in progress
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Thu, 11 Oct 2012 19:54:24 +0000 (19:54 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Thu, 11 Oct 2012 19:54:24 +0000 (19:54 +0000)
forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb

index 69a6bc4..3620fc5 100644 (file)
@@ -20,280 +20,282 @@ require 'date'
 
 module Evoruby
 
-    class PhylogeniesDecorator
-
-        DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
-        # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
-        #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
-        DECORATOR_OPTIONS_DOMAINS = '-r=1'
-        IDS_MAPFILE_SUFFIX        = '.nim'
-        DOMAINS_MAPFILE_SUFFIX    = '.dff'
-        SLEEP_TIME                = 0.1
-        REMOVE_NI                 = true
-        TMP_FILE                  = '___PD___'
-        LOG_FILE                  = '00_phylogenies_decorator.log'
-        FORESTER_HOME             = ENV[Constants::FORESTER_HOME_ENV_VARIABLE]
-        JAVA_HOME                 = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
-
-        PRG_NAME       = "phylogenies_decorator"
-        PRG_DATE       = "2008.09.02"
-        PRG_DESC       = "decoration of phylogenies with sequence/species names and domain architectures"
-        PRG_VERSION    = "1.0.1"
-        COPYRIGHT      = "2008-2009 Christian M Zmasek"
-        CONTACT        = "phylosoft@gmail.com"
-        WWW            = "www.phylosoft.org"
-
-        IDS_ONLY_OPTION     = "n"
-        DOMAINS_ONLY_OPTION = "d"
-        HELP_OPTION_1       = "help"
-        HELP_OPTION_2       = "h"
-
-        NL = Constants::LINE_DELIMITER
-
-        def run
-
-            Util.print_program_information( PRG_NAME,
-                PRG_VERSION,
-                PRG_DESC,
-                PRG_DATE,
-                COPYRIGHT,
-                CONTACT,
-                WWW,
-                STDOUT )
-
-            if ( ARGV == nil || ARGV.length > 3 || ARGV.length < 2  )
-                print_help
-                exit( -1 )
-            end
-
-            if FORESTER_HOME == nil || FORESTER_HOME.length < 1
-                Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::FORESTER_HOME_ENV_VARIABLE} has not been set" )
-            end
-            if JAVA_HOME == nil ||  JAVA_HOME.length < 1
-                Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::JAVA_HOME_ENV_VARIABLE} has not been set" )
-            end
-
-            if !File.exist?( FORESTER_HOME )
-                Util.fatal_error( PRG_NAME, '[' + FORESTER_HOME + '] does not exist' )
-            end
-            if !File.exist?( JAVA_HOME )
-                Util.fatal_error( PRG_NAME, '[' + JAVA_HOME + '] does not exist' )
-            end
-
-            decorator = JAVA_HOME + '/bin/java -cp ' + FORESTER_HOME + '/java/forester.jar org.forester.application.decorator'
-
+  class PhylogeniesDecorator
+
+    #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
+    DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+    # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
+    #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
+    #DECORATOR_OPTIONS_DOMAINS = '-r=1'
+    DECORATOR_OPTIONS_DOMAINS = '-p -t'
+    IDS_MAPFILE_SUFFIX        = '.nim'
+    DOMAINS_MAPFILE_SUFFIX    = '.dff'
+    SLEEP_TIME                = 0.1
+    REMOVE_NI                 = true
+    TMP_FILE                  = '___PD___'
+    LOG_FILE                  = '00_phylogenies_decorator.log'
+    FORESTER_HOME             = ENV[Constants::FORESTER_HOME_ENV_VARIABLE]
+    JAVA_HOME                 = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
+
+    PRG_NAME       = "phylogenies_decorator"
+    PRG_DATE       = "2012.10.11"
+    PRG_DESC       = "decoration of phylogenies with sequence/species names and domain architectures"
+    PRG_VERSION    = "1.02"
+    COPYRIGHT      = "2012 Christian M Zmasek"
+    CONTACT        = "phylosoft@gmail.com"
+    WWW            = "www.phylosoft.org"
+
+    IDS_ONLY_OPTION     = "n"
+    DOMAINS_ONLY_OPTION = "d"
+    HELP_OPTION_1       = "help"
+    HELP_OPTION_2       = "h"
+
+    NL = Constants::LINE_DELIMITER
+
+    def run
+
+      Util.print_program_information( PRG_NAME,
+        PRG_VERSION,
+        PRG_DESC,
+        PRG_DATE,
+        COPYRIGHT,
+        CONTACT,
+        WWW,
+        STDOUT )
+
+      if ( ARGV == nil || ARGV.length > 3 || ARGV.length < 2  )
+        print_help
+        exit( -1 )
+      end
+
+      if FORESTER_HOME == nil || FORESTER_HOME.length < 1
+        Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::FORESTER_HOME_ENV_VARIABLE} has not been set" )
+      end
+      if JAVA_HOME == nil ||  JAVA_HOME.length < 1
+        Util.fatal_error( PRG_NAME, "apparently environment variable #{Constants::JAVA_HOME_ENV_VARIABLE} has not been set" )
+      end
+
+      if !File.exist?( FORESTER_HOME )
+        Util.fatal_error( PRG_NAME, '[' + FORESTER_HOME + '] does not exist' )
+      end
+      if !File.exist?( JAVA_HOME )
+        Util.fatal_error( PRG_NAME, '[' + JAVA_HOME + '] does not exist' )
+      end
+
+      decorator = JAVA_HOME + '/bin/java -cp ' + FORESTER_HOME + '/java/forester.jar org.forester.application.decorator'
+
+      begin
+        cla = CommandLineArguments.new( ARGV )
+      rescue ArgumentError => e
+        Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+      end
+
+      if ( cla.is_option_set?( HELP_OPTION_1 ) ||
+           cla.is_option_set?( HELP_OPTION_2 ) )
+        print_help
+        exit( 0 )
+      end
+
+      if File.exist?( LOG_FILE )
+        Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
+      end
+
+      allowed_opts = Array.new
+      allowed_opts.push( IDS_ONLY_OPTION )
+      allowed_opts.push( DOMAINS_ONLY_OPTION )
+
+      disallowed = cla.validate_allowed_options_as_str( allowed_opts )
+      if ( disallowed.length > 0 )
+        Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
+      end
+
+      ids_only = false
+      domains_only = false
+
+      in_suffix = cla.get_file_name( 0 )
+      out_suffix = cla.get_file_name( 1 )
+
+      if cla.is_option_set?( IDS_ONLY_OPTION )
+        ids_only = true
+      end
+      if cla.is_option_set?( DOMAINS_ONLY_OPTION )
+        domains_only = true
+      end
+
+      if ( ids_only && domains_only )
+        Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' )
+      end
+
+      log = String.new
+
+      now = DateTime.now
+      log << "Program              : " + PRG_NAME + NL
+      log << "Version              : " + PRG_VERSION + NL
+      log << "Program date         : " + PRG_DATE + NL
+      log << "Options for seq names: " + DECORATOR_OPTIONS_SEQ_NAMES + NL
+      log << "Options for domains  : " + DECORATOR_OPTIONS_DOMAINS + NL
+      log << "FORESTER_HOME        : " + FORESTER_HOME + NL
+      log << "JAVA_HOME            : " + JAVA_HOME + NL + 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 << 'input suffix     : ' + in_suffix + NL
+      log << 'output suffix    : ' + out_suffix + NL
+
+      if ( File.exists?( TMP_FILE ) )
+        File.delete( TMP_FILE )
+      end
+
+      files = Dir.entries( "." )
+
+      counter = 0
+
+      files.each { | phylogeny_file |
+        if ( !File.directory?( phylogeny_file ) &&
+             phylogeny_file !~ /^\./ &&
+             phylogeny_file !~ /^00/ &&
+             phylogeny_file !~ /#{out_suffix}$/ &&
+             phylogeny_file =~ /#{in_suffix}$/ )
+          begin
+            Util.check_file_for_readability( phylogeny_file )
+          rescue ArgumentError
+            Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
+          end
+
+          counter += 1
+
+          outfile = phylogeny_file.sub( /#{in_suffix}$/, out_suffix )
+
+          if REMOVE_NI
+            outfile = outfile.sub( /_ni_/, '_' )
+          end
+
+          if File.exists?( outfile )
+            msg = counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile +
+             ' : already exists, skipping'
+            Util.print_message( PRG_NAME, msg  )
+            log << msg + NL
+            next
+          end
+
+          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 )
+
+          ids_mapfile_name = nil
+          domains_mapfile_name = nil
+
+          if ids_only
+            ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
+          elsif domains_only
+            domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+          else
+            ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
+            domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+          end
+
+          if domains_mapfile_name != nil
             begin
-                cla = CommandLineArguments.new( ARGV )
-            rescue ArgumentError => e
-                Util.fatal_error( PRG_NAME, "error: " + e.to_s )
+              Util.check_file_for_readability( domains_mapfile_name )
+            rescue ArgumentError
+              Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
             end
+          end
 
-            if ( cla.is_option_set?( HELP_OPTION_1 ) ||
-                     cla.is_option_set?( HELP_OPTION_2 ) )
-                print_help
-                exit( 0 )
-            end
-
-            if File.exist?( LOG_FILE )
-                Util.fatal_error( PRG_NAME, 'logfile [' + LOG_FILE + '] already exists' )
-            end
-
-            allowed_opts = Array.new
-            allowed_opts.push( IDS_ONLY_OPTION )
-            allowed_opts.push( DOMAINS_ONLY_OPTION )
-
-            disallowed = cla.validate_allowed_options_as_str( allowed_opts )
-            if ( disallowed.length > 0 )
-                Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
-            end
-
-            ids_only = false
-            domains_only = false
-
-            in_suffix = cla.get_file_name( 0 )
-            out_suffix = cla.get_file_name( 1 )
-
-            if cla.is_option_set?( IDS_ONLY_OPTION )
-                ids_only = true
-            end
-            if cla.is_option_set?( DOMAINS_ONLY_OPTION )
-                domains_only = true
-            end
-
-            if ( ids_only && domains_only )
-                Util.fatal_error( PRG_NAME, 'attempt to use ids only and domains only at the same time' )
-            end
-
-            log = String.new
-
-            now = DateTime.now
-            log << "Program              : " + PRG_NAME + NL
-            log << "Version              : " + PRG_VERSION + NL
-            log << "Program date         : " + PRG_DATE + NL
-            log << "Options for seq names: " + DECORATOR_OPTIONS_SEQ_NAMES + NL
-            log << "Options for domains  : " + DECORATOR_OPTIONS_DOMAINS + NL
-            log << "FORESTER_HOME        : " + FORESTER_HOME + NL
-            log << "JAVA_HOME            : " + JAVA_HOME + NL + 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 << 'input suffix     : ' + in_suffix + NL
-            log << 'output suffix    : ' + out_suffix + NL
-
-            if ( File.exists?( TMP_FILE ) )
-                File.delete( TMP_FILE )
+          if ids_mapfile_name != nil
+            begin
+              Util.check_file_for_readability( ids_mapfile_name )
+            rescue ArgumentError
+              Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
             end
+          end
 
-            files = Dir.entries( "." )
-
-            counter = 0
-
-            files.each { | phylogeny_file |
-                if ( !File.directory?( phylogeny_file ) &&
-                         phylogeny_file !~ /^\./ &&
-                         phylogeny_file !~ /^00/ &&
-                         phylogeny_file !~ /#{out_suffix}$/ &&
-                         phylogeny_file =~ /#{in_suffix}$/ )
-                    begin
-                        Util.check_file_for_readability( phylogeny_file )
-                    rescue ArgumentError
-                        Util.fatal_error( PRG_NAME, 'can not read from: ' + phylogeny_file + ': '+ $! )
-                    end
-
-                    counter += 1
-
-                    outfile = phylogeny_file.sub( /#{in_suffix}$/, out_suffix )
-
-                    if REMOVE_NI
-                        outfile = outfile.sub( /_ni_/, '_' )
-                    end
-
-                    if File.exists?( outfile )
-                        msg = counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile +
-                         ' : already exists, skipping'
-                        Util.print_message( PRG_NAME, msg  )
-                        log << msg + NL
-                        next
-                    end
-
-                    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 )
-
-                    ids_mapfile_name = nil
-                    domains_mapfile_name = nil
-
-                    if ids_only
-                        ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
-                    elsif domains_only
-                        domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
-                    else
-                        ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
-                        domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
-                    end
-
-                    if domains_mapfile_name != nil
-                        begin
-                            Util.check_file_for_readability( domains_mapfile_name )
-                        rescue ArgumentError
-                            Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
-                        end
-                    end
-
-                    if ids_mapfile_name != nil
-                        begin
-                            Util.check_file_for_readability( ids_mapfile_name )
-                        rescue ArgumentError
-                            Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
-                        end
-                    end
-
-                    if domains_mapfile_name != nil
-                        if ids_mapfile_name != nil
-                            my_outfile = TMP_FILE
-                        else
-                            my_outfile = outfile
-                        end
-                        cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
-                         '-f=d ' + phylogeny_file + ' ' +
-                         domains_mapfile_name + ' ' + my_outfile
-                        execute_cmd( cmd, log )
-                    end
-
-                    if ids_mapfile_name != nil
-                        if domains_mapfile_name != nil
-                            my_infile = TMP_FILE
-                        else
-                            my_infile = phylogeny_file
-                        end
-                        cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
-                         '-f=s ' + my_infile + ' ' +
-                         ids_mapfile_name + ' ' + outfile
-                        execute_cmd( cmd, log )
-                    end
-
-                    if ( File.exists?( TMP_FILE ) )
-                        File.delete( TMP_FILE )
-                    end
-                end
-            }
-            open( LOG_FILE, 'w' ) do | f |
-                f.write( log )
-            end
-            puts
-            Util.print_message( PRG_NAME, 'OK' )
-            puts
-        end # def run
-
-        def execute_cmd( cmd, log )
-            log << 'excuting ' + cmd + NL
-            IO.popen( cmd , 'r+' ) do | pipe |
-                pipe.close_write
-                log << pipe.read + NL + NL
+          if domains_mapfile_name != nil
+            if ids_mapfile_name != nil
+              my_outfile = TMP_FILE
+            else
+              my_outfile = outfile
             end
-            sleep( SLEEP_TIME )
-        end
-
-
-        def get_id( phylogeny_file_name )
-            phylogeny_file_name =~ /^([^_]+)/
-            $1
-        end
-
-        def get_file( files_in_dir, phylogeny_id, suffix_pattern )
-            matching_files = Array.new
-            files_in_dir.each { | file |
-
-                if ( !File.directory?( file ) &&
-                         file !~ /^\./ &&
-                         file !~ /^00/ &&
-                         file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
-                    matching_files << file
-                end
-            }
-            if matching_files.length < 1
-                Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
-                     '_] [' + suffix_pattern + '] present in current directory' )
-            elsif matching_files.length > 1
-                Util.fatal_error( PRG_NAME, 'more than one file matching [' + phylogeny_id +
-                     '_] [' + suffix_pattern + '] present in current directory' )
+            cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
+             '-f=d ' + phylogeny_file + ' ' +
+             domains_mapfile_name + ' ' + my_outfile
+            execute_cmd( cmd, log )
+          end
+
+          if ids_mapfile_name != nil
+            if domains_mapfile_name != nil
+              my_infile = TMP_FILE
+            else
+              my_infile = phylogeny_file
             end
-            matching_files[ 0 ]
+            cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+             '-f=s ' + my_infile + ' ' +
+             ids_mapfile_name + ' ' + outfile
+            execute_cmd( cmd, log )
+          end
+
+          if ( File.exists?( TMP_FILE ) )
+            File.delete( TMP_FILE )
+          end
         end
-
-        def print_help()
-            puts( "Usage:" )
-            puts()
-            puts( "  " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
-            puts()
-            puts( "  options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
-            puts( "           -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures" )
-            puts()
+      }
+      open( LOG_FILE, 'w' ) do | f |
+        f.write( log )
+      end
+      puts
+      Util.print_message( PRG_NAME, 'OK' )
+      puts
+    end # def run
+
+    def execute_cmd( cmd, log )
+      log << 'excuting ' + cmd + NL
+      IO.popen( cmd , 'r+' ) do | pipe |
+        pipe.close_write
+        log << pipe.read + NL + NL
+      end
+      sleep( SLEEP_TIME )
+    end
+
+
+    def get_id( phylogeny_file_name )
+      phylogeny_file_name =~ /^([^_]+)/
+      $1
+    end
+
+    def get_file( files_in_dir, phylogeny_id, suffix_pattern )
+      matching_files = Array.new
+      files_in_dir.each { | file |
+
+        if ( !File.directory?( file ) &&
+             file !~ /^\./ &&
+             file !~ /^00/ &&
+             file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
+          matching_files << file
         end
-    end # class PhylogenyiesDecorator
+      }
+      if matching_files.length < 1
+        Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
+           '_] [' + suffix_pattern + '] present in current directory' )
+      elsif 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 print_help()
+      puts( "Usage:" )
+      puts()
+      puts( "  " + PRG_NAME + ".rb [options] <suffix of intrees to be decorated> <suffix for decorated outtrees> " )
+      puts()
+      puts( "  options: -" + IDS_ONLY_OPTION + ": decorate with sequence/species names only" )
+      puts( "           -" + DOMAINS_ONLY_OPTION + ": decorate with domain structures" )
+      puts()
+    end
+  end # class PhylogenyiesDecorator
 
 end # module Evoruby