in progress...

diff --git a/forester/ruby/evoruby/lib/evo/msa/msa.rb b/forester/ruby/evoruby/lib/evo/msa/msa.rb
index 2d2f93b..1cdc78d 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/msa/msa.rb
+++ b/forester/ruby/evoruby/lib/evo/msa/msa.rb
@@ -17,6 +17,15 @@ module Evoruby
       @identical_seqs_detected = Array.new
       @name_to_seq_indices = Hash.new
       @namestart_to_seq_indices = Hash.new
+      @name = nil
+    end
+
+    def get_name
+      @name
+    end
+
+    def set_name( name )
+      @name = name
     end
 
     def add_sequence( sequence )
@@ -397,7 +406,7 @@ module Evoruby
       removed
     end
 
-    def trim!( first, last )
+    def trim!( first, last, name_suffix = nil )
       cols = Array.new()
       for i in 0 ... get_length()
         if ( i < first || i > last )
@@ -405,6 +414,58 @@ module Evoruby
         end
       end
       remove_columns!( cols )
+      if name_suffix != nil
+        n = get_number_of_seqs
+        for s in 0 ... n
+          seq = get_sequence( s )
+          seq.set_name( seq.get_name() + name_suffix );
+        end
+      end
+    end
+
+    def extract( first, last )
+      if !is_aligned()
+        error_msg = "attempt to extract from unaligned msa"
+        raise StandardError, error_msg, caller
+      end
+      if first < 0
+        error_msg = "first < 0"
+        raise StandardError, error_msg, caller
+      end
+      if last >= get_length()
+        error_msg = "last > length"
+        raise StandardError, error_msg, caller
+      end
+      if first >= last
+        error_msg = "first >= last"
+        raise StandardError, error_msg, caller
+      end
+      msa = Msa.new()
+      for i in 0 ... get_number_of_seqs
+        msa.add_sequence( get_sequence( i ).get_subsequence( first, last ) )
+      end
+      msa
+    end
+
+    def sliding_extraction( step, size )
+      counter = 0
+      done = false
+      msas = Array.new()
+      while !done
+        first = counter * step
+        last = first + size - 1
+        if last > get_length() - 1
+          last = get_length() - 1
+          done = true
+        end
+        unless first >= last
+          counter +=1
+          res = extract( first, last)
+          res.set_name(first.to_s + "-" + last.to_s)
+          msas << res
+        end
+      end
+      msas
     end
 
     def get_gap_only_columns()

diff --git a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
index e71a36f..48bb6c1 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
@@ -25,9 +25,9 @@ module Evoruby
   class MsaProcessor
 
     PRG_NAME       = "msa_pro"
-    PRG_DATE       = "170215"
+    PRG_DATE       = "170609"
     PRG_DESC       = "processing of multiple sequence alignments"
-    PRG_VERSION    = "1.08"
+    PRG_VERSION    = "1.09"
     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
 
     NAME_LENGTH_DEFAULT                = 10
@@ -50,6 +50,7 @@ module Evoruby
     REMOVE_MATCHING_SEQUENCES_OPTION   = "mr"
 
     TRIM_OPTION                        = "t"
+    SLIDING_EXTRACTION_OPTION          = "se"
     REMOVE_SEQS_GAP_RATIO_OPTION       = "rsgr"
     REMOVE_SEQS_NON_GAP_LENGTH_OPTION  = "rsl"
     SPLIT                              = "split"
@@ -88,6 +89,9 @@ module Evoruby
       @split_by_os      = false
       @first            = -1
       @last             = -1
+      @window = false
+      @step = -1
+      @size =  -1
     end
 
     def run()
@@ -144,6 +148,7 @@ module Evoruby
       allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
       allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
       allowed_opts.push( DIE_IF_NAME_TOO_LONG )
+      allowed_opts.push( SLIDING_EXTRACTION_OPTION )
 
       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
       if ( disallowed.length > 0 )
@@ -275,6 +280,15 @@ module Evoruby
         puts( "Split            : " + @split.to_s )
         log << "Split            : " + @split.to_s + ld
       end
+      if @window
+        puts( "Sliding window extraction: true"  )
+        log << "Sliding window extraction: true" + ld
+        puts( "Sliding window step      : " + @step.to_s )
+        log << "Sliding window step      : " + @step.to_s + ld
+        puts( "Sliding window size      : " +  @size.to_s )
+        log << "Sliding window size      : " +  @size.to_s + ld
+      end
+
       puts()
 
       f = MsaFactory.new()
@@ -359,8 +373,48 @@ module Evoruby
         end
 
         if ( @trim )
-          msa.trim!( @first, @last )
+          msa.trim!( @first, @last, '_S' )
+        end
+
+        if @window
+          msas = msa.sliding_extraction( @step, @size )
+          begin
+            io = MsaIO.new()
+            w = MsaWriter
+            if ( @pi_output )
+              w = PhylipSequentialWriter.new()
+              w.clean( @clean )
+              w.set_max_name_length( @name_length )
+            elsif( @fasta_output )
+              w = FastaWriter.new()
+              w.set_line_width( @width )
+              w.clean( @clean )
+              if ( @name_length_set )
+                w.set_max_name_length( @name_length )
+              end
+            elsif( @nexus_output )
+              w = NexusWriter.new()
+              w.clean( @clean )
+              w.set_max_name_length( @name_length )
+            end
+            i = 0
+            for m in msas
+              i = i + 1
+              name = output + "_" + m.get_name
+              if @fasta_output
+                name += ".fasta"
+              elsif @nexus_output
+                name += ".nex"
+              end
+              io.write_to_file( m, name, w )
+            end
+            Util.print_message( PRG_NAME, "wrote " + msas.length.to_s + " files"  )
+            log << "wrote " + msas.length.to_s + " files" + ld
+          rescue Exception => e
+            Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+          end
         end
+
         if( @rgr >= 0 )
           msa.remove_gap_columns_w_gap_ratio!( @rgr )
         elsif ( @rgc )
@@ -505,7 +559,7 @@ module Evoruby
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
       end
 
-      if (@split <= 0) && (!@split_by_os)
+      if (@split <= 0) && (!@split_by_os) && (!@window)
 
         unless ( @rg )
           if ( msa.is_aligned() )
@@ -757,6 +811,25 @@ module Evoruby
       @trim             = false
       @first            = -1
       @last             = -1
+      @window           = false
+    end
+
+    def set_window()
+      @split            = -1
+      @split_by_os      = false
+      @rgc              = false
+      @rgoc             = false
+      @rg               = false  # fasta only
+      @rgr              = -1
+      @rsgr             = -1
+      @rsl              = -1
+      @seqs_name_file   = nil
+      @remove_seqs      = false
+      @keep_seqs        = false
+      @trim             = false
+      @first            = -1
+      @last             = -1
+      @window           = true
     end
 
     def analyze_command_line( cla )
@@ -863,6 +936,29 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
         end
       end
+      if ( cla.is_option_set?( SLIDING_EXTRACTION_OPTION ) )
+        begin
+          s = cla.get_option_value( SLIDING_EXTRACTION_OPTION )
+          if ( s =~ /(\d+)\/(\d+)/ )
+            set_window
+            @window = true
+            @step = $1.to_i()
+            @size = $2.to_i()
+          else
+            puts( "illegal argument" )
+            print_help
+            exit( -1 )
+          end
+          if (@step <= 0) || (@size <= 0)
+            puts( "illegal argument" )
+            print_help
+            exit( -1 )
+          end
+        rescue ArgumentError => e
+          Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+        end
+      end
+
       if ( cla.is_option_set?( REMOVE_SEQS_GAP_RATIO_OPTION ) )
         begin
           f = cla.get_option_value_as_float( REMOVE_SEQS_GAP_RATIO_OPTION )
@@ -921,8 +1017,8 @@ module Evoruby
       puts()
       puts( "  " + PRG_NAME + ".rb [options] <input alignment> <output>" )
       puts()
-      puts( "  options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
-      puts( "           -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
+      puts( "  options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta (default), p for phylip/selex type" )
+      puts( "           -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta (default), n for nexus, p for phylip sequential" )
       puts( "           -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
       puts( "           -" + DIE_IF_NAME_TOO_LONG + ": die if sequence name too long" )
       puts( "           -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
@@ -940,6 +1036,7 @@ module Evoruby
       puts( "           -" + KEEP_MATCHING_SEQUENCES_OPTION + "=<s> keep only sequences with names containing s" )
       puts( "           -" + SPLIT + "=<n> split a fasta file into n files of equal number of sequences (expect for " )
       puts( "            last one), cannot be used with other options" )
+      puts( "           -" + SLIDING_EXTRACTION_OPTION + "=<step>/<window size>: sliding window extraction, cannot be used with other options" )
       puts( "           -" + REM_RED_OPTION + ": remove redundant sequences" )
       puts()
     end

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index a811899..b2f6446 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -21,7 +21,6 @@ module Evoruby
 
     DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -mp -or'
     DECORATOR_OPTIONS_DOMAINS   = '-p -t'
-    DOMAINS_MAPFILE_SUFFIX      = '.dff'
     SLEEP_TIME                  = 0.01
     REMOVE_NI                   = true
     TMP_FILE_1                  = '___PD1___'
@@ -31,9 +30,9 @@ module Evoruby
     JAVA_HOME                   = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
 
     PRG_NAME       = "phylogenies_decorator"
-    PRG_DATE       = "170427"
+    PRG_DATE       = "170428"
     PRG_DESC       = "decoration of phylogenies with sequence/species names and domain architectures"
-    PRG_VERSION    = "1.04"
+    PRG_VERSION    = "1.05"
     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
 
     HELP_OPTION_1                           = "help"
@@ -86,7 +85,7 @@ module Evoruby
         exit( 0 )
       end
 
-      if ( cla.get_number_of_files != 2 )
+      if ( cla.get_number_of_files != 2 && cla.get_number_of_files != 3 )
         print_help
         exit( -1 )
       end
@@ -124,30 +123,54 @@ module Evoruby
         verbose = true
       end
 
-      if File.exist?( LOG_FILE )
+      if File.exist? LOG_FILE
         Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
       end
 
       in_suffix = cla.get_file_name( 0 )
       out_suffix = cla.get_file_name( 1 )
 
+      mapping_files_dir = nil
+
+      if cla.get_number_of_files == 3
+        mapping_files_dir = cla.get_file_name( 2 )
+      else
+        mapping_files_dir = Dir.getwd
+      end
+      unless File.exist? mapping_files_dir
+        Util.fatal_error( PRG_NAME, 'mapping files directory [' + mapping_files_dir + '] does not exist' )
+      end
+      unless File.directory? mapping_files_dir
+        Util.fatal_error( PRG_NAME, '[' + mapping_files_dir + '] is not a directory' )
+      end
+      if Dir.entries(mapping_files_dir).length <= 2
+        Util.fatal_error( PRG_NAME, 'mapping files directory [' + mapping_files_dir + '] is empty' )
+      end
+
+      mapping_files_dir = Util.canonical_path( mapping_files_dir.to_s )
+
       log = String.new
 
       now = DateTime.now
       log << "Program              : " + PRG_NAME + NL
       log << "Version              : " + PRG_VERSION + NL
       log << "Program date         : " + PRG_DATE + NL
+      log << "Input/Output dir     : " + Dir.getwd + NL
+      log << "Mappings file dir    : " + mapping_files_dir + NL
+      log << "Input suffix         : " + in_suffix + NL
+      log << "Output suffix        : " + out_suffix + NL
       log << "No domains data      : " + no_domains.to_s + NL
       log << "No mol seq data      : " + no_seqs_files.to_s + NL
       log << "Extract tax codes    : " + extr_bracketed_tc.to_s + NL
-      log << "Date/time: " + now.to_s + NL
-      log << "Directory: " + Dir.getwd  + NL + NL
-
-      Util.print_message( PRG_NAME, 'input suffix     : ' + in_suffix )
-      Util.print_message( PRG_NAME, 'output suffix    : ' + out_suffix )
+      log << "Date/time: " + now.to_s + NL + NL
 
-      log << 'input suffix     : ' + in_suffix + NL
-      log << 'output suffix    : ' + out_suffix + NL
+      Util.print_message( PRG_NAME, 'Input/Output dir : ' + Dir.getwd )
+      Util.print_message( PRG_NAME, 'Mappings file dir: ' + mapping_files_dir )
+      Util.print_message( PRG_NAME, 'Input suffix     : ' + in_suffix )
+      Util.print_message( PRG_NAME, 'Output suffix    : ' + out_suffix )
+      Util.print_message( PRG_NAME, 'No domains data  : ' + no_domains.to_s )
+      Util.print_message( PRG_NAME, 'No mol seq data  : ' + no_seqs_files.to_s )
+      Util.print_message( PRG_NAME, 'Extract tax codes: ' + extr_bracketed_tc.to_s )
 
       if ( File.exist?( TMP_FILE_1 ) )
         File.delete( TMP_FILE_1 )
@@ -169,7 +192,7 @@ module Evoruby
           begin
             Util.check_file_for_readability( phylogeny_file )
           rescue ArgumentError
-            Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
+            Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $!.to_s )
           end
 
           counter += 1
@@ -194,7 +217,7 @@ module Evoruby
           Util.print_message( PRG_NAME, counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile )
           log << counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile + NL
 
-          phylogeny_id = get_id( phylogeny_file )
+          phylogeny_id = phylogeny_file
           if  phylogeny_id == nil || phylogeny_id.size < 1
             Util.fatal_error( PRG_NAME, 'could not get id from ' + phylogeny_file.to_s )
           end
@@ -203,75 +226,80 @@ module Evoruby
           end
           log << "Id: " + phylogeny_id + NL
 
-          ids_mapfile_name = nil
-          domains_mapfile_name = nil
-          seqs_file_name = nil
+          ids_mapfile_path = nil
+          domains_mapfile_path = nil
+          seqs_file_path = nil
 
-          ids_mapfile_name = get_file( ".", phylogeny_id, Constants::ID_MAP_FILE_SUFFIX )
+          ids_mapfile_name = get_file( mapping_files_dir, phylogeny_id, Constants::ID_MAP_FILE_SUFFIX )
+          ids_mapfile_path = Util.canonical_path(mapping_files_dir, ids_mapfile_name)
 
           begin
-            Util.check_file_for_readability( ids_mapfile_name )
+            Util.check_file_for_readability( ids_mapfile_path)
           rescue IOError
-            Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
+            Util.fatal_error( PRG_NAME, "failed to read from [#{ids_mapfile_path}]: " + $!.to_s )
           end
           if verbose
-            Util.print_message( PRG_NAME, "Ids mapfile: " + ids_mapfile_name )
+            Util.print_message( PRG_NAME, "Ids mapfile: " + ids_mapfile_path )
           end
-          log << "Ids mapfile: " + ids_mapfile_name + NL
+          log << "Ids mapfile: " + ids_mapfile_path + NL
 
           unless no_seqs_files
-            seqs_file_name = get_file( ".", phylogeny_id, Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX )
+            seqs_file_name = get_file( mapping_files_dir, phylogeny_id, Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX )
+            seqs_file_path = Util.canonical_path(mapping_files_dir, seqs_file_name)
             begin
-              Util.check_file_for_readability( seqs_file_name  )
+              Util.check_file_for_readability( seqs_file_path  )
             rescue IOError
-              Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
+              Util.fatal_error( PRG_NAME, "failed to read from [#{seqs_file_path}]: " + $!.to_s )
             end
             if verbose
-              Util.print_message( PRG_NAME, "Seq file: " + seqs_file_name )
+              Util.print_message( PRG_NAME, "Seq file: " + seqs_file_path )
             end
-            log << "Seq file: " + seqs_file_name + NL
+            log << "Seq file: " + seqs_file_path + NL
           end
 
           unless no_domains
-            domains_mapfile_name = get_file( ".", phylogeny_id, Constants::DOMAINS_TO_FORESTER_OUTFILE_SUFFIX  )
+            domains_mapfile_name = get_file( mapping_files_dir , phylogeny_id, Constants::DOMAINS_TO_FORESTER_OUTFILE_SUFFIX  )
+            domains_mapfile_path = Util.canonical_path(mapping_files_dir, domains_mapfile_name)
             begin
-              Util.check_file_for_readability( domains_mapfile_name )
+              Util.check_file_for_readability( domains_mapfile_path )
             rescue IOError
-              Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
+              Util.fatal_error( PRG_NAME, "failed to read from [#{domains_mapfile_path}]: " + $!.to_s )
             end
             if verbose
-              Util.print_message( PRG_NAME, "Domains file: " + domains_mapfile_name )
+              Util.print_message( PRG_NAME, "Domains file: " + domains_mapfile_path )
             end
-            log << "Domains file: " + domains_mapfile_name + NL
+            log << "Domains file: " + domains_mapfile_path + NL
           end
 
+          log <<  NL + NL
+
           if no_seqs_files
             FileUtils.cp(phylogeny_file, TMP_FILE_1)
           else
             cmd = decorator +
             ' -t -p -f=m ' + phylogeny_file + ' ' +
-            seqs_file_name  + ' ' + TMP_FILE_1
+            seqs_file_path  + ' ' + TMP_FILE_1
             if verbose
               puts cmd
             end
             begin
               execute_cmd( cmd, log )
-            rescue Error
-              Util.fatal_error( PRG_NAME, 'error: ' + $! )
+            rescue Exception
+              Util.fatal_error( PRG_NAME, 'error: ' + $!.to_s )
             end
           end
 
           unless no_domains
             cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
             '-f=d ' + TMP_FILE_1 + ' ' +
-            domains_mapfile_name + ' ' + TMP_FILE_2
+            domains_mapfile_path + ' ' + TMP_FILE_2
             if verbose
               puts cmd
             end
             begin
               execute_cmd( cmd, log )
-            rescue Error
-              Util.fatal_error( PRG_NAME, 'error: ' + $! )
+            rescue Exception
+              Util.fatal_error( PRG_NAME, 'error: ' + $!.to_s )
             end
           end
 
@@ -282,26 +310,26 @@ module Evoruby
 
           if no_domains
             cmd = decorator + ' ' + opts + ' -f=n ' + TMP_FILE_1 + ' ' +
-            ids_mapfile_name + ' ' + outfile
+            ids_mapfile_path + ' ' + outfile
             if verbose
               puts cmd
             end
             begin
               execute_cmd( cmd, log )
-            rescue Error
-              Util.fatal_error( PRG_NAME, 'error: ' + $! )
+            rescue Exception
+              Util.fatal_error( PRG_NAME, 'error: ' + $!.to_s )
             end
             File.delete( TMP_FILE_1 )
           else
             cmd = decorator + ' ' + opts + ' -f=n ' + TMP_FILE_2 + ' ' +
-            ids_mapfile_name + ' ' + outfile
+            ids_mapfile_path + ' ' + outfile
             if verbose
               puts cmd
             end
             begin
               execute_cmd( cmd, log )
-            rescue Error
-              Util.fatal_error( PRG_NAME, 'error: ' + $! )
+            rescue Exception
+              Util.fatal_error( PRG_NAME, 'error: ' + $!.to_s )
             end
             File.delete( TMP_FILE_1 )
             File.delete( TMP_FILE_2 )
@@ -324,73 +352,41 @@ module Evoruby
         pipe.close_write
         log << pipe.read + NL + NL
       end
+      if $?.to_i != 0
+        raise StandardError, "failed to execute " + cmd
+      end
       sleep( SLEEP_TIME )
     end
 
-    def get_id( phylogeny_file_name )
-      return phylogeny_file_name
-      #if phylogeny_file_name =~ /^(.+?_DA)_/
-      #  return $1
-      #elsif phylogeny_file_name =~ /^(.+?)_/
-      #  return $1
-      #end
-      #nil
-    end
-
     def get_file( files_in_dir, phylogeny_id, suffix_pattern )
-      Util.get_matching_file( files_in_dir, phylogeny_id, suffix_pattern )
-      #      matching_files = Util.get_matching_files( files_in_dir, phylogeny_id, suffix_pattern )
-      #      if matching_files.length < 1
-      #        Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
-      #        '...' + suffix_pattern + '] present in current directory' )
-      #      end
-      #      if matching_files.length > 1
-      #        Util.fatal_error( PRG_NAME, 'more than one file matching [' +
-      #        phylogeny_id  + '...' + suffix_pattern + '] present in current directory' )
-      #      end
-      #      matching_files[ 0 ]
-    end
-
-    def get_seq_file( files_in_dir, phylogeny_id )
-      matching_files = Array.new
-
-      files_in_dir.each { | file |
-
-        if ( !File.directory?( file ) &&
-        file !~ /^\./ &&
-        file !~ /^00/ &&
-        ( file =~ /^#{phylogeny_id}__.+\d$/ || file =~ /^#{phylogeny_id}_.*\.fasta$/ ) )
-          matching_files << file
-        end
-      }
-
-      if matching_files.length < 1
-        Util.fatal_error( PRG_NAME, 'no seq file matching [' +
-        phylogeny_id + '_] present in current directory' )
-      end
-      if matching_files.length > 1
-        Util.fatal_error( PRG_NAME, 'more than one seq file matching [' +
-        phylogeny_id + '_] present in current directory' )
+      begin
+        Util.get_matching_file( files_in_dir, phylogeny_id, suffix_pattern )
+      rescue Exception
+        Util.fatal_error( PRG_NAME, 'error: ' + $!.to_s )
       end
-      matching_files[ 0 ]
     end
 
     def print_help()
       puts "Usage:"
       puts
-      puts "   " + PRG_NAME + ".rb <suffix of in-trees to be decorated> <suffix for decorated out-trees> "
+      puts "   " + PRG_NAME + ".rb [options] <suffix of in-trees to be decorated> <suffix for decorated out-trees> [mapping files directory, default: current dir]"
       puts
-      puts "   required files (in this dir): " + "name mappings       : .nim"
-      puts "                                 " + "sequences           : _ni.fasta"
-      puts "                                 " + "domain architectures: .dff"
+      puts "   " + PRG_NAME + ".rb [options] <input directory> <output directory> <mapping files directory>"
       puts
-      puts "   options: -" + NO_DOMAINS_OPTION  + ": to not add domain architecture information (.dff file)"
-      puts "            -" + NO_SEQS_OPTION   + ": to not add molecular sequence information (_ni.fasta file)"
+      puts "   required file  (in mapping files directory): " + "name mappings       : #{Constants::ID_MAP_FILE_SUFFIX}"
+      puts "   optional files (in mapping files directory): " + "sequences           : #{Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX}"
+      puts "                                                " + "domain architectures: #{Constants::DOMAINS_TO_FORESTER_OUTFILE_SUFFIX}"
+      puts
+      puts "   options: -" + NO_DOMAINS_OPTION  + ": to not add domain architecture information (#{Constants::DOMAINS_TO_FORESTER_OUTFILE_SUFFIX} file)"
+      puts "            -" + NO_SEQS_OPTION   + ": to not add molecular sequence information (#{Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX} file)"
       puts "            -" + EXTRACT_BRACKETED_TAXONOMIC_CODE_OPTION  + ": to extract bracketed taxonomic codes, e.g. [NEMVE]"
-      puts "            -" + VERBOSE_OPTION  + ":  verbose"
+      puts "            -" + VERBOSE_OPTION  + " : verbose"
       puts
       puts "Examples: " + PRG_NAME + ".rb .xml _d.xml"
       puts "          " + PRG_NAME + ".rb -#{NO_DOMAINS_OPTION} -#{NO_SEQS_OPTION} .xml _d.xml"
+      puts "          " + PRG_NAME + ".rb -#{NO_DOMAINS_OPTION} -#{NO_SEQS_OPTION} .xml _d.xml mappings_dir"
+      puts
+      puts "          " + PRG_NAME + ".rb in_trees_dir out_dir mappings_dir"
       puts
     end
   end # class PhylogenyiesDecorator

diff --git a/forester/ruby/evoruby/lib/evo/util/util.rb b/forester/ruby/evoruby/lib/evo/util/util.rb
index df28bc5..7e8b554 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/util/util.rb
+++ b/forester/ruby/evoruby/lib/evo/util/util.rb
@@ -6,10 +6,25 @@
 #
 # Last modified: 2017/04/27
 
+require 'pathname'
 require 'lib/evo/util/constants'
 
 module Evoruby
   class Util
+    def Util.canonical_path( parent, child = nil )
+      if child == nil
+        return  File.expand_path(Pathname.new(parent).cleanpath.to_s).to_s
+      end
+
+      s = nil
+      if parent.end_with?('/')
+        s = parent + child
+      else
+        s = parent + '/' + child
+      end
+      File.expand_path(Pathname.new(s).cleanpath.to_s).to_s
+    end
+
     def Util.get_matching_files( files, prefix_pattern, suffix_pattern )
       matching_files = Array.new
       files.each { | file |
@@ -48,7 +63,7 @@ module Evoruby
       the_one = nil;
 
       loop do
-        puts my_prefix #TODO remove me
+
         matches = 0
         matching_files.each { | file |
           if file.start_with?( my_prefix )
@@ -68,8 +83,7 @@ module Evoruby
           done = true
         else
           if my_prefix.length <= 1
-            raise IOError, "no file matching \"" + removeFileExtension( prefix )
-            + "\" and ending with \"" + suffix + "\" found in [" + dir_name + "]"
+            raise IOError, "no file matching \"" + prefix + "\" and ending with \"" + suffix + "\" found in [" + dir_name + "]"
           end
           my_prefix = my_prefix[ 0 ... ( my_prefix.length - 1 ) ]