forester/ruby/evoruby/lib/evo/apps/multi_sequence_extractor.rb

   1 #
   2 # = lib/evo/apps/multi_sequence_extractor.rb - MultiSequenceExtractor class
   3 #
   4 # Copyright::  Copyright (C) 2006-2008 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: multi_sequence_extractor.rb,v 1.10 2010/12/13 19:00:11 cmzmasek Exp $
   8
   9
  10 require 'lib/evo/util/constants'
  11 require 'lib/evo/util/util'
  12 require 'lib/evo/msa/msa'
  13 require 'lib/evo/msa/msa_factory'
  14 require 'lib/evo/io/msa_io'
  15 require 'lib/evo/io/parser/fasta_parser'
  16 require 'lib/evo/io/writer/fasta_writer'
  17 require 'lib/evo/util/command_line_arguments'
  18
  19
  20
  21 module Evoruby
  22
  23   class MultiSequenceExtractor
  24
  25     PRG_NAME                           = "mse"
  26     PRG_VERSION                        = "1.0.0"
  27     PRG_DESC                           = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
  28     PRG_DATE                           = "2008.08.13"
  29     COPYRIGHT                          = "2008-2009 Christian M Zmasek"
  30     CONTACT                            = "phylosoft@gmail.com"
  31     WWW                                = "www.phylosoft.org"
  32     HELP_OPTION_1                      = 'help'
  33     HELP_OPTION_2                      = 'h'
  34
  35     LOG_SUFFIX                          = ".mse_log"
  36     FASTA_SUFFIX                        = ".fasta"
  37     FASTA_WITH_NORMALIZED_IDS_SUFFIX    = ".ni.fasta"
  38     NORMALIZED_IDS_MAP_SUFFIX           = ".nim"
  39     PROTEINS_LIST_FILE_SEPARATOR        = "\t"
  40
  41     def run()
  42
  43       Util.print_program_information( PRG_NAME,
  44         PRG_VERSION,
  45         PRG_DESC ,
  46         PRG_DATE,
  47         COPYRIGHT,
  48         CONTACT,
  49         WWW,
  50         STDOUT )
  51
  52       ld = Constants::LINE_DELIMITER
  53
  54       begin
  55         cla = CommandLineArguments.new( ARGV )
  56       rescue ArgumentError => e
  57         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  58       end
  59
  60       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
  61            cla.is_option_set?( HELP_OPTION_2 ) )
  62         print_help
  63         exit( 0 )
  64       end
  65
  66       if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
  67         print_help
  68         exit( -1 )
  69       end
  70
  71       allowed_opts = Array.new
  72
  73       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  74       if ( disallowed.length > 0 )
  75         Util.fatal_error( PRG_NAME,
  76           "unknown option(s): " + disallowed,
  77           STDOUT )
  78       end
  79
  80       seq_names_files_suffix = cla.get_file_name( 0 )
  81       input_dir              = cla.get_file_name( 1 )
  82       out_dir                = cla.get_file_name( 2 )
  83       out_dir_doms           = cla.get_file_name( 3 )
  84       mapping_file            = nil
  85
  86       if ( cla.get_number_of_files == 5 )
  87         mapping_file = cla.get_file_name( 4 )
  88         begin
  89           Util.check_file_for_readability( mapping_file )
  90         rescue ArgumentError => e
  91           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  92         end
  93       end
  94
  95       if  !File.exist?( input_dir )
  96         Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
  97       end
  98       if  !File.exist?( out_dir )
  99         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
 100       end
 101       if  !File.exist?( out_dir_doms )
 102         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" )
 103       end
 104       if !File.directory?( input_dir )
 105         Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
 106       end
 107       if !File.directory?( out_dir )
 108         Util.fatal_error( PRG_NAME, "error:  [#{out_dir}] is not a directory" )
 109       end
 110       if !File.directory?( out_dir_doms )
 111         Util.fatal_error( PRG_NAME, "error:  [#{out_dir_doms}] is not a directory" )
 112       end
 113
 114
 115       log = String.new
 116
 117       log << "Program            : " + PRG_NAME + ld
 118       log << "Version            : " + PRG_VERSION + ld
 119       log << "Program date       : " + PRG_DATE + ld
 120
 121       puts()
 122       puts( "Sequence names files suffix: " + seq_names_files_suffix )
 123       log << "Sequence names files suffix: " + seq_names_files_suffix + ld
 124       puts( "Input dir                  : " + input_dir )
 125       log << "Input dir                  : " + input_dir + ld
 126       puts( "Output dir                 : " + out_dir )
 127       log << "Output dir                 : " + out_dir + ld
 128       puts( "Output dir domains         : " + out_dir_doms )
 129       log << "Output dir domains         : " + out_dir_doms + ld
 130       if ( mapping_file != nil )
 131         puts( "Mapping file               : " + mapping_file )
 132         log << "Mapping file               : " + mapping_file + ld
 133       end
 134       log << "Date                       : " + Time.now.to_s + ld
 135       puts
 136
 137       if ( mapping_file != nil )
 138         species_codes_to_paths = extract_mappings( mapping_file )
 139       end
 140
 141       input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
 142
 143       counter = 0
 144
 145       input_files.each { |input_file|
 146         counter += 1
 147         puts
 148         puts
 149         puts counter.to_s + "/" + input_files.size.to_s
 150         read_seq_family_file( input_file,
 151           seq_names_files_suffix,
 152           input_dir,
 153           species_codes_to_paths,
 154           log,
 155           out_dir,
 156           out_dir_doms,
 157           mapping_file )
 158       }
 159       puts
 160       Util.print_message( PRG_NAME, "OK" )
 161       puts
 162
 163     end
 164
 165
 166     def read_seq_family_file( input_file,
 167         seq_names_files_suffix,
 168         input_dir,
 169         species_codes_to_paths,
 170         log,
 171         out_dir,
 172         out_dir_doms,
 173         mapping_file )
 174
 175       begin
 176         Util.check_file_for_readability( input_file )
 177       rescue ArgumentError => e
 178         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 179       end
 180       basename = File.basename( input_file, seq_names_files_suffix )
 181       out_file_path_fasta_file                = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
 182       out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
 183       out_file_path_ids_map                   = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
 184       doms_out_file_path_fasta_file           = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains" + FASTA_SUFFIX
 185       begin
 186         Util.check_file_for_writability( out_file_path_fasta_file )
 187         Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
 188         Util.check_file_for_writability( out_file_path_ids_map  )
 189         Util.check_file_for_writability( doms_out_file_path_fasta_file  )
 190       rescue ArgumentError => e
 191         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 192       end
 193
 194       ids_map_writer = nil
 195       begin
 196         ids_map_writer = File.open( out_file_path_ids_map, 'a' )
 197       rescue Exception => e
 198         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 199       end
 200
 201       current_species         = ""
 202       current_msa            = nil
 203       new_msa                = Msa.new
 204       new_msa_normalized_ids = Msa.new
 205       new_msa_domains = Msa.new
 206       per_species_counter = 0
 207
 208       puts basename
 209
 210       File.open( input_file ) do | file |
 211         while line = file.gets
 212           if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 213             values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
 214
 215             if ( values.length < 2 )
 216               Util.fatal_error( PRG_NAME, "unexpected format: " + line )
 217             end
 218             species = values[ 0 ]
 219             if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
 220               next
 221             end
 222             seq_name = values[ 1 ]
 223             domain_ranges = nil
 224             if ( values.length > 3 )
 225               domain_ranges_block = values[ 3 ]
 226               domain_ranges = domain_ranges_block.split( "/" )
 227             end
 228             if ( species != current_species )
 229               current_species = species
 230               my_file = input_dir + Constants::FILE_SEPARATOR + current_species
 231
 232               if ( !File.exist?( my_file ) )
 233                 if species_codes_to_paths == nil
 234                   Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
 235                 elsif ( !species_codes_to_paths.has_key?( current_species ) )
 236                   Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
 237                 end
 238                 my_file = species_codes_to_paths[ current_species ]
 239               end
 240               my_path = File.expand_path( my_file )
 241               my_readlink = my_path
 242               if ( File.symlink?( my_path ) )
 243                 my_readlink = File.readlink( my_path )
 244               end
 245               current_msa = read_fasta_file( my_file )
 246
 247               if ( per_species_counter > 0 )
 248                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 249                 per_species_counter = 0
 250               end
 251               puts " " + current_species + " [" + my_readlink + "]"
 252               log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
 253             end
 254             puts "   " + seq_name
 255             log << "   " + seq_name + Constants::LINE_DELIMITER
 256             per_species_counter = per_species_counter + 1
 257             seq = nil
 258
 259             if current_msa.find_by_name_start( seq_name, true ).size > 0
 260               begin
 261                 seq = current_msa.get_by_name_start( seq_name, true ).copy
 262               rescue ArgumentError => e
 263                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 264               end
 265             else
 266               # Not found, try finding by partial match.
 267               begin
 268                 seq = current_msa.get_by_name( seq_name, true, true )
 269               rescue ArgumentError => e
 270                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 271               end
 272             end
 273
 274             normalized_id = per_species_counter.to_s( 16 ).upcase +
 275              "_" + current_species
 276
 277             per_species_counter.to_i
 278
 279             ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
 280
 281             orig_name = nil
 282             if ( seq != nil )
 283               orig_name = seq.get_name
 284               seq.set_name( seq.get_name + " [" + current_species + "]" )
 285               new_msa.add_sequence( seq )
 286             else
 287               Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
 288             end
 289
 290             if  domain_ranges != nil
 291               domain_ranges.each { |range|
 292                 if range != nil && range.length > 0
 293                   s= range.split("-")
 294                   from = s[ 0 ]
 295                   to = s[ 1 ]
 296                   new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from.to_i..to.to_i] ) )
 297                 end
 298               }
 299             end
 300
 301             new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
 302
 303           end
 304         end
 305
 306       end
 307
 308       ids_map_writer.close
 309
 310       if ( per_species_counter > 0 )
 311         print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 312       end
 313
 314       io = MsaIO.new()
 315
 316       fasta_writer = FastaWriter.new()
 317       fasta_writer.remove_gap_chars
 318       fasta_writer.clean
 319
 320       begin
 321         io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
 322       rescue Exception => e
 323         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 324       end
 325
 326       if  new_msa_domains != nil
 327         begin
 328           io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer )
 329         rescue Exception => e
 330           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 331         end
 332       end
 333
 334       begin
 335         io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
 336       rescue Exception => e
 337         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 338       end
 339
 340       begin
 341         f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LOG_SUFFIX , 'a' )
 342         f.print( log )
 343         f.close
 344       rescue Exception => e
 345         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 346       end
 347
 348     end
 349
 350     def obtain_inputfiles( input_dir, seq_names_files_suffix )
 351       input_files = Array.new()
 352       Dir.foreach( input_dir ) { |file_name|
 353         if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
 354           input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
 355         end
 356       }
 357       input_files
 358     end
 359
 360     def extract_mappings( mapping_file )
 361       species_code_to_path = Hash.new()
 362       File.open( mapping_file ) do | file |
 363         while line = file.gets
 364           if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 365             if ( line =~ /(\S+)\s+(\S+)/ )
 366               species = $1
 367               path = $2
 368               if ( species_code_to_path.has_key?( species ) )
 369                 Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
 370               end
 371               if ( species_code_to_path.has_value?( path ) )
 372                 Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
 373               end
 374               if ( !File.exist?( path ) )
 375                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
 376               end
 377               if ( !File.file?( path ) )
 378                 Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
 379               end
 380               if ( !File.readable?( path ) )
 381                 Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
 382               end
 383               if ( File.size( path ) < 10000 )
 384                 Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
 385               end
 386               if ( !Util.looks_like_fasta?( path ) )
 387                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
 388               end
 389               species_code_to_path[ species ] = path
 390               puts species + " -> " + path
 391             end
 392           end
 393         end
 394       end
 395       species_code_to_path
 396     end
 397
 398     def print_counts( per_species_counter, log, ld )
 399       puts "   [sum: " + per_species_counter.to_s + "]"
 400       log << "   [sum: " + per_species_counter.to_s + "]" + ld
 401     end
 402
 403     def read_fasta_file( input )
 404       f = MsaFactory.new()
 405       msa = nil
 406       begin
 407         msa = f.create_msa_from_file( input, FastaParser.new() )
 408       rescue Exception => e
 409         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 410       end
 411       msa
 412     end
 413
 414     def print_help()
 415       puts( "Usage:" )
 416       puts()
 417       puts( "  " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
 418          "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
 419          "genome multiple-sequence ('fasta') files not in input dir]" )
 420       puts()
 421       puts( "  " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" )
 422       puts()
 423     end
 424
 425   end # class MultiSequenceExtractor
 426 end