pcm2pwm.rb in bioinform-0.1.8

- old
+ new
@@ -1,40 +1,40 @@
-require 'bioinform'
+require_relative '../../bioinform'
 require 'docopt'
 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)
+          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)
 
-Usage:
-  #{__FILE__} [options] [<pcm-files>...]
+          Usage:
+            #{__FILE__} [options] [<pcm-files>...]
 
-Options:
-  -h --help           Show this screen.
-  -e --extension EXT  Extension of output files [default: pwm]
-  -f --folder FOLDER  Where to save output files [default: .]
+          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)
 
-        if options['<pcm-files>'].empty?
-          filelist = $stdin.read.shellsplit
-        else
-          filelist = options['<pcm-files>']
-        end
-
+        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
 
-        filelist.each do |pcm_filename|
-          pwm = Bioinform::PCM.new( File.read(pcm_filename) ).to_pwm
-          File.open(Bioinform::CLI.output_filename(pcm_filename, options['--extension'], folder), 'w') do |f|
+        filelist.each do |filename|
+          pwm = Bioinform::PCM.new( File.read(filename) ).to_pwm
+          File.open(change_folder_and_extension(filename, extension, folder), 'w') do |f|
             f.puts pwm
           end
         end
 
       rescue Docopt::Exit => e
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