inprogress

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

diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
index b499c72..31f0272 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@ -25,10 +25,10 @@ module Evoruby
     PRG_NAME                           = "mse"
     PRG_VERSION                        = "1.02"
     PRG_DESC                           = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
-    PRG_DATE                           = "2012.07.20"
-    COPYRIGHT                          = "2008-2012 Christian M Zmasek"
+    PRG_DATE                           = "130322"
+    COPYRIGHT                          = "2008-2013 Christian M Zmasek"
     CONTACT                            = "phylosoft@gmail.com"
-    WWW                                = "www.phylosoft.org"
+    WWW                                = "https://sites.google.com/site/cmzmasek/home/software/forester"
     HELP_OPTION_1                      = 'help'
     HELP_OPTION_2                      = 'h'
 
@@ -254,9 +254,9 @@ module Evoruby
               Util.fatal_error( PRG_NAME, "unexpected format: " + line )
             end
             species = values[ 0 ]
-            if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
-              next
-            end
+            #if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
+            #  next
+            #end
             seq_name = values[ 1 ]
             domain_ranges = nil
             if ( values.length > 3 )
@@ -314,7 +314,7 @@ module Evoruby
 
             per_species_counter.to_i
 
-            ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
+            ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER )
 
             orig_name = nil
             if seq != nil