in progress

diff --git a/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb b/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
index 098cf05..f6335ea 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/domain_sequence_extractor_new.rb
@@ -114,10 +114,10 @@ module Evoruby
       end
 
       add_species = false
       end
 
       add_species = false

-      if cla.is_option_set? ADD_SPECIES 
+      if cla.is_option_set? ADD_SPECIES

         add_species = true
       end
         add_species = true
       end

-      
+

       if ( add_domain_number_as_letter && add_domain_number_as_digit )
         puts( "attempt to add domain number as letter and digit at the same time" )
         print_help
       if ( add_domain_number_as_letter && add_domain_number_as_digit )
         puts( "attempt to add domain number as letter and digit at the same time" )
         print_help

@@ -223,7 +223,7 @@ module Evoruby
           add_domain_number_as_digit,
           add_domain_number_as_letter,
           trim,
           add_domain_number_as_digit,
           add_domain_number_as_letter,
           trim,

-           add_species,
+          add_species,

           log )
       rescue ArgumentError, IOError, StandardError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
           log )
       rescue ArgumentError, IOError, StandardError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )

diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
index 3bf3fb7..c7d8146 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb
@@ -37,7 +37,7 @@ module Evoruby
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,

-         add_species,
+        add_species,

         log )
 
       Util.check_file_for_readability( hmmsearch_output )
         log )
 
       Util.check_file_for_readability( hmmsearch_output )

@@ -82,8 +82,8 @@ module Evoruby
             if domain_id != target_name
               next
             end
             if domain_id != target_name
               next
             end

-            
-            
+
+

             sequence = $4
             number   = $10.to_i
             out_of   = $11.to_i
             sequence = $4
             number   = $10.to_i
             out_of   = $11.to_i

@@ -227,7 +227,7 @@ module Evoruby
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,
         add_domain_number_as_digit,
         add_domain_number_as_letter,
         trim_name,

-        add_species      )
+        add_species )

       if ( number < 1 || out_of < 1 || number > out_of )
         error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
         raise ArgumentError, error_msg
       if ( number < 1 || out_of < 1 || number > out_of )
         error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
         raise ArgumentError, error_msg

@@ -247,11 +247,11 @@ module Evoruby
       end
       # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
       seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
       end
       # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
       seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )

-      
+

       orig_name = seq.get_name
       orig_name = seq.get_name

-      
+

       seq.set_name( orig_name.split[ 0 ] )
       seq.set_name( orig_name.split[ 0 ] )

-      
+

       if add_position
         seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
       end
       if add_position
         seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
       end

@@ -272,18 +272,18 @@ module Evoruby
         elsif ( add_domain_number )
           seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
         end
         elsif ( add_domain_number )
           seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
         end

-        
+

         if add_species
           a = orig_name.rindex "["
           b = orig_name.rindex "]"
           unless a && b
         if add_species
           a = orig_name.rindex "["
           b = orig_name.rindex "]"
           unless a && b

-               error_msg = "species not found in " + orig_name
-               raise StandardError, error_msg
+            error_msg = "species not found in " + orig_name
+            raise StandardError, error_msg

           end
           species = orig_name[ a .. b ]
           seq.set_name( seq.get_name + " [" + species + "]" )
           end
           species = orig_name[ a .. b ]
           seq.set_name( seq.get_name + " [" + species + "]" )

-        end  
-          
+        end
+

       end
 
       # if ( seq.get_name.length > 10 )
       end
 
       # if ( seq.get_name.length > 10 )