-  module CLI  
+  module CLI
     module PCM2PWM
       extend Bioinform::CLI::Helpers
       def self.main(argv)
-        doc = <<-DOCOPT
-          PCM to PWM converter.
-          It transforms files with PCMs into files with PWMs. Folder for resulting files to save files can be specified. Resulting PWM files have the same name as original file but have another extension (.pwm by default).
-          When filelist is empty, it's obtained from STDIN. One can use it: `ls -b pcm_folder/*.pcm | pcm2pwm` (ls -b option escape spaces in filenames)
+        options = {folder: '.', extension: 'pwm'}
+        opt_parser = OptionParser.new do |opts|
+          opts.banner = "PCM to PWM converter.\n" +
+                        "It transforms files with PCMs into files with PWMs.\n" +
+                        "Folder for resulting files to save files can be specified.\n" +
+                        "Resulting PWM files have the same name as original file but have another extension (.pwm by default).\n" +
+                        "When filelist is empty, it's obtained from STDIN.\n" +
+                        "One can use it: `ls -b pcm_folder/*.pcm | pcm2pwm` (ls -b option escape spaces in filenames)\n" +
+                        "\n" +
+                        "Usage:\n" +
+                        "  pcm2pwm [options] [<pcm-files>...]"
+          opts.version = ::Bioinform::VERSION
+          opts.on('-e', '--extension EXT', 'Extension of output files [default: pwm]') do |v|
+            options[:extension] = v
+          end
+          opts.on('-f', '--folder FOLDER', 'Where to save output files') do |v|
+            options[:folder] = v
+          end
+        end
 
-          Usage:
-            pcm2pwm [options] [<pcm-files>...]
+        opt_parser.parse!(argv)
+        pcm_files = argv
+        folder = options[:folder]
+        extension = options[:extension]
 
-          Options:
-            -h --help           Show this screen.
-            -e --extension EXT  Extension of output files [default: pwm]
-            -f --folder FOLDER  Where to save output files [default: .]
-        DOCOPT
-
-        doc.gsub!(/^#{doc[/\A +/]}/,'')
-        options = Docopt::docopt(doc, argv: argv)
-
-        pcm_files = options['<pcm-files>']
-        folder = options['--folder']
-        extension = options['--extension']
-
         Dir.mkdir(folder)  unless Dir.exist?(folder)
         filelist = (pcm_files.empty?)  ?  $stdin.read.shellsplit  :  pcm_files
 
+        converter = ConversionAlgorithms::PCM2PWMConverter.new()
+
         filelist.each do |filename|
-          pwm = Bioinform::PCM.new( File.read(filename) ).to_pwm
+          input = File.read(filename)
+          motif_data = MatrixParser.new.parse(input)
+          pcm = MotifModel::PCM.new(motif_data[:matrix]).named(motif_data[:name])
+          pwm = converter.convert(pcm)
           File.open(change_folder_and_extension(filename, extension, folder), 'w') do |f|
             f.puts pwm
           end
         end
-
-      rescue Docopt::Exit => e
-        puts e.message
       end
 
     end
   end
-end
\ No newline at end of file
+end