X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Fphylogenies_decorator.rb;h=1eea808704e646c8b56b43306940e43f07f4ff79;hb=2d569f0ff0e0c8fa5d21ca6b3446a152132ff1de;hp=85e247830d746ebd01fb8f0775e5d770cd70c358;hpb=156517428746b21481eb815bf860ffb6cb0314ef;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 85e2478..1eea808 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -30,8 +30,8 @@ module Evoruby
     #DECORATOR_OPTIONS_DOMAINS = '-r=1'
     DECORATOR_OPTIONS_DOMAINS = '-p -t'
     IDS_MAPFILE_SUFFIX        = '.nim'
-    DOMAINS_MAPFILE_SUFFIX    = '.dff'
-    SLEEP_TIME                = 0.1
+    DOMAINS_MAPFILE_SUFFIX    = '_hmmscan_10.dff'
+    SLEEP_TIME                = 0.05
     REMOVE_NI                 = true
     TMP_FILE_1                  = '___PD1___'
     TMP_FILE_2                  = '___PD2___'
@@ -40,10 +40,10 @@ module Evoruby
     JAVA_HOME                 = ENV[Constants::JAVA_HOME_ENV_VARIABLE]
 
     PRG_NAME       = "phylogenies_decorator"
-    PRG_DATE       = "2012.10.11"
+    PRG_DATE       = "2013.11.15"
     PRG_DESC       = "decoration of phylogenies with sequence/species names and domain architectures"
     PRG_VERSION    = "1.02"
-    COPYRIGHT      = "2012 Christian M Zmasek"
+    COPYRIGHT      = "2013 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
 
@@ -166,6 +166,12 @@ module Evoruby
           log << counter.to_s + ': ' + phylogeny_file + ' -> ' +  outfile + NL
 
           phylogeny_id = get_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
+          puts
+          Util.print_message( PRG_NAME, "id: " + phylogeny_id )
+          log << "id: " + phylogeny_id + NL
 
           ids_mapfile_name = nil
           domains_mapfile_name = nil
@@ -175,7 +181,6 @@ module Evoruby
           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
@@ -195,22 +200,34 @@ module Evoruby
           end
 
           cmd = decorator +
-           ' -p -f=m ' + phylogeny_file + ' ' +
+           ' -t -p -f=m ' + phylogeny_file + ' ' +
            seqs_file_name  + ' ' + TMP_FILE_1
           puts cmd
-          execute_cmd( cmd, log )
+          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
-          execute_cmd( cmd, log )
+          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
-          execute_cmd( cmd, log )
+          begin
+            execute_cmd( cmd, log )
+          rescue Error
+            Util.fatal_error( PRG_NAME, 'error: ' + $! )
+          end
 
           File.delete( TMP_FILE_1 )
           File.delete( TMP_FILE_2 )
@@ -236,13 +253,17 @@ module Evoruby
 
 
     def get_id( phylogeny_file_name )
-      phylogeny_file_name =~ /^([^_]+)/
-      $1
+      if phylogeny_file_name =~ /^(.+?)__/
+        return $1
+      elsif phylogeny_file_name =~ /^(.+?)_/
+        return $1
+      end
+      nil
     end
 
     def get_file( files_in_dir, phylogeny_id, suffix_pattern )
       matching_files = Array.new
-      matching_suffix_files = Array.new
+
       files_in_dir.each { | file |
 
         if ( !File.directory?( file ) &&
@@ -251,24 +272,14 @@ module Evoruby
              file =~ /^#{phylogeny_id}.*#{suffix_pattern}$/ )
           matching_files << file
         end
-        if ( !File.directory?( file ) &&
-             file !~ /^\./ &&
-             file !~ /^00/ &&
-             file =~ /#{suffix_pattern}$/ )
-          matching_suffix_files << file
-        end
       }
-      if matching_files.length < 1 && matching_suffix_files.length == 1
-        return matching_suffix_files[ 0 ]
-      end
-
-      if matching_files.length < 1 && matching_suffix_files.length < 1
+      if matching_files.length < 1
         Util.fatal_error( PRG_NAME, 'no file matching [' + phylogeny_id +
-           '_] [' + suffix_pattern + '] present in current directory' )
+           '...' + 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' )
+        Util.fatal_error( PRG_NAME, 'more than one file matching [' +
+           phylogeny_id  + '...' + suffix_pattern + '] present in current directory' )
       end
       matching_files[ 0 ]
     end
@@ -281,17 +292,18 @@ module Evoruby
         if ( !File.directory?( file ) &&
              file !~ /^\./ &&
              file !~ /^00/ &&
-             file =~ /^#{phylogeny_id}.+\d$/ )
+             ( file =~ /^#{phylogeny_id}__.+\d$/ || 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' )
+        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' )
+        Util.fatal_error( PRG_NAME, 'more than one seq file matching [' +
+           phylogeny_id + '_] present in current directory' )
       end
       matching_files[ 0 ]
     end