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                        = "1.01"
  27     PRG_DESC                           = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
  28     PRG_DATE                           = "2012.07.19"
  29     COPYRIGHT                          = "2008-2012 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     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
  45     def run()
  46
  47       Util.print_program_information( PRG_NAME,
  48         PRG_VERSION,
  49         PRG_DESC ,
  50         PRG_DATE,
  51         COPYRIGHT,
  52         CONTACT,
  53         WWW,
  54         STDOUT )
  55
  56       ld = Constants::LINE_DELIMITER
  57
  58       begin
  59         cla = CommandLineArguments.new( ARGV )
  60       rescue ArgumentError => e
  61         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  62       end
  63
  64       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
  65            cla.is_option_set?( HELP_OPTION_2 ) )
  66         print_help
  67         exit( 0 )
  68       end
  69
  70       if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
  71         print_help
  72         exit( -1 )
  73       end
  74
  75       allowed_opts = Array.new
  76       allowed_opts.push(EXT_OPTION)
  77       allowed_opts.push(EXTRACT_LINKERS_OPTION)
  78
  79       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  80       if ( disallowed.length > 0 )
  81         Util.fatal_error( PRG_NAME,
  82           "unknown option(s): " + disallowed,
  83           STDOUT )
  84       end
  85
  86       seq_names_files_suffix = cla.get_file_name( 0 )
  87       input_dir              = cla.get_file_name( 1 )
  88       out_dir                = cla.get_file_name( 2 )
  89       out_dir_doms           = cla.get_file_name( 3 )
  90       mapping_file            = nil
  91
  92       if ( cla.get_number_of_files == 5 )
  93         mapping_file = cla.get_file_name( 4 )
  94         begin
  95           Util.check_file_for_readability( mapping_file )
  96         rescue ArgumentError => e
  97           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
  98         end
  99       end
 100
 101       extension = 0
 102       if cla.is_option_set?(EXT_OPTION)
 103         extension = cla.get_option_value_as_int(EXT_OPTION)
 104         if extension < 0
 105           extension = 0
 106         end
 107       end
 108
 109       extract_linkers = false
 110       if cla.is_option_set?(EXTRACT_LINKERS_OPTION)
 111         extract_linkers = true
 112       end
 113
 114       if  !File.exist?( input_dir )
 115         Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
 116       end
 117       if  !File.exist?( out_dir )
 118         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
 119       end
 120       if  !File.exist?( out_dir_doms )
 121         Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" )
 122       end
 123       if !File.directory?( input_dir )
 124         Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
 125       end
 126       if !File.directory?( out_dir )
 127         Util.fatal_error( PRG_NAME, "error:  [#{out_dir}] is not a directory" )
 128       end
 129       if !File.directory?( out_dir_doms )
 130         Util.fatal_error( PRG_NAME, "error:  [#{out_dir_doms}] is not a directory" )
 131       end
 132
 133
 134       log = String.new
 135
 136       log << "Program            : " + PRG_NAME + ld
 137       log << "Version            : " + PRG_VERSION + ld
 138       log << "Program date       : " + PRG_DATE + ld
 139
 140       puts()
 141       puts( "Sequence names files suffix: " + seq_names_files_suffix )
 142       log << "Sequence names files suffix: " + seq_names_files_suffix + ld
 143       puts( "Input dir                  : " + input_dir )
 144       log << "Input dir                  : " + input_dir + ld
 145       puts( "Output dir                 : " + out_dir )
 146       log << "Output dir                 : " + out_dir + ld
 147       puts( "Output dir domains         : " + out_dir_doms )
 148       log << "Output dir domains         : " + out_dir_doms + ld
 149       if ( mapping_file != nil )
 150         puts( "Mapping file               : " + mapping_file )
 151         log << "Mapping file               : " + mapping_file + ld
 152       end
 153       if ( extension > 0 )
 154         puts( "Extension                  : " + extension.to_s )
 155         log << "Extension                  : " + extension.to_s + ld
 156       end
 157       log << "Date                       : " + Time.now.to_s + ld
 158       puts
 159
 160       if ( mapping_file != nil )
 161         species_codes_to_paths = extract_mappings( mapping_file )
 162       end
 163
 164       input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
 165
 166       counter = 0
 167
 168       input_files.each { |input_file|
 169         counter += 1
 170         puts
 171         puts
 172         puts counter.to_s + "/" + input_files.size.to_s
 173         read_seq_family_file( input_file,
 174           seq_names_files_suffix,
 175           input_dir,
 176           species_codes_to_paths,
 177           log,
 178           out_dir,
 179           out_dir_doms,
 180           mapping_file,
 181           extension,
 182           extract_linkers )
 183       }
 184       puts
 185       Util.print_message( PRG_NAME, "OK" )
 186       puts
 187
 188     end
 189
 190
 191     def read_seq_family_file( input_file,
 192         seq_names_files_suffix,
 193         input_dir,
 194         species_codes_to_paths,
 195         log,
 196         out_dir,
 197         out_dir_doms,
 198         mapping_file,
 199         extension,
 200         extract_linkers )
 201
 202       begin
 203         Util.check_file_for_readability( input_file )
 204       rescue ArgumentError => e
 205         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 206       end
 207       basename = File.basename( input_file, seq_names_files_suffix )
 208       out_file_path_fasta_file                = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX
 209       out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX
 210       out_file_path_ids_map                   = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX
 211       doms_out_file_path_fasta_file           = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains" + FASTA_SUFFIX
 212       doms_ext_out_file_path_fasta_file           = nil
 213       if extension > 0
 214         doms_ext_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains_ext_" + extension.to_s + FASTA_SUFFIX
 215       end
 216       begin
 217         Util.check_file_for_writability( out_file_path_fasta_file )
 218         Util.check_file_for_writability( out_file_path_normalized_ids_fasta_file )
 219         Util.check_file_for_writability( out_file_path_ids_map  )
 220         Util.check_file_for_writability( doms_out_file_path_fasta_file  )
 221       rescue ArgumentError => e
 222         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 223       end
 224
 225       ids_map_writer = nil
 226       begin
 227         ids_map_writer = File.open( out_file_path_ids_map, 'a' )
 228       rescue Exception => e
 229         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 230       end
 231
 232       current_species         = ""
 233       current_msa            = nil
 234       new_msa                = Msa.new
 235       new_msa_normalized_ids = Msa.new
 236       new_msa_domains = Msa.new
 237       new_msa_domains_extended = Msa.new
 238       per_species_counter = 0
 239       linkers = ""
 240
 241       puts basename
 242
 243       File.open( input_file ) do | file |
 244         while line = file.gets
 245           line.strip!
 246           if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
 247             values = line.split( PROTEINS_LIST_FILE_SEPARATOR )
 248             mod_line = nil
 249             if ( values.length < 2 )
 250               Util.fatal_error( PRG_NAME, "unexpected format: " + line )
 251             end
 252             species = values[ 0 ]
 253             if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA"  || species == "EIMTE"
 254               next
 255             end
 256             seq_name = values[ 1 ]
 257             domain_ranges = nil
 258             if ( values.length > 3 )
 259               domain_ranges_block = values[ 3 ]
 260               domain_ranges = domain_ranges_block.split( "/" )
 261             end
 262             if ( species != current_species )
 263               current_species = species
 264               my_file = input_dir + Constants::FILE_SEPARATOR + current_species
 265
 266               if ( !File.exist?( my_file ) )
 267                 if species_codes_to_paths == nil
 268                   Util.fatal_error( PRG_NAME, "error: [#{my_file}] not found and no mapping file provided" )
 269                 elsif ( !species_codes_to_paths.has_key?( current_species ) )
 270                   Util.fatal_error( PRG_NAME, "error: species [#{current_species}] not found in mapping file [#{mapping_file}]" )
 271                 end
 272                 my_file = species_codes_to_paths[ current_species ]
 273               end
 274               my_path = File.expand_path( my_file )
 275               my_readlink = my_path
 276               if ( File.symlink?( my_path ) )
 277                 my_readlink = File.readlink( my_path )
 278               end
 279               current_msa = read_fasta_file( my_file )
 280
 281               if ( per_species_counter > 0 )
 282                 print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 283                 per_species_counter = 0
 284               end
 285               puts " " + current_species + " [" + my_readlink + "]"
 286               log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
 287             end
 288             puts "   " + seq_name
 289             log << "   " + seq_name + Constants::LINE_DELIMITER
 290             per_species_counter = per_species_counter + 1
 291             seq = nil
 292
 293             if current_msa.find_by_name_start( seq_name, true ).size > 0
 294               begin
 295                 seq = current_msa.get_by_name_start( seq_name, true ).copy
 296               rescue ArgumentError => e
 297                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 298               end
 299             else
 300               # Not found, try finding by partial match.
 301               begin
 302                 seq = current_msa.get_by_name( seq_name, true, true )
 303               rescue ArgumentError => e
 304                 Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 305               end
 306             end
 307
 308             normalized_id = per_species_counter.to_s( 16 ).upcase +
 309              "_" + current_species
 310
 311             per_species_counter.to_i
 312
 313             ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
 314
 315             orig_name = nil
 316             if seq != nil
 317               orig_name = seq.get_name
 318               seq.set_name( seq.get_name + " [" + current_species + "]" )
 319               new_msa.add_sequence( seq )
 320             else
 321               Util.fatal_error( PRG_NAME, "unexected error: seq is nil" )
 322             end
 323
 324             if domain_ranges != nil
 325               first = true
 326               prev_to = -1
 327
 328               domain_ranges.each { |range|
 329                 if range != nil && range.length > 0
 330                   s = range.split("-")
 331                   from = s[ 0 ].to_i
 332                   to = s[ 1 ].to_i
 333                   new_msa_domains.add_sequence( Sequence.new( orig_name +
 334                        " [" + from.to_s +
 335                        "-" + to.to_s +
 336                        "] [" + basename + "] [" +
 337                        current_species + "]",
 338                       seq.get_sequence_as_string[from..to] ) )
 339                   if extension > 0
 340                     from_e = from - extension
 341                     if from_e < 0
 342                       from_e = 0
 343                     end
 344                     to_e = to + extension
 345                     if to_e > seq.get_sequence_as_string.length - 1
 346                       to_e = seq.get_sequence_as_string.length - 1
 347                     end
 348                     new_msa_domains_extended.add_sequence( Sequence.new( orig_name +
 349                          " [" + from.to_s +
 350                          "-" + to.to_s  +
 351                          "] [extended by " +
 352                          extension.to_s +
 353                          "] [" + basename + "] [" +
 354                          current_species + "]",
 355                         seq.get_sequence_as_string[ from_e..to_e ] ) )
 356                   end # extension > 0
 357                   if  extract_linkers
 358                     if first
 359                       first = false
 360                       f = 0
 361                       t = from - 1
 362                       if extension > 0
 363                         f = t - extension
 364                       end
 365                       mod_line = line + "\t[" + get_linker_sequence( f, t, seq ) + "|"
 366                     else
 367                       mod_line += get_linker_sequence( prev_to + 1, from - 1, seq ) + "|"
 368                     end
 369                     prev_to = to
 370                   end
 371                 end # range != nil && range.length > 0
 372               }
 373               if extract_linkers && prev_to > 0
 374                 f = prev_to + 1
 375                 t = seq.get_sequence_as_string.length - 1
 376                 if extension > 0
 377                   t = f + extension
 378                 end
 379                 mod_line += get_linker_sequence( f, t, seq ) + "]"
 380               end
 381             end
 382
 383             new_msa_normalized_ids.add_sequence( Sequence.new( normalized_id, seq.get_sequence_as_string ) )
 384             if mod_line
 385               linkers << mod_line + Constants::LINE_DELIMITER
 386             end
 387           end # !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
 388         end # while line = file.gets
 389
 390       end
 391
 392       ids_map_writer.close
 393
 394       if ( per_species_counter > 0 )
 395         print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
 396       end
 397
 398       io = MsaIO.new()
 399
 400       fasta_writer = FastaWriter.new()
 401       fasta_writer.remove_gap_chars
 402       fasta_writer.clean
 403
 404       begin
 405         io.write_to_file( new_msa, out_file_path_fasta_file, fasta_writer )
 406       rescue Exception => e
 407         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 408       end
 409
 410       if new_msa_domains != nil
 411         begin
 412           io.write_to_file( new_msa_domains, doms_out_file_path_fasta_file, fasta_writer )
 413         rescue Exception => e
 414           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 415         end
 416       end
 417
 418       if extension > 0 && new_msa_domains_extended != nil
 419         begin
 420           io.write_to_file( new_msa_domains_extended, doms_ext_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       begin
 427         io.write_to_file( new_msa_normalized_ids, out_file_path_normalized_ids_fasta_file, fasta_writer )
 428       rescue Exception => e
 429         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 430       end
 431
 432       begin
 433         f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LOG_SUFFIX , 'a' )
 434         f.print( log )
 435         f.close
 436       rescue Exception => e
 437         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 438       end
 439
 440       if extract_linkers
 441         begin
 442           f = File.open( out_dir + Constants::FILE_SEPARATOR + basename +  LINKERS_SUFFIX , 'a' )
 443           f.print( linkers )
 444           f.close
 445         rescue Exception => e
 446           Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 447         end
 448       end
 449
 450
 451     end
 452
 453
 454     def get_linker_sequence( from, to, seq )
 455       if from < 0
 456         from = 0
 457       end
 458       if to > seq.get_sequence_as_string.length - 1
 459         to = seq.get_sequence_as_string.length - 1
 460       end
 461       if from > to
 462         return ""
 463       else
 464         return from.to_s + "-" + to.to_s + ":" + seq.get_sequence_as_string[ from..to ]
 465       end
 466     end
 467
 468     def obtain_inputfiles( input_dir, seq_names_files_suffix )
 469       input_files = Array.new()
 470       Dir.foreach( input_dir ) { |file_name|
 471         if file_name.index( seq_names_files_suffix ) == ( file_name.size - seq_names_files_suffix.size )
 472           input_files.push( input_dir + Constants::FILE_SEPARATOR + file_name )
 473         end
 474       }
 475       input_files
 476     end
 477
 478     def extract_mappings( mapping_file )
 479       species_code_to_path = Hash.new()
 480       File.open( mapping_file ) do | file |
 481         while line = file.gets
 482           if ( !Util.is_string_empty?( line ) && !(line =~ /\s*#/ ) )
 483             if ( line =~ /(\S+)\s+(\S+)/ )
 484               species = $1
 485               path = $2
 486               if ( species_code_to_path.has_key?( species ) )
 487                 Util.fatal_error( PRG_NAME, "error: species code [#{species}] is not unique" )
 488               end
 489               if ( species_code_to_path.has_value?( path ) )
 490                 Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
 491               end
 492               if ( !File.exist?( path ) )
 493                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
 494               end
 495               if ( !File.file?( path ) )
 496                 Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
 497               end
 498               if ( !File.readable?( path ) )
 499                 Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
 500               end
 501               if ( File.size( path ) < 10000 )
 502                 Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
 503               end
 504               if ( !Util.looks_like_fasta?( path ) )
 505                 Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
 506               end
 507               species_code_to_path[ species ] = path
 508               puts species + " -> " + path
 509             end
 510           end
 511         end
 512       end
 513       species_code_to_path
 514     end
 515
 516     def print_counts( per_species_counter, log, ld )
 517       puts "   [sum: " + per_species_counter.to_s + "]"
 518       log << "   [sum: " + per_species_counter.to_s + "]" + ld
 519     end
 520
 521     def read_fasta_file( input )
 522       f = MsaFactory.new()
 523       msa = nil
 524       begin
 525         msa = f.create_msa_from_file( input, FastaParser.new() )
 526       rescue Exception => e
 527         Util.fatal_error( PRG_NAME, "error: " + e.to_s )
 528       end
 529       msa
 530     end
 531
 532     def print_help()
 533       puts( "Usage:" )
 534       puts()
 535       puts( "  " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
 536          "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
 537          "genome multiple-sequence ('fasta') files not in input dir]" )
 538       puts()
 539       puts( "  option: -" + EXT_OPTION  + "=<int>: to extend extracted domains" )
 540       puts( "          -" + EXTRACT_LINKERS_OPTION  + "      : to extract linkers" )
 541       puts()
 542       puts( "  " + "Example: \"mse.rb .prot . protein_seqs domain_seqs ../genome_locations.txt\"" )
 543       puts()
 544     end
 545
 546   end # class MultiSequenceExtractor
 547 end