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

   1 #
   2 # = lib/evo/io/writer/fasta_writer.rb - FastaWriter class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: fasta_writer.rb,v 1.6 2008/09/12 23:52:11 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 FastaWriter < MsaWriter
  16
  17         LINE_WIDTH_DEFAULT      = 60
  18         MAX_NAME_LENGTH_DEFAULT = 0
  19
  20         def initialize()
  21             @line_width       = LINE_WIDTH_DEFAULT
  22             @max_name_length  = MAX_NAME_LENGTH_DEFAULT
  23             @remove_gap_chars = false
  24             @clean            = false
  25         end
  26
  27
  28         def set_line_width( line_width = LINE_WIDTH_DEFAULT )
  29             if ( line_width < 1 )
  30                 line_width = LINE_WIDTH_DEFAULT
  31             end
  32             @line_width = line_width
  33         end
  34
  35         def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
  36             if ( length < 1 )
  37                 length = MAX_NAME_LENGTH_DEFAULT
  38             end
  39             @max_name_length = length
  40         end
  41
  42         def remove_gap_chars( remove_gap_chars = true )
  43             @remove_gap_chars = remove_gap_chars
  44         end
  45
  46         def clean( clean = true )
  47             @clean = clean
  48         end
  49
  50         def write( msa, path )
  51             Util.check_file_for_writability( path )
  52             f = File.open( path, "a" )
  53             for i in 0 ... msa.get_number_of_seqs()
  54                 seq_obj = msa.get_sequence( i )
  55                 name = seq_obj.get_name()
  56                 f.print( ">" )
  57                 if ( @max_name_length != MAX_NAME_LENGTH_DEFAULT )
  58                     name = Util.normalize_seq_name( name, @max_name_length )
  59                 end
  60                 f.print( name )
  61                 counter = 0
  62                 for j in 0 ... seq_obj.get_length()
  63                     unless @remove_gap_chars && Util.is_aa_gap_character?( seq_obj.get_character_code( j ) )
  64                         char = seq_obj.get_residue( j )
  65                         if ( @clean )
  66                             char = Util.clean_seq_str( char )
  67                             if ( char.length < 1 )
  68                                 next
  69                             end
  70                         end
  71                         if counter % @line_width == 0
  72                             f.print( Evoruby::Constants::LINE_DELIMITER )
  73                         end
  74                         f.print( char )
  75                         counter += 1
  76                     end
  77                 end
  78                 f.print( Evoruby::Constants::LINE_DELIMITER )
  79             end
  80             f.close()
  81         end
  82
  83     end # class FastaWriter
  84
  85 end # module Evoruby
  86