forester/ruby/evoruby/lib/evo/tool/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                        = "1.03"
  27     PRG_DESC                           = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
  28     PRG_DATE                           = "131127"
  29     COPYRIGHT                          = "2008-2013 Christian M Zmasek"
  30     CONTACT                            = "phylosoft@gmail.com"
  31     WWW                                = "https://sites.google.com/site/cmzmasek/home/software/forester"
  32     HELP_OPTION_1                      = 'help'
  33     HELP_OPTION_2                      = 'h'
  34
  35     EXT_OPTION                          = 'e'
  36     EXTRACT_LINKERS_OPTION              = 'l'
  37     LOG_SUFFIX                          = ".mse_log"
  38     LINKERS_SUFFIX                      = ".linkers"
  39     FASTA_SUFFIX                        = ".fasta"
  40     FASTA_WITH_NORMALIZED_IDS_SUFFIX    = ".ni.fasta"
  41     NORMALIZED_IDS_MAP_SUFFIX           = ".nim"
  42     PROTEINS_LIST_FILE_SEPARATOR        = "\t"
  43
  44     def initialize()
  45       @file_to_msa = Hash.new
  46       @seqs = 0
  47     end
  48
  49     def run()
  50
  51       Util.print_program_information( PRG_NAME,
  52         PRG_VERSION,
  53         PRG_DESC ,
  54         PRG_DATE,
  55         COPYRIGHT,
  56         CONTACT,
  57         WWW,
  58         STDOUT )
  59
  60       ld = Constants::LINE_DELIMITER
  61
  62       begin
  63         cla = CommandLineArguments.new( ARGV )
  64       rescue ArgumentError => e
  65         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  66       end
  67
  68       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
  69            cla.is_option_set?( HELP_OPTION_2 ) )
  70         print_help
  71         exit( 0 )
  72       end
  73
  74       if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
  75         print_help
  76         exit( -1 )
  77       end
  78
  79       allowed_opts = Array.new
  80       allowed_opts.push(EXT_OPTION)
  81       allowed_opts.push(EXTRACT_LINKERS_OPTION)
  82
  83       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  84       if ( disallowed.length > 0 )
  85         Util.fatal_error( PRG_NAME,
  86           "unknown option(s): " + disallowed,
  87           STDOUT )
  88       end
  89
  90       seq_names_files_suffix = cla.get_file_name( 0 )
  91       input_dir              = cla.get_file_name( 1 )
  92       out_dir                = cla.get_file_name( 2 )
  93       out_dir_doms           = cla.get_file_name( 3 )
  94       mapping_file            = nil
  95
  96       if ( cla.get_number_of_files == 5 )
  97         mapping_file = cla.get_file_name( 4 )
  98         begin
  99           Util.check_file_for_readability( mapping_file )
 100         rescue ArgumentError => e
 101           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 102         end
 103       end
 104
 105       extension = 0
 106       if cla.is_option_set?(EXT_OPTION)
 107         extension = cla.get_option_value_as_int(EXT_OPTION)
 108         if extension < 0
 109           extension = 0
 110         end
 111       end
 112
 113       extract_linkers = false
 114       if cla.is_option_set?(EXTRACT_LINKERS_OPTION)
 115         extract_linkers = true
 116       end
 117
 118       if  !File.exist?( input_dir )
 119         Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
 120       end
 121       if  !File.exist?( out_dir )
 122         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
 123       end
 124       if  !File.exist?( out_dir_doms )
 125         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" )
 126       end
 127       if !File.directory?( input_dir )
 128         Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
 129       end
 130       if !File.directory?( out_dir )
 131         Util.fatal_error( PRG_NAME, "error:  [#{out_dir}] is not a directory" )
 132       end
 133       if !File.directory?( out_dir_doms )
 134         Util.fatal_error( PRG_NAME, "error:  [#{out_dir_doms}] is not a directory" )
 135       end
 136
 137
 138       log = String.new
 139
 140       log << "Program            : " + PRG_NAME + ld
 141       log << "Version            : " + PRG_VERSION + ld
 142       log << "Program date       : " + PRG_DATE + ld
 143
 144       puts()
 145       puts( "Sequence names files suffix: " + seq_names_files_suffix )
 146       log << "Sequence names files suffix: " + seq_names_files_suffix + ld
 147       puts( "Input dir                  : " + input_dir )
 148       log << "Input dir                  : " + input_dir + ld
 149       puts( "Output dir                 : " + out_dir )
 150       log << "Output dir                 : " + out_dir + ld
 151       puts( "Output dir domains         : " + out_dir_doms )
 152       log << "Output dir domains         : " + out_dir_doms + ld
 153       if ( mapping_file != nil )
 154         puts( "Mapping file               : " + mapping_file )
 155         log << "Mapping file               : " + mapping_file + ld
 156       end
 157       if extension > 0
 158         puts( "Extension                  : " + extension.to_s )
 159         log << "Extension                  : " + extension.to_s + ld
 160       end
 161       if extract_linkers
 162         puts( "Extract linkers            : true" )
 163         log << "Extract linkers            : true" + ld
 164       end
 165       log << "Date                       : " + Time.now.to_s + ld
 166       puts
 167
 168       if ( mapping_file != nil )
 169         species_codes_to_paths = extract_mappings( mapping_file )
 170       end
 171
 172       input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
 173
 174       counter = 0
 175
 176       input_files.each { |input_file|
 177         counter += 1
 178         puts
 179         puts
 180         puts counter.to_s + "/" + input_files.size.to_s
 181         read_seq_family_file( input_file,
 182           seq_names_files_suffix,
 183           input_dir,
 184           species_codes_to_paths,
 185           log,
 186           out_dir,
 187           out_dir_doms,
 188           mapping_file,
 189           extension,
 190           extract_linkers )
 191       }
 192       puts
 193       Util.print_message( PRG_NAME, "OK" )
 194       puts
 195
 196     end
 197
 198
 199     def read_seq_family_file( input_file,
 200         seq_names_files_suffix,
 201         input_dir,
 202         species_codes_to_paths,
 203         log,
 204         out_dir,
 205         out_dir_doms,
 206         mapping_file,
 207         extension,
 208         extract_linkers )
 209
 210       begin
 211         Util.check_file_for_readability( input_file )
 212       rescue ArgumentError => e
 213         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 214       end
 215       basename = File.basename( input_file, seq_names_files_suffix )
 216       out_file_path_fasta_file                = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
 217       out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
 218       out_file_path_ids_map                   = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
 219       doms_out_file_path_fasta_file           = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains" + FASTA_SUFFIX
 220       doms_ext_out_file_path_fasta_file           = nil
 221       if extension > 0
 222         doms_ext_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains_ext_" + extension.to_s + FASTA_SUFFIX
 223       end
 224       begin
 225         Util.check_file_for_writability( out_file_path_fasta_file )
 226         Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
 227         Util.check_file_for_writability( out_file_path_ids_map  )
 228         Util.check_file_for_writability( doms_out_file_path_fasta_file  )
 229       rescue ArgumentError => e
 230         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 231       end
 232
 233       ids_map_writer = nil
 234       begin
 235         ids_map_writer = File.open( out_file_path_ids_map, 'a' )
 236       rescue Exception => e
 237         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 238       end
 239
 240       current_species         = ""
 241       current_msa            = nil
 242       new_msa                = Msa.new
 243       new_msa_normalized_ids = Msa.new
 244       new_msa_domains = Msa.new
 245       new_msa_domains_extended = Msa.new
 246       per_species_counter = 0
 247       linkers = ""
 248
 249       puts basename
 250
 251       File.open( input_file ) do | file |
 252         species_counter = 1
 253         while line = file.gets
 254           line.strip!
 255           if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
 256             values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
 257             mod_line = nil
 258             if ( values.length < 2 )
 259               Util.fatal_error( PRG_NAME, "unexpected format: " + line )
 260             end
 261             species = values[ 0 ]
 262             #if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
 263             #  next
 264             #end
 265             seq_name = values[ 1 ]
 266             domain_ranges = nil
 267             if ( values.length > 3 )
 268               domain_ranges_block = values[ 3 ]
 269               domain_ranges = domain_ranges_block.split( "/" )
 270             end
 271             if ( species != current_species )
 272               current_species = species
 273               my_file = input_dir + Constants::FILE_SEPARATOR + current_species
 274
 275               if ( !File.exist?( my_file ) )
 276                 if species_codes_to_paths == nil
 277                   Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
 278                 elsif ( !species_codes_to_paths.has_key?( current_species ) )
 279                   Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
 280                 end
 281                 my_file = species_codes_to_paths[ current_species ]
 282               end
 283               my_path = File.expand_path( my_file )
 284               my_readlink = my_path
 285               if ( File.symlink?( my_path ) )
 286                 my_readlink = File.readlink( my_path )
 287               end
 288               current_msa = read_fasta_file( my_file )
 289
 290               if ( per_species_counter > 0 )
 291                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 292                 per_species_counter = 0
 293               end
 294               puts " " + species_counter.to_s +  ":" + current_species + " [" + my_readlink + "]"
 295               log << species_counter.to_s <<  ": " << current_species << " [" + my_readlink + "]" << Constants::LINE_DELIMITER
 296               species_counter += 1
 297             end
 298             log << "   " << seq_name << Constants::LINE_DELIMITER
 299             per_species_counter = per_species_counter + 1
 300             seq = nil
 301
 302             indices = current_msa.find_by_name_start( seq_name, true )
 303             if indices.size == 1
 304               seq =  current_msa.get_sequence( indices[ 0 ] )
 305             elsif indices.size == 0
 306               # Not found, try finding by partial match.
 307               begin
 308                 seq = current_msa.get_by_name( seq_name, true, true )
 309               rescue ArgumentError => e
 310                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 311               end
 312             else
 313               Util.fatal_error( PRG_NAME, "error: seq name \"" + seq_name + "\" not unique"  )
 314             end
 315
 316             normalized_id = per_species_counter.to_s( 16 ).upcase +
 317              "_" + current_species
 318
 319             per_species_counter.to_i
 320
 321             ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER )
 322
 323             orig_name = nil
 324             if seq != nil
 325               orig_name = seq.get_name
 326               seq.set_name( seq.get_name + " [" + current_species + "]" )
 327               new_msa.add_sequence( seq )
 328             else
 329               Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
 330             end
 331
 332             if domain_ranges != nil
 333               first = true
 334               prev_to = -1
 335
 336               domain_ranges.each { |range|
 337                 if range != nil && range.length > 0
 338                   s = range.split("-")
 339                   from = s[ 0 ].to_i
 340                   to = s[ 1 ].to_i
 341                   new_msa_domains.add_sequence( Sequence.new( orig_name +
 342                        " [" + from.to_s +
 343                        "-" + to.to_s +
 344                        "] [" + basename + "] [" +
 345                        current_species + "]",
 346                       seq.get_sequence_as_string[from..to] ) )
 347                   if extension > 0
 348                     from_e = from - extension
 349                     if from_e < 0
 350                       from_e = 0
 351                     end
 352                     to_e = to + extension
 353                     if to_e > seq.get_sequence_as_string.length - 1
 354                       to_e = seq.get_sequence_as_string.length - 1
 355                     end
 356                     new_msa_domains_extended.add_sequence( Sequence.new( orig_name +
 357                          " [" + from.to_s +
 358                          "-" + to.to_s  +
 359                          "] [extended by " +
 360                          extension.to_s +
 361                          "] [" + basename + "] [" +
 362                          current_species + "]",
 363                         seq.get_sequence_as_string[ from_e..to_e ] ) )
 364                   end # extension > 0
 365                   if  extract_linkers
 366                     if first
 367                       first = false
 368                       f = 0
 369                       t = from - 1
 370                       if extension > 0
 371                         f = from - extension
 372                       end
 373                       mod_line = line + "\t[" + get_linker_sequence( f, t, seq ) + "|"
 374                     else
 375                       mod_line += get_linker_sequence( prev_to + 1, from - 1, seq ) + "|"
 376                     end
 377                     prev_to = to
 378                   end
 379                 end # range != nil && range.length > 0
 380               }
 381               if extract_linkers && prev_to > 0
 382                 f = prev_to + 1
 383                 t = seq.get_sequence_as_string.length - 1
 384                 if extension > 0
 385                   t = prev_to + extension
 386                 end
 387                 mod_line += get_linker_sequence( f, t, seq ) + "]"
 388               end
 389             end
 390
 391             new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
 392             if mod_line
 393               linkers << mod_line + Constants::LINE_DELIMITER
 394             end
 395           end # !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
 396         end # while line = file.gets
 397
 398       end
 399
 400       ids_map_writer.close
 401
 402       if ( per_species_counter > 0 )
 403         print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 404       end
 405
 406       io = MsaIO.new()
 407
 408       fasta_writer = FastaWriter.new()
 409       fasta_writer.remove_gap_chars
 410       fasta_writer.clean
 411
 412       begin
 413         io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
 414       rescue Exception => e
 415         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 416       end
 417
 418       if new_msa_domains != nil
 419         begin
 420           io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer )
 421         rescue Exception => e
 422           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 423         end
 424       end
 425
 426       if extension > 0 && new_msa_domains_extended != nil
 427         begin
 428           io.write_to_file( new_msa_domains_extended, doms_ext_out_file_path_fasta_file, fasta_writer )
 429         rescue Exception => e
 430           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 431         end
 432       end
 433
 434       begin
 435         io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
 436       rescue Exception => e
 437         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 438       end
 439
 440       begin
 441         f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LOG_SUFFIX , 'a' )
 442         f.print( log )
 443         f.close
 444       rescue Exception => e
 445         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 446       end
 447
 448       if extract_linkers && linkers != nil
 449         begin
 450           f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LINKERS_SUFFIX , 'a' )
 451           f.print( linkers )
 452           f.close
 453         rescue Exception => e
 454           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 455         end
 456       end
 457     end
 458
 459
 460     def get_linker_sequence( from, to, seq )
 461       if from < 0
 462         from = 0
 463       end
 464       if to > seq.get_sequence_as_string.length - 1
 465         to = seq.get_sequence_as_string.length - 1
 466       end
 467       if from > to
 468         return ""
 469       else
 470         return from.to_s + "-" + to.to_s + ":" + seq.get_sequence_as_string[ from..to ]
 471       end
 472     end
 473
 474     def obtain_inputfiles( input_dir, seq_names_files_suffix )
 475       input_files = Array.new()
 476       Dir.foreach( input_dir ) { |file_name|
 477         if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
 478           input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
 479         end
 480       }
 481       input_files
 482     end
 483
 484     def extract_mappings( mapping_file )
 485       species_code_to_path = Hash.new()
 486       File.open( mapping_file ) do | file |
 487         while line = file.gets
 488           if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 489             if ( line =~ /(\S+)\s+(\S+)/ )
 490               species = $1
 491               path = $2
 492               if ( species_code_to_path.has_key?( species ) )
 493                 Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
 494               end
 495               if ( species_code_to_path.has_value?( path ) )
 496                 Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
 497               end
 498               if ( !File.exist?( path ) )
 499                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
 500               end
 501               if ( !File.file?( path ) )
 502                 Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
 503               end
 504               if ( !File.readable?( path ) )
 505                 Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
 506               end
 507               if ( File.size( path ) < 10000 )
 508                 Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
 509               end
 510               if ( !Util.looks_like_fasta?( path ) )
 511                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
 512               end
 513               species_code_to_path[ species ] = path
 514               puts species + " -> " + path
 515             end
 516           end
 517         end
 518       end
 519       species_code_to_path
 520     end
 521
 522     def print_counts( per_species_counter, log, ld )
 523       puts "   sum: " + per_species_counter.to_s
 524       log << "   sum: " + per_species_counter.to_s + ld
 525     end
 526
 527     def read_fasta_file( input )
 528       if @file_to_msa.has_key?( input )
 529         return @file_to_msa[ input ]
 530       end
 531
 532       f = MsaFactory.new()
 533       msa = nil
 534       begin
 535         msa = f.create_msa_from_file( input, FastaParser.new() )
 536       rescue Exception => e
 537         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 538       end
 539       if @seqs <= 400000
 540         @file_to_msa[ input ] = msa
 541         @seqs += msa.get_number_of_seqs
 542         puts "   total seqs in memory: " + @seqs.to_s
 543       end
 544       msa
 545     end
 546
 547     def print_help()
 548       puts( "Usage:" )
 549       puts()
 550       puts( "  " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
 551          "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
 552          "genome multiple-sequence ('fasta') files not in input dir]" )
 553       puts()
 554       puts( "  option: -" + EXT_OPTION  + "=<int>: to extend extracted domains" )
 555       puts( "          -" + EXTRACT_LINKERS_OPTION  + "      : to extract linkers" )
 556       puts()
 557       puts( "  " + "Example: \"mse.rb .prot . protein_seqs domain_seqs ../genome_locations.txt\"" )
 558       puts()
 559     end
 560
 561   end # class MultiSequenceExtractor
 562 end