JAL-2797 first attempt

[jalview.git] / forester / ruby / scripts / hmm_split.rb

diff --git a/forester/ruby/scripts/hmm_split.rb b/forester/ruby/scripts/hmm_split.rb
index 8ae000d..69edd90 100755 (executable)
--- a/forester/ruby/scripts/hmm_split.rb
+++ b/forester/ruby/scripts/hmm_split.rb
@@ -1,80 +1,68 @@
 #!/usr/local/bin/ruby -w
 #
-# = hmm_split 
-#
-# Copyright::  Copyright (C) 2006-2008 Christian M. Zmasek
-# License::    GNU Lesser General Public License (LGPL)
-#
-# $Id: hmm_split.rb,v 1.5 2008/11/17 22:32:43 cmzmasek Exp $
-#
-# To split a Pfam HMM file into one file for each HMM.
+# = hmm_split
 #
-
+# Copyright::    Copyright (C) 2017 Christian M Zmasek
+# License::      GNU Lesser General Public License (LGPL)
 
 module ForesterScripts
-    
-    if RUBY_VERSION !~ /1.9/
-                      puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
-                      exit( -1 )
-                end     
-    
-    
-    if ( ARGV == nil || ARGV.length != 3 )
-        puts( "usage: hmm_split.rb <Pfam HMM file> <outfile suffix> <outdir>" )         
-        exit( -1 )
-    end    
-       
-       hmmfile = ARGV[ 0 ]
-       suffix  = ARGV[ 1 ]
-       outdir  = ARGV[ 2 ]
-     
-       if ( !File.exists?( outdir ) )
-           puts( "outdir [" + outdir + "] does not exist" )
-           exit( -1 ) 
-       end 
-       if ( !File.exists?( hmmfile ) ) 
-           puts( "Pfam HMM file [" + hmmfile + "] does not exist" )
-           exit( -1 ) 
-       end                
-       
-       data = String.new
-       name = String.new
-       line_count = 0
-       count = 0
-       
-       File.open( hmmfile ) do | file |
-           while line = file.gets
-               data = data + line
-               line_count += 1
-               if ( line =~ /NAME\s+(.+)/ )
-                   if name.length > 0
-                       puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
-                       exit( -1 )                        
-                   end    
-                   name = $1    
-               elsif ( line =~ /\/\// )
-                   if name.length < 1
-                       puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
-                       exit( -1 )                        
-                   end
-                                       
-                   outfile = outdir + '/' + name + suffix
-                   if ( File.exists?( outfile ) ) 
-                       puts( "file [" + outfile + "] already exists" )
-                       exit( -1 )  
-                   end                   
-                   open( outfile, 'w' ) do | out |
-                       out.write( data )
-                   end
-                   count += 1
-                   puts( count.to_s + ": " + name )
-                   data = String.new
-                   name = String.new                                      
-               end
-           end
-       end 
-         
-       puts()
-       puts( "wrote " + count.to_s + " individual HMM files to " + outdir )    
-    
+
+  if ( ARGV == nil || ARGV.length != 3 )
+    puts( "usage: hmm_split.rb <Pfam HMM file> <outfile suffix> <outdir>" )
+    exit( -1 )
+  end
+
+  hmmfile = ARGV[ 0 ]
+  suffix  = ARGV[ 1 ]
+  outdir  = ARGV[ 2 ]
+
+  if ( !File.exist?( outdir ) )
+    puts( "outdir [" + outdir + "] does not exist" )
+    exit( -1 )
+  end
+  if ( !File.exist?( hmmfile ) )
+    puts( "Pfam HMM file [" + hmmfile + "] does not exist" )
+    exit( -1 )
+  end
+
+  data = String.new
+  name = String.new
+  line_count = 0
+  count = 0
+
+  File.open( hmmfile ) do | file |
+    while line = file.gets
+      data = data + line
+      line_count += 1
+      if ( line =~ /NAME\s+(.+)/ )
+        if name.length > 0
+          puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
+          exit( -1 )
+        end
+        name = $1
+      elsif ( line =~ /\/\// )
+        if name.length < 1
+          puts( "Pfam HMM file [" + hmmfile + "] format error [line: " + line + "]" )
+          exit( -1 )
+        end
+
+        outfile = outdir + '/' + name + suffix
+        if ( File.exist?( outfile ) )
+          puts( "file [" + outfile + "] already exists" )
+          exit( -1 )
+        end
+        open( outfile, 'w' ) do | out |
+          out.write( data )
+        end
+        count += 1
+        puts( count.to_s + ": " + name )
+        data = String.new
+        name = String.new
+      end
+    end
+  end
+
+  puts()
+  puts( "wrote " + count.to_s + " individual HMM files to " + outdir )
+
 end    
\ No newline at end of file