forester/ruby/evoruby/lib/evo/tool/new_tap.rb

   1 #
   2 # = lib/evo/apps/ -  class
   3 #
   4 # Copyright::  Copyright (C) 2009 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: new_tap.rb,v 1.4 2010/12/13 19:00:11 cmzmasek Exp $
   8
   9
  10 require 'lib/evo/util/util'
  11 require 'lib/evo/msa/msa_factory'
  12 require 'lib/evo/msa/msa'
  13 require 'lib/evo/io/msa_io'
  14 require 'lib/evo/io/parser/fasta_parser'
  15 require 'lib/evo/io/parser/general_msa_parser'
  16 require 'lib/evo/io/writer/fasta_writer'
  17 require 'lib/evo/io/writer/phylip_sequential_writer'
  18 require 'lib/evo/util/command_line_arguments'
  19
  20 module Evoruby
  21
  22     class TaxonomyProcessor
  23
  24         PRG_NAME       = ""
  25         PRG_DATE       = "2009.10.09"
  26         PRG_DESC       = "replacement of labels in multiple sequence files"
  27         PRG_VERSION    = "1.00"
  28         COPYRIGHT      = "2009 Christian M Zmasek"
  29         CONTACT        = "phylosoft@gmail.com"
  30         WWW            = "www.phylosoft.org"
  31
  32         REMOVE_REDUNDANT_SEQS_OPTION = "rr"
  33
  34         def initialize()
  35             @taxonomies = Hash.new()
  36         end
  37
  38         def run()
  39
  40             Util.print_program_information( PRG_NAME,
  41                 PRG_VERSION,
  42                 PRG_DESC,
  43                 PRG_DATE,
  44                 COPYRIGHT,
  45                 CONTACT,
  46                 WWW,
  47                 STDOUT )
  48
  49             if ( ARGV == nil || ( ARGV.length != 3 && ARGV.length != 4 ) )
  50                 puts( "Usage: #{PRG_NAME}.rb <input sequences> <output sequences> <output map>" )
  51                 puts()
  52                 puts( "  options: -" + REMOVE_REDUNDANT_SEQS_OPTION + ": to remove redundant sequences" )
  53                 puts()
  54                 exit( -1 )
  55             end
  56
  57             begin
  58                 cla = CommandLineArguments.new( ARGV )
  59             rescue ArgumentError => e
  60                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  61             end
  62
  63             input     = cla.get_file_name( 0 )
  64             output    = cla.get_file_name( 1 )
  65             map_file = cla.get_file_name( 2 )
  66
  67             allowed_opts = Array.new
  68             allowed_opts.push( REMOVE_REDUNDANT_SEQS_OPTION )
  69
  70             disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  71             if ( disallowed.length > 0 )
  72                 Util.fatal_error( PRG_NAME, "unknown option(s): " + disallowed )
  73             end
  74
  75
  76             remove_redudant = false
  77             if ( cla.is_option_set?( REMOVE_REDUNDANT_SEQS_OPTION ) )
  78                 remove_redudant = true
  79             end
  80
  81             if ( File.exists?( output ) )
  82                 Util.fatal_error( PRG_NAME, "outfile [" + output + "] already exists" )
  83             end
  84             if ( File.exists?( map_file ) )
  85                 Util.fatal_error( PRG_NAME, "map file [" + map_file + "] already exists" )
  86             end
  87             if ( !File.exists?( input) )
  88                 Util.fatal_error( PRG_NAME, "infile [" + input + "] does not exist" )
  89             end
  90
  91             fasta_like = Util.looks_like_fasta?( input )
  92
  93             puts()
  94             puts( "Input alignment : " + input )
  95             puts( "Output alignment: " + output )
  96             puts( "Output map      : " + map_file )
  97             if ( fasta_like )
  98                 puts( "Format          : Fasta"  )
  99             else
 100                 puts( "Format          : Phylip like" )
 101             end
 102             puts()
 103
 104             species_map = Hash.new
 105
 106             f = MsaFactory.new()
 107             begin
 108                 if ( fasta_like )
 109                     msa = f.create_msa_from_file( input, FastaParser.new() )
 110                 else
 111                     msa = f.create_msa_from_file( input, GeneralMsaParser.new() )
 112                 end
 113             rescue Exception => e
 114                 Util.fatal_error( PRG_NAME, "failed to read file: " + e.to_s )
 115             end
 116
 117             if ( msa == nil || msa.get_number_of_seqs() < 1 )
 118                 Util.fatal_error( PRG_NAME, "failed to read MSA" )
 119             end
 120             begin
 121                 Util.check_file_for_writability( map_file )
 122             rescue Exception => e
 123                 Util.fatal_error( PRG_NAME, "error: " + e.to_, STDOUT )
 124             end
 125
 126             if ( remove_redudant )
 127                 removed = msa.remove_redundant_sequences!( true )
 128                 if removed.size > 0
 129                     Util.print_message( PRG_NAME, "going to ignore the following " + removed.size.to_s + " redundant sequences:" )
 130                     removed.each { | seq_name |
 131                         puts seq_name
 132                     }
 133                     Util.print_message( PRG_NAME, "will process " + msa.get_number_of_seqs.to_s + " non redundant sequences" )
 134                 end
 135             end
 136
 137             lf = File.open( map_file, "a" )
 138             for i in 0 ... msa.get_number_of_seqs
 139                 seq  = msa.get_sequence( i )
 140             end
 141
 142             io = MsaIO.new()
 143             w = nil
 144             if ( fasta_like )
 145                 w = FastaWriter.new()
 146             else
 147                 w = PhylipSequentialWriter.new()
 148             end
 149             w.set_max_name_length( 10 )
 150             w.clean( true )
 151             begin
 152                 io.write_to_file( msa, output, w )
 153             rescue Exception => e
 154                 Util.fatal_error( PRG_NAME, "failed to write file: " + e.to_s )
 155             end
 156             lf.close()
 157             if ( @taxonomies.length > 0 )
 158                 Util.print_message( PRG_NAME, "number of unique taxonomies: " + @taxonomies.length.to_s )
 159             end
 160             Util.print_message( PRG_NAME, "wrote: " + map_file )
 161             Util.print_message( PRG_NAME, "wrote: " + output )
 162             Util.print_message( PRG_NAME, "OK" )
 163         end
 164
 165     end # class
 166
 167 end # module Evoruby