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             @ex_if_name_too_long = false
  26         end
  27
  28
  29         def set_line_width( line_width = LINE_WIDTH_DEFAULT )
  30             if ( line_width < 1 )
  31                 line_width = LINE_WIDTH_DEFAULT
  32             end
  33             @line_width = line_width
  34         end
  35
  36         def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
  37             if ( length < 1 )
  38                 length = MAX_NAME_LENGTH_DEFAULT
  39             end
  40             @max_name_length = length
  41         end
  42
  43         def remove_gap_chars( remove_gap_chars = true )
  44             @remove_gap_chars = remove_gap_chars
  45         end
  46
  47         def clean( clean = true )
  48             @clean = clean
  49         end
  50
  51         def set_exception_if_name_too_long( exception_if_name_too_long )
  52           @ex_if_name_too_long = exception_if_name_too_long
  53         end
  54
  55         def write( msa, path )
  56             Util.check_file_for_writability( path )
  57             f = File.open( path, "a" )
  58             for i in 0 ... msa.get_number_of_seqs()
  59                 seq_obj = msa.get_sequence( i )
  60                 name = seq_obj.get_name()
  61                 f.print( ">" )
  62                 if ( @max_name_length != MAX_NAME_LENGTH_DEFAULT )
  63                     name = Util.normalize_seq_name( name, @max_name_length, @ex_if_name_too_long )
  64                 end
  65                 f.print( name )
  66                 counter = 0
  67                 for j in 0 ... seq_obj.get_length()
  68                     unless @remove_gap_chars && Util.is_aa_gap_character?( seq_obj.get_character_code( j ) )
  69                         char = seq_obj.get_residue( j )
  70                         if ( @clean )
  71                             char = Util.clean_seq_str( char )
  72                             if ( char.length < 1 )
  73                                 next
  74                             end
  75                         end
  76                         if counter % @line_width == 0
  77                             f.print( Evoruby::Constants::LINE_DELIMITER )
  78                         end
  79                         f.print( char )
  80                         counter += 1
  81                     end
  82                 end
  83                 f.print( Evoruby::Constants::LINE_DELIMITER )
  84             end
  85             f.close()
  86         end
  87
  88     end # class FastaWriter
  89
  90 end # module Evoruby
  91