in progress

[jalview.git] / forester / ruby / evoruby / lib / evo / tool / phylogenies_decorator.rb

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 535b1fa..973286c 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -178,14 +178,14 @@ module Evoruby
           seqs_file_name = nil
 
           ids_mapfile_name = get_file( files, phylogeny_id, IDS_MAPFILE_SUFFIX )
-          domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
-          seqs_file_name = get_seq_file( files, phylogeny_id )
+         # domains_mapfile_name = get_file( files, phylogeny_id, DOMAINS_MAPFILE_SUFFIX )
+         # seqs_file_name = get_seq_file( files, phylogeny_id )
 
-          begin
-            Util.check_file_for_readability( domains_mapfile_name )
-          rescue ArgumentError
-            Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
-          end
+#          begin
+#            Util.check_file_for_readability( domains_mapfile_name )
+#          rescue ArgumentError
+#            Util.fatal_error( PRG_NAME, 'failed to read from [#{domains_mapfile_name}]: ' + $! )
+#          end
 
           begin
             Util.check_file_for_readability( ids_mapfile_name )
@@ -193,32 +193,54 @@ module Evoruby
             Util.fatal_error( PRG_NAME, 'failed to read from [#{ids_mapfile_name}]: ' + $! )
           end
 
-          begin
-            Util.check_file_for_readability( seqs_file_name  )
-          rescue ArgumentError
-            Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
-          end
-
-          cmd = decorator +
-           ' -p -f=m ' + phylogeny_file + ' ' +
-           seqs_file_name  + ' ' + TMP_FILE_1
-          puts cmd
-          execute_cmd( cmd, log )
-
-          cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
-           '-f=d ' + TMP_FILE_1 + ' ' +
-           domains_mapfile_name + ' ' +TMP_FILE_2
-          puts cmd
-          execute_cmd( cmd, log )
+#          begin
+#            Util.check_file_for_readability( seqs_file_name  )
+#          rescue ArgumentError
+#            Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! )
+#          end
+
+#          cmd = decorator +
+#           ' -t -p -f=m ' + phylogeny_file + ' ' +
+#           seqs_file_name  + ' ' + TMP_FILE_1
+#          puts cmd
+#          begin
+#            execute_cmd( cmd, log )
+#          rescue Error
+#            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#          end
+#
+#          cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
+#           '-f=d ' + TMP_FILE_1 + ' ' +
+#           domains_mapfile_name + ' ' +TMP_FILE_2
+#          puts cmd
+#          begin
+#            execute_cmd( cmd, log )
+#          rescue Error
+#            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#          end
 
           cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
-           '-f=n ' + TMP_FILE_2 + ' ' +
+           '-f=n ' + phylogeny_file + ' ' +
            ids_mapfile_name + ' ' + outfile
           puts cmd
-          execute_cmd( cmd, log )
-
-          File.delete( TMP_FILE_1 )
-          File.delete( TMP_FILE_2 )
+          begin
+            execute_cmd( cmd, log )
+          rescue Error
+            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+          end
+          
+#          cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
+#                    '-f=n ' + TMP_FILE_2 + ' ' +
+#                    ids_mapfile_name + ' ' + outfile
+#                   puts cmd
+#                   begin
+#                     execute_cmd( cmd, log )
+#                   rescue Error
+#                     Util.fatal_error( PRG_NAME, 'error: ' + $! )
+#                   end
+
+        #  File.delete( TMP_FILE_1 )
+        #  File.delete( TMP_FILE_2 )
 
         end
       }
@@ -231,7 +253,7 @@ module Evoruby
     end # def run
 
     def execute_cmd( cmd, log )
-      log << 'excuting ' + cmd + NL
+      log << 'executing ' + cmd + NL
       IO.popen( cmd , 'r+' ) do | pipe |
         pipe.close_write
         log << pipe.read + NL + NL
@@ -241,8 +263,14 @@ module Evoruby
 
 
     def get_id( phylogeny_file_name )
-      phylogeny_file_name =~ /^(.+?)__/
-      $1
+      if phylogeny_file_name =~ /^(.+?_.+?)_/
+        return $1
+      elsif phylogeny_file_name =~ /^(.+?)__/
+        return $1
+      elsif phylogeny_file_name =~ /^(.+?)_/
+        return $1
+      end
+      nil
     end
 
     def get_file( files_in_dir, phylogeny_id, suffix_pattern )
@@ -276,18 +304,18 @@ module Evoruby
         if ( !File.directory?( file ) &&
              file !~ /^\./ &&
              file !~ /^00/ &&
-             ( file =~ /^#{phylogeny_id}__.+\d$/ || file =~ /^#{phylogeny_id}__.*\.fasta$/ ) )
+             ( 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' )
+           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' )
+           phylogeny_id + '_] present in current directory' )
       end
       matching_files[ 0 ]
     end