forester/ruby/evoruby/lib/evo/io/writer/nexus_writer.rb

   1 #
   2 # = lib/evo/io/writer/nexus_writer.rb - NexusWriter class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: nexus_writer.rb,v 1.4 2009/11/04 01:50:59 cmzmasek Exp $
   8 #
   9 # last modified: 05/16/2007
  10
  11 require 'lib/evo/io/writer/msa_writer'
  12
  13 module Evoruby
  14
  15     class NexusWriter < MsaWriter
  16
  17         MAX_NAME_LENGTH_DEFAULT = 10
  18
  19         def initialize()
  20             @max_name_length = MAX_NAME_LENGTH_DEFAULT
  21             @clean           = false
  22         end
  23
  24         def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
  25             if length < 1
  26                 length = MAX_NAME_LENGTH_DEFAULT
  27             end
  28             @max_name_length = length
  29         end
  30
  31         def clean( clean = true )
  32             @clean = clean
  33         end
  34
  35         def write( msa, path )
  36             if ( !msa.is_aligned() )
  37                 error_msg = "attempt to write unaligned msa in nexus format"
  38                 raise StandardError, error_msg, caller
  39             end
  40
  41             Util.check_file_for_writability( path )
  42
  43             f = File.open( path, "a" )
  44
  45             f.print( "Begin Data;" )
  46             f.print( Evoruby::Constants::LINE_DELIMITER )
  47             f.print( "   Dimensions NTax=" )
  48             f.print( msa.get_number_of_seqs().to_s() )
  49             f.print( " NChar=" )
  50             f.print( msa.get_length().to_s() )
  51             f.print( ";" )
  52             f.print( Evoruby::Constants::LINE_DELIMITER )
  53             f.print( "   Format DataType=Protein Interleave=No gap=-;" )
  54             f.print( Evoruby::Constants::LINE_DELIMITER )
  55             f.print( "   Matrix" )
  56             f.print( Evoruby::Constants::LINE_DELIMITER )
  57             for i in 0 ... msa.get_number_of_seqs()
  58                 seq_obj = msa.get_sequence( i )
  59                 name = seq_obj.get_name()
  60                 seq  = seq_obj.get_sequence_as_string()
  61                 name = name.gsub( /\s+$/, '')
  62                 name = name.gsub( /\s+/, '_')
  63                 name = Util.normalize_seq_name( name, @max_name_length )
  64                 f.print( "      " )
  65                 f.print( name )
  66                 f.print( " " )
  67                 if ( @clean )
  68                     seq = Util.clean_seq_str( seq )
  69                 end
  70                 f.print( seq )
  71                 f.print( Evoruby::Constants::LINE_DELIMITER )
  72             end
  73             f.print( "   ;" )
  74             f.print( Evoruby::Constants::LINE_DELIMITER )
  75             f.print( "End;" )
  76             f.print( Evoruby::Constants::LINE_DELIMITER )
  77             f.close()
  78         end
  79
  80     end # class NexusWriter
  81
  82 end # module Evoruby