inprogress

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

diff --git a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
index 6299417..d952277 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/msa_processor.rb
@@ -27,9 +27,9 @@ module Evoruby
   class MsaProcessor
 
     PRG_NAME       = "msa_pro"
-    PRG_DATE       = "2012.05.11"
+    PRG_DATE       = "131112"
     PRG_DESC       = "processing of multiple sequence alignments"
-    PRG_VERSION    = "1.06"
+    PRG_VERSION    = "1.08"
     COPYRIGHT      = "2008-2010 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "www.phylosoft.org"
@@ -40,6 +40,7 @@ module Evoruby
     INPUT_TYPE_OPTION                  = "i"
     OUTPUT_TYPE_OPTION                 = "o"
     MAXIMAL_NAME_LENGTH_OPTION         = "n"
+    DIE_IF_NAME_TOO_LONG               = "d"
     WIDTH_OPTION                       = "w"
     CLEAN_UP_SEQ_OPTION                = "c"
     REM_RED_OPTION                     = "rem_red"
@@ -78,6 +79,7 @@ module Evoruby
       @rgoc             = false
       @rg               = false  # fasta only
       @rem_red          = false
+      @die_if_name_too_long  = false
       @rgr              = -1
       @rsgr             = -1
       @rsl              = -1
@@ -148,6 +150,7 @@ module Evoruby
       allowed_opts.push( REM_RED_OPTION )
       allowed_opts.push( KEEP_MATCHING_SEQUENCES_OPTION )
       allowed_opts.push( REMOVE_MATCHING_SEQUENCES_OPTION )
+      allowed_opts.push( DIE_IF_NAME_TOO_LONG )
 
       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
       if ( disallowed.length > 0 )
@@ -162,13 +165,13 @@ module Evoruby
 
       begin
         Util.check_file_for_readability( input )
-      rescue ArgumentError => e
+      rescue IOError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
 
       begin
         Util.check_file_for_writability( output )
-      rescue ArgumentError => e
+      rescue IOError => e
         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
       end
 
@@ -298,8 +301,8 @@ module Evoruby
         Util.print_message( PRG_NAME, "Gap-proportion of original alignment : " + gp.to_s )
         log << "Gap-proportion of original alignment : " +  gp.to_s + ld
       else
-        Util.print_message( PRG_NAME, "the input is not aligned" )
-        log << "The input is not aligned" + ld
+        Util.print_message( PRG_NAME, "Input is not aligned" )
+        log << "Input is not aligned" + ld
       end
 
       all_names = Set.new()
@@ -481,8 +484,32 @@ module Evoruby
             Util.print_message( PRG_NAME, "Gap-proportion of processed alignment: " + gp.to_s )
             log << "Gap-proportion of processed alignment: " +  gp.to_s + ld
           else
-            Util.print_warning_message( PRG_NAME, "output is not aligned" )
-            log << "output is not aligned" + ld
+            min = 0
+            max = 0
+            sum = 0
+            first = true
+            for s in 0 ... msa.get_number_of_seqs
+              seq = msa.get_sequence( s )
+              l = seq.get_length
+              sum += l
+              if l > max
+                max = l
+              end
+              if first || l < min
+                min = l
+              end
+              first = false
+            end
+            avg = sum / msa.get_number_of_seqs
+            Util.print_message( PRG_NAME, "Output is not aligned" )
+            log << "Output is not aligned" + ld
+            Util.print_message( PRG_NAME, "Shortest sequence                    : " + min.to_s )
+            log <<  "Shortest sequence                    : " + min.to_s + ld
+            Util.print_message( PRG_NAME, "Longest sequence                     : " + max.to_s )
+            log <<  "Longest sequence                     : " + max.to_s + ld
+            Util.print_message( PRG_NAME, "Average length                       : " + avg.to_s )
+            log <<  "Average length                       : " + avg.to_s + ld
+
           end
         end
 
@@ -511,6 +538,7 @@ module Evoruby
           w = PhylipSequentialWriter.new()
           w.clean( @clean )
           w.set_max_name_length( @name_length )
+          w.set_exception_if_name_too_long( @die_if_name_too_long )
         elsif( @fasta_output )
           w = FastaWriter.new()
           w.set_line_width( @width )
@@ -522,20 +550,24 @@ module Evoruby
           w.clean( @clean )
           if ( @name_length_set )
             w.set_max_name_length( @name_length )
+            w.set_exception_if_name_too_long( @die_if_name_too_long )
           end
         elsif( @nexus_output )
           w = NexusWriter.new()
           w.clean( @clean )
           w.set_max_name_length( @name_length )
+          w.set_exception_if_name_too_long( @die_if_name_too_long )
         end
 
-
         begin
           io.write_to_file( msa, output, w )
         rescue Exception => e
           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
         end
 
+        Util.print_message( PRG_NAME, "Number of sequences in output        : " + msa.get_number_of_seqs.to_s )
+        log << "Number of sequences in output        : " + msa.get_number_of_seqs.to_s + ld
+
         begin
           f = File.open( output + LOG_SUFFIX, 'a' )
           f.print( log )
@@ -661,6 +693,7 @@ module Evoruby
         @last             = -1
       end
     end
+
     def analyze_command_line( cla )
       if ( cla.is_option_set?( INPUT_TYPE_OPTION ) )
         begin
@@ -806,6 +839,9 @@ module Evoruby
           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
         end
       end
+      if ( cla.is_option_set?( DIE_IF_NAME_TOO_LONG ) )
+        @die_if_name_too_long = true
+      end
 
 
     end
@@ -819,6 +855,7 @@ module Evoruby
       puts( "  options: -" + INPUT_TYPE_OPTION + "=<input type>: f for fasta, p for phylip selex type" )
       puts( "           -" + OUTPUT_TYPE_OPTION + "=<output type>: f for fasta, n for nexus, p for phylip sequential (default)" )
       puts( "           -" + MAXIMAL_NAME_LENGTH_OPTION + "=<n>: n=maximal name length (default for phylip 10, for fasta: unlimited )" )
+      puts( "           -" + DIE_IF_NAME_TOO_LONG + ": die if sequence name too long" )
       puts( "           -" + WIDTH_OPTION + "=<n>: n=width (fasta output only, default is 60)" )
       puts( "           -" + CLEAN_UP_SEQ_OPTION + ": clean up sequences" )
       puts( "           -" + REMOVE_GAP_COLUMNS_OPTION + ": remove gap columns" )