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