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             species_to_genomes = Hash.new()
 145
 146             input_files.each { |input_file|
 147                 counter += 1
 148                 puts
 149                 puts
 150                 puts counter.to_s + "/" + input_files.size.to_s
 151                 read_seq_family_file( input_file,
 152                     seq_names_files_suffix,
 153                     input_dir,
 154                     species_codes_to_paths,
 155                     species_to_genomes,
 156                     log,
 157                     out_dir,
 158                     out_dir_doms,
 159                     mapping_file )
 160             }
 161             puts
 162             Util.print_message( PRG_NAME, "OK" )
 163             puts
 164
 165         end
 166
 167
 168         def read_seq_family_file( input_file,
 169                 seq_names_files_suffix,
 170                 input_dir,
 171                 species_codes_to_paths,
 172                 species_to_genomes,
 173                 log,
 174                 out_dir,
 175                 out_dir_doms,
 176                 mapping_file )
 177
 178             begin
 179                 Util.check_file_for_readability( input_file )
 180             rescue ArgumentError => e
 181                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 182             end
 183             basename = File.basename( input_file, seq_names_files_suffix )
 184             out_file_path_fasta_file                = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
 185             out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
 186             out_file_path_ids_map                   = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
 187             doms_out_file_path_fasta_file           = out_dir_doms + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
 188             begin
 189                 Util.check_file_for_writability( out_file_path_fasta_file )
 190                 Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
 191                 Util.check_file_for_writability( out_file_path_ids_map  )
 192                 Util.check_file_for_writability( doms_out_file_path_fasta_file  )
 193             rescue ArgumentError => e
 194                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 195             end
 196
 197             ids_map_writer = nil
 198             begin
 199                 ids_map_writer = File.open( out_file_path_ids_map, 'a' )
 200             rescue Exception => e
 201                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 202             end
 203
 204             current_species         = ""
 205             current_msa            = nil
 206             new_msa                = Msa.new
 207             new_msa_normalized_ids = Msa.new
 208             new_msa_domains = Msa.new
 209             per_species_counter = 0
 210
 211             puts basename
 212
 213             File.open( input_file ) do | file |
 214                 while line = file.gets
 215                     if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 216                         values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
 217
 218                         if ( values.length < 2 )
 219                             Util.fatal_error( PRG_NAME, "unexpected format: " + line )
 220                         end
 221                         species = values[ 0 ]
 222                         if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
 223                           next
 224                         end
 225                         seq_name = values[ 1 ]
 226                         domain_ranges = nil
 227                         if ( values.length > 2 )
 228                           domain_ranges_block = values[ 2 ]
 229                           domain_ranges = domain_ranges_block.split( "/" )
 230                         end
 231                         if ( species != current_species )
 232                             current_species = species
 233                             my_file = input_dir + Constants::FILE_SEPARATOR + current_species
 234
 235                             if ( !File.exist?( my_file ) )
 236                                 if species_codes_to_paths == nil
 237                                     Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
 238                                 elsif ( !species_codes_to_paths.has_key?( current_species ) )
 239                                     Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
 240                                 end
 241                                 my_file = species_codes_to_paths[ current_species ]
 242                             end
 243                             my_path = File.expand_path( my_file )
 244                             my_readlink = my_path
 245                             if ( File.symlink?( my_path ) )
 246                                 my_readlink = File.readlink( my_path )
 247                             end
 248                             current_msa = read_fasta_file( my_file )
 249                             end
 250
 251                             if ( per_species_counter > 0 )
 252                                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 253                                 per_species_counter = 0
 254                             end
 255                             puts " " + current_species + " [" + my_readlink + "]"
 256                             log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
 257                         end
 258                         puts "   " + seq_name
 259                         log << "   " + seq_name + Constants::LINE_DELIMITER
 260                         per_species_counter = per_species_counter + 1
 261                         seq = nil
 262
 263                         if current_msa.find_by_name_start( seq_name, true ).size > 0
 264                             begin
 265                                 seq = current_msa.get_by_name_start( seq_name, true ).copy
 266                             rescue ArgumentError => e
 267                                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 268                             end
 269                         elsif
 270                             # Not found, try finding by partial match.
 271                             begin
 272                                 seq = current_msa.get_by_name( seq_name, true, true )
 273                             rescue ArgumentError => e
 274                                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 275                             end
 276                         end
 277
 278                         normalized_id = per_species_counter.to_s( 16 ).upcase +
 279                          "_" + current_species
 280
 281                         per_species_counter.to_i
 282
 283                         ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
 284
 285                         orig_name = nil
 286                         if ( seq != nil )
 287                             orig_name = seq.get_name
 288                             seq.set_name( seq.get_name + " [" + current_species + "]" )
 289                             new_msa.add_sequence( seq )
 290                         else
 291                             Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
 292                         end
 293
 294                         if  domain_ranges != nil
 295                             domain_ranges.each { |range|
 296                                 if range != nil
 297                                     s= range.split("-")
 298                                     from = s[ 0 ]
 299                                     to = s[ 1 ]
 300                                     puts from + "-" + to
 301                                     new_msa_domains.add_sequence( Sequence.new( orig_name + "/" + from + "-" + to + " [" + basename + "] [" + current_species + "]", seq.get_sequence_as_string[from..to] ) )
 302                                 end
 303                             }
 304                         end
 305
 306                         new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
 307
 308                     end
 309                 end
 310
 311             end
 312
 313             ids_map_writer.close
 314
 315             if ( per_species_counter > 0 )
 316                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 317             end
 318
 319             io = MsaIO.new()
 320
 321             fasta_writer = FastaWriter.new()
 322             fasta_writer.remove_gap_chars
 323             fasta_writer.clean
 324
 325             begin
 326                 io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
 327             rescue Exception => e
 328                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 329             end
 330
 331             if  new_msa_domains != nil
 332                 begin
 333                     io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer )
 334                 rescue Exception => e
 335                     Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 336                 end
 337            end
 338
 339             begin
 340                 io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
 341             rescue Exception => e
 342                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 343             end
 344
 345             begin
 346                 f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LOG_SUFFIX , 'a' )
 347                 f.print( log )
 348                 f.close
 349             rescue Exception => e
 350                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 351             end
 352
 353         end
 354
 355         def obtain_inputfiles( input_dir, seq_names_files_suffix )
 356             input_files = Array.new()
 357             Dir.foreach( input_dir ) { |file_name|
 358                 if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
 359                     input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
 360                 end
 361             }
 362             input_files
 363         end
 364
 365         def extract_mappings( mapping_file )
 366             species_code_to_path = Hash.new()
 367             File.open( mapping_file ) do | file |
 368                 while line = file.gets
 369                     if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 370                         if ( line =~ /(\S+)\s+(\S+)/ )
 371                             species = $1
 372                             path = $2
 373                             if ( species_code_to_path.has_key?( species ) )
 374                                 Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
 375                             end
 376                             if ( species_code_to_path.has_value?( path ) )
 377                                 Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
 378                             end
 379                             if ( !File.exist?( path ) )
 380                                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
 381                             end
 382                             if ( !File.file?( path ) )
 383                                 Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
 384                             end
 385                             if ( !File.readable?( path ) )
 386                                 Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
 387                             end
 388                             if ( File.size( path ) < 10000 )
 389                                 Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
 390                             end
 391                             if ( !Util.looks_like_fasta?( path ) )
 392                                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
 393                             end
 394                             species_code_to_path[ species ] = path
 395                             puts species + " -> " + path
 396                         end
 397                     end
 398                 end
 399             end
 400             species_code_to_path
 401         end
 402
 403         def print_counts( per_species_counter, log, ld )
 404             puts "   [sum: " + per_species_counter.to_s + "]"
 405             log << "   [sum: " + per_species_counter.to_s + "]" + ld
 406         end
 407
 408         def read_fasta_file( input )
 409             f = MsaFactory.new()
 410             msa = nil
 411             begin
 412                 msa = f.create_msa_from_file( input, FastaParser.new() )
 413             rescue Exception => e
 414                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 415             end
 416             msa
 417         end
 418
 419         def print_help()
 420             puts( "Usage:" )
 421             puts()
 422             puts( "  " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
 423                  "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
 424                  "genome multiple-sequence ('fasta') files not in input dir]" )
 425             puts()
 426             puts( "  " + "Example: \"mse.rb .prot . seqs doms ../genome_locations.txt\"" )
 427             puts()
 428         end
 429
 430     end # class MultiSequenceExtractor
 431 end