forester/ruby/evoruby/exe/test.rb

   1 #!/usr/local/bin/ruby -w
   2 #
   3 # = exe/test - Test class
   4 #
   5 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   6 # License::    GNU Lesser General Public License (LGPL)
   7 #
   8 # $Id: test.rb,v 1.18 2010/10/08 22:04:17 cmzmasek Exp $
   9 #
  10 # last modified: 05/15/2007
  11
  12
  13 require 'lib/evo/util/constants'
  14 require 'lib/evo/taxonomy/taxonomy'
  15 require 'lib/evo/sequence/sequence'
  16 require 'lib/evo/msa/msa'
  17 require 'lib/evo/msa/msa_factory'
  18 require 'lib/evo/sequence/domain_structure'
  19 require 'lib/evo/sequence/protein_domain'
  20 require 'lib/evo/table/basic_table'
  21 require 'lib/evo/io/msa_io'
  22 require 'lib/evo/io/writer/phylip_sequential_writer'
  23 require 'lib/evo/io/writer/nexus_writer'
  24 require 'lib/evo/io/writer/fasta_writer'
  25 require 'lib/evo/io/parser/fasta_parser'
  26 require 'lib/evo/io/parser/ncbi_tseq_parser'
  27 require 'lib/evo/io/parser/hmmsearch_domain_extractor'
  28 require 'lib/evo/tool/domain_sequence_extractor'
  29 require 'lib/evo/tool/hmmscan_summary'
  30 require 'lib/evo/tool/domains_to_forester'
  31 require 'lib/evo/io/parser/general_msa_parser'
  32 require 'lib/evo/io/parser/basic_table_parser'
  33 require 'lib/evo/util/command_line_arguments'
  34 require 'lib/evo/soft/fastme'
  35 require 'lib/evo/soft/tree_puzzle'
  36
  37
  38
  39 module Evoruby
  40
  41     class Test
  42
  43         GENERAL_MSA_FILE = "files/test/general_msa_file.txt"
  44         FASTA_FILE       = "files/test/fasta_file.txt"
  45         TSEQ_FILE        = "files/test/ncbi_tseq.xml"
  46
  47         def initialize()
  48             @failures  = 0
  49             @successes = 0
  50         end
  51
  52
  53
  54         def test_taxonomy()
  55             begin
  56                 tax = Taxonomy.new( "pig" )
  57
  58                 if tax.get_name != "pig"
  59                     return false
  60                 end
  61
  62                 tax1 = Taxonomy.new( "dog", "id", "source" )
  63                 tax2 = tax1.copy
  64
  65                 if tax2.get_name != "dog"
  66                     return false
  67                 end
  68                 if tax2.get_id != "id"
  69                     return false
  70                 end
  71                 if tax2.get_id_source != "source"
  72                     return false
  73                 end
  74
  75                 if !( tax1 == tax2 )
  76                     return false
  77                 end
  78
  79                 if !( tax1 == tax1 )
  80                     return false
  81                 end
  82
  83                 tax3 = Taxonomy.new( "dog", "id"  )
  84                 if ( tax1 == tax3 )
  85                     return false
  86                 end
  87
  88                 tax4 = Taxonomy.new( "dog" )
  89                 tax5 = Taxonomy.new( "dog" )
  90                 if !( tax4 == tax5 )
  91                     return false
  92                 end
  93
  94             rescue Exception => e
  95                 puts()
  96                 puts( e.to_s )
  97                 puts()
  98                 return false
  99             end
 100             return true
 101         end
 102
 103
 104         def test_sequence()
 105             begin
 106                 seq = Sequence.new( "seq1", "WLIQ" )
 107                 if ( seq.get_length != 4 )
 108                     return false
 109                 end
 110                 if ( seq.get_residue( 3 ) != "Q" )
 111                     return false
 112                 end
 113                 seq.append!( "E?-*X_Y" )
 114                 if ( seq.get_length != 11 )
 115                     return false
 116                 end
 117                 if ( seq.get_residue( 3 ) != "Q" )
 118                     return false
 119                 end
 120                 if ( seq.get_residue( 4 ) != "E" )
 121                     return false
 122                 end
 123                 seq.append!( "A V_" )
 124                 if ( seq.get_length != 15 )
 125                     return false
 126                 end
 127                 if ( !Test::same?( seq.get_gap_length, 5 ) )
 128                     return false
 129                 end
 130                 if ( !Test::same?( seq.get_gap_ratio, 5.0 / 15.0 ) )
 131                     return false
 132                 end
 133                 seq.delete_residue!( 0 )
 134                 seq.delete_residue!( 2 )
 135                 seq2 = seq.copy()
 136                 seq.delete_residue!( 0 )
 137                 seq.delete_residue!( 0 )
 138                 seq = nil
 139                 if ( seq2.get_length != 13 )
 140                     return false
 141                 end
 142                 if ( seq2.get_sequence_as_string != "LIE?-*X_YA V_" )
 143                     return false
 144                 end
 145                 if ( seq2.get_slice( 2, 2 ) != "E?" )
 146                     return false
 147                 end
 148                 if ( seq2.get_slice( 0, 1 ) != "L" )
 149                     return false
 150                 end
 151                 if ( seq2.get_subsequence( 1, 4 ).get_sequence_as_string != "IE?-" )
 152                     return false
 153                 end
 154                 if ( seq2.get_name() != "seq1" )
 155                     return false
 156                 end
 157                 if ( seq2.get_slice!( 2, 2 ) != "E?" )
 158                     return false
 159                 end
 160                 if ( seq2.get_sequence_as_string != "LI-*X_YA V_" )
 161                     return false
 162                 end
 163                 if ( seq2.get_length != 11 )
 164                     return false
 165                 end
 166                 if ( seq2.get_character_code( 0 ) != 76 )
 167                     return false
 168                 end
 169                 str_0 = " Li-*X_YA V_ 3 3    1212 ?? B1J OU.Z "
 170                 if ( Util.clean_seq_str( str_0 ) != "LI-X-YAV-XXXXXX-X" )
 171                     return false
 172                 end
 173
 174                 tax = Taxonomy.new( "dog", "tax_id", "tax_source" )
 175                 seqn = Sequence.new( "seqn", "VVVVV", "acc", "acc source", tax, "symbol", "2accession", "2source" )
 176                 seqc = seqn.copy
 177                 if ( seqc.get_name() != "seqn" )
 178                     return false
 179                 end
 180                 if ( seqc.get_accession() != "acc" )
 181                     return false
 182                 end
 183                 if ( seqc.get_accession_source() != "acc source" )
 184                     return false
 185                 end
 186                 if ( seqc.get_taxonomy.get_name != "dog" )
 187                     return false
 188                 end
 189                 if ( seqc.get_taxonomy.get_id != "tax_id" )
 190                     return false
 191                 end
 192                 if ( seqc.get_symbol != "symbol" )
 193                     return false
 194                 end
 195                 if ( seqc.get_secondary_accession != "2accession" )
 196                     return false
 197                 end
 198                 if ( seqc.get_secondary_accession_source != "2source" )
 199                     return false
 200                 end
 201
 202             rescue Exception => e
 203                 puts()
 204                 puts( e.to_s )
 205                 puts()
 206                 return false
 207             end
 208             return true
 209         end
 210
 211
 212         def test_msa()
 213             begin
 214                 msa = Msa.new()
 215                 seq0 = Sequence.new( "seq 0", "a-*-_ x-ijklmnopqrstuvwxyz" )
 216                 seq1 = Sequence.new( "seq 1", "ab--_ X-ijklmnopqrstuvwxyz" )
 217                 seq2 = Sequence.new( "seq 2", "abc-_?x-ijklmnopqrstuvwxyz" )
 218                 seq3 = Sequence.new( "seq 3", "abcd_?x-ijklmnopqrstuvwxyz" )
 219                 seq4 = Sequence.new( "seq 4", "abcde?x-ijklmnopqrstuvwxyz" )
 220                 seq5 = Sequence.new( "seq 5", "abcdefx-ijklmnopqrstuvwxyz" )
 221                 msa.add_sequence( seq0 );
 222                 msa.add_sequence( seq1 );
 223                 msa.add_sequence( seq2 );
 224                 msa.add_sequence( seq3 );
 225                 msa.add_sequence( seq4 );
 226                 msa.add_sequence( seq5 );
 227                 msa.add(                      "seq 6", "abcdefg-ijklmnopqrstuvwxyz" );
 228                 if ( msa.get_sequence( 0 ).get_name() != "seq 0" )
 229                     return false
 230                 end
 231                 if ( msa.get_by_name( "Eq 1", false, true ).get_name != "seq 1" )
 232                     return false
 233                 end
 234                 if ( msa.find_by_name( "Eq 2", false, true )[ 0 ] != 2 )
 235                     return false
 236                 end
 237                 if ( !msa.is_aligned )
 238                     return false
 239                 end
 240                 if ( msa.get_number_of_seqs != 7 )
 241                     return false
 242                 end
 243                 if ( msa.get_length != 26 )
 244                     return false
 245                 end
 246                 msa.add( "seq 7", "abcdefgqijklmnopqrstuvwxyz" );
 247                 if ( msa.get_number_of_seqs != 8 )
 248                     return false
 249                 end
 250                 msa.remove_sequence!( 7 )
 251                 if ( msa.get_number_of_seqs != 7 )
 252                     return false
 253                 end
 254                 msa.remove_gap_only_columns!()
 255                 if ( msa.get_length() != 25 )
 256                     return false
 257                 end
 258                 if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
 259                     return false
 260                 end
 261                 msa.remove_gap_columns_w_gap_ratio!( 6.1 / 7.0 )
 262                 if ( msa.get_length() != 25 )
 263                     return false
 264                 end
 265                 msa.remove_gap_columns_w_gap_ratio!( 6.0 / 7.0 )
 266                 if ( msa.get_length() != 25 )
 267                     return false
 268                 end
 269                 if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
 270                     return false
 271                 end
 272                 msa.remove_gap_columns_w_gap_ratio!( 5.0 / 7.0 )
 273                 if ( msa.get_length() != 25 )
 274                     return false
 275                 end
 276                 if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-*-_ xijklmnopqrstuvwxyz" )
 277                     return false
 278                 end
 279                 msa.remove_gap_columns_w_gap_ratio!( 2.0 / 7.0 )
 280                 if ( msa.get_length() != 23 )
 281                     return false
 282                 end
 283                 if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-* xijklmnopqrstuvwxyz" )
 284                     puts msa.get_by_name( "seq 0" ).get_sequence_as_string
 285                     return false
 286                 end
 287                 msa.remove_gap_columns_w_gap_ratio!( 1.0 / 7.0 )
 288                 if ( msa.get_length() != 21 )
 289                     return false
 290                 end
 291                 if ( msa.get_by_name( "seq 0" ).get_sequence_as_string != "a-xijklmnopqrstuvwxyz" )
 292                     return false
 293                 end
 294                 msa2 = Evoruby::Msa.new()
 295                 msa2.add( "seq0", "abcdefgh" );
 296                 msa2.add( "seq1", "a-cdefgh" );
 297                 msa2.add( "seq2", "a--defgh" );
 298                 msa2.add( "seq3", "a---efgh" );
 299                 msa2.add( "seq4", "a----fgh" );
 300                 msa2.add( "seq5", "a" );
 301                 if ( msa2.is_aligned )
 302                     return false
 303                 end
 304                 msa2.remove_sequence!( 5 )
 305                 if ( !msa2.is_aligned )
 306                     return false
 307                 end
 308                 if ( msa2.get_number_of_seqs != 5 )
 309                     return false
 310                 end
 311                 msa2.remove_gap_only_columns!()
 312
 313                 if ( msa2.get_length != 8 )
 314                     return false
 315                 end
 316
 317                 msa2.remove_sequences_by_gap_ratio!( 4.0 / 8.0 )
 318                 if ( msa2.get_number_of_seqs != 5 )
 319                     return false
 320                 end
 321                 msa2.remove_sequences_by_gap_ratio!( 3.0 / 8.0 )
 322                 if ( msa2.get_number_of_seqs != 4 )
 323                     return false
 324                 end
 325                 msa2.remove_sequences_by_gap_ratio!( 1.0 / 8.0 )
 326                 if ( msa2.get_number_of_seqs != 2 )
 327                     return false
 328                 end
 329                 msa2.remove_sequences_by_gap_ratio!( 0.0 )
 330                 if ( msa2.get_number_of_seqs != 1 )
 331                     return false
 332                 end
 333                 msa2.add( "seq1", "a-cdefgh" );
 334                 msa2.add( "seq2", "a--defgh" );
 335                 msa2.add( "seq3", "a---efgh" );
 336                 msa2.add( "seq4", "a----fgh" );
 337
 338                 msa2.remove_sequences_by_non_gap_length!( 4 )
 339                 if ( msa2.get_number_of_seqs != 5 )
 340                     return false
 341                 end
 342                 msa2.remove_sequences_by_non_gap_length!( 5 )
 343                 if ( msa2.get_number_of_seqs != 4 )
 344                     return false
 345                 end
 346                 msa2.remove_sequences_by_non_gap_length!( 8 )
 347                 if ( msa2.get_number_of_seqs != 1 )
 348                     return false
 349                 end
 350                 msa2.add( "seq1", "a-cdefgh" );
 351                 msa2.add( "seq2", "a--defgh" );
 352                 msa2.add( "seq3", "a---efgh" );
 353                 msa2.add( "seq4", "a----fgh" );
 354                 msa2.trim!( 0, 7 )
 355                 if ( msa2.get_by_name( "seq0" ).get_sequence_as_string != "abcdefgh" )
 356                     return false
 357                 end
 358                 msa2.trim!( 3, 4 )
 359                 if ( msa2.get_by_name( "seq0" ).get_sequence_as_string != "de" )
 360                     return false
 361                 end
 362                 msa3 = Evoruby::Msa.new()
 363                 msa3.add( "seq0", "abcdefgh-abcdef--*" );
 364                 msa3.add( "seq1", "b-deefgh-a____f--*" );
 365                 msa3.add( "seq2", "A________abcdef--*" );
 366                 msa3.add( "seq3", "A   Efgh---------*" );
 367                 msa3.add( "seq4", "    eFhh---------*" );
 368                 msa3.add( "seq5", "----------------ee" );
 369                 if ( !Test::same?( msa3.calculate_overlap( 0, 0 ), 14 ) )
 370                     return false
 371                 end
 372                 if ( !Test::same?( msa3.calculate_overlap( 0, 1 ), 9 ) )
 373                     return false
 374                 end
 375                 if ( !Test::same?( msa3.calculate_overlap( 0, 5 ), 0 ) )
 376                     return false
 377                 end
 378                 if ( !Test::same?( msa3.calculate_overlap( 4, 5 ), 0 ) )
 379                     return false
 380                 end
 381                 if ( !msa3.overlap?( 2, 3 ) )
 382                     return false
 383                 end
 384                 if ( msa3.overlap?( 2, 3, 2 ) )
 385                     return false
 386                 end
 387                 if ( msa3.overlap?( 4, 5 ) )
 388                     return false
 389                 end
 390                 if ( !Test::same?( msa3.calculate_identities( 4, 5 ), 0 ) )
 391                     return false
 392                 end
 393                 if ( !Test::same?( msa3.calculate_identities( 3, 4 ), 3 ) )
 394                     return false
 395                 end
 396                 if ( msa3.split_into_overlapping_msa.length != 3 )
 397                     return false
 398                 end
 399                 if ( msa3.split_into_overlapping_msa( 5 ).length != 4 )
 400                     return false
 401                 end
 402
 403
 404                 msa4 = Msa.new()
 405                 seq0 = Sequence.new( "seq 0", "ABCDED" )
 406                 seq1 = Sequence.new( "seq 1", "ABCDEE" )
 407                 seq2 = Sequence.new( "seq 2", "abcded" )
 408                 seq3 = Sequence.new( "seq 3", " ABCDEE" )
 409                 seq4 = Sequence.new( "seq 4", "ABCDEV" )
 410                 seq5 = Sequence.new( "seq 5", "ABCDED" )
 411                 seq6 = Sequence.new( "seq 6", "AB.DEI" )
 412                 seq7 = Sequence.new( "seq 7", "aB-DEi*" )
 413                 seq8 = Sequence.new( "seq 8", "ABCDED" )
 414                 seq9 = Sequence.new( "seq 9", "ABCDED" )
 415                 seq10 = Sequence.new( "seq 10", "ABCDED" )
 416                 seq11 = Sequence.new( "seq 11", "ABCDED" )
 417                 msa4.add_sequence( seq0 );
 418                 msa4.add_sequence( seq1 );
 419                 msa4.add_sequence( seq2 );
 420                 msa4.add_sequence( seq3 );
 421                 msa4.add_sequence( seq4 );
 422                 msa4.add_sequence( seq5 );
 423                 msa4.add_sequence( seq6 );
 424                 msa4.add_sequence( seq7 );
 425                 msa4.add_sequence( seq8 );
 426                 msa4.add_sequence( seq9 );
 427                 msa4.add_sequence( seq10 );
 428                 msa4.add_sequence( seq11 );
 429
 430                 msa4.remove_redundant_sequences!
 431
 432                 puts msa4.to_str
 433
 434                 if msa4.get_number_of_seqs != 4
 435                     return false
 436                 end
 437
 438                 if msa4.get_sequence( 0 ).get_name != "seq 0"
 439                     return false
 440                 end
 441                 if msa4.get_sequence( 1 ).get_name != "seq 1"
 442                     return false
 443                 end
 444                 if msa4.get_sequence( 2 ).get_name != "seq 4"
 445                     return false
 446                 end
 447                 if msa4.get_sequence( 3 ).get_name != "seq 6"
 448                     return false
 449                 end
 450
 451             rescue Exception => e
 452                 puts()
 453                 puts( e.to_s )
 454                 puts()
 455                 return false
 456             end
 457             return true
 458         end
 459
 460         def test_msa_factory()
 461             begin
 462                 f = MsaFactory.new()
 463             rescue Exception => e
 464                 puts()
 465                 puts( e.to_s )
 466                 puts()
 467                 return false
 468             end
 469             return true
 470         end
 471
 472         def test_domain_structure()
 473             begin
 474                 ds = DomainStructure.new( 190 )
 475             rescue Exception => e
 476                 puts()
 477                 puts( e.to_s )
 478                 puts()
 479                 return false
 480             end
 481             return true
 482         end
 483
 484         def test_protein_domain()
 485             begin
 486                 ds = ProteinDomain.new( "domain", 23, 466, "d1", 0.4 )
 487             rescue Exception => e
 488                 puts()
 489                 puts( e.to_s )
 490                 puts()
 491                 return false
 492             end
 493             return true
 494         end
 495
 496         def test_basic_table()
 497             begin
 498                 t = BasicTable.new()
 499                 t.set_value( 233, 923, "snake" )
 500                 t.set_value( 233, 923, "lizard" )
 501                 if ( t.get_value_as_string( 233, 923 ) != "lizard" )
 502                     return false
 503                 end
 504                 if ( t.get_value_as_string( 33, 23 ) != "" )
 505                     return false
 506                 end
 507             rescue Exception => e
 508                 puts()
 509                 puts( e.to_s )
 510                 puts()
 511                 return false
 512             end
 513             return true
 514         end
 515
 516         def test_msa_io()
 517             begin
 518                 msaio = MsaIO.new()
 519             rescue Exception => e
 520                 puts()
 521                 puts( e.to_s )
 522                 puts()
 523                 return false
 524             end
 525             return true
 526         end
 527
 528         def test_phylip_sequentialwriter()
 529             begin
 530                 p = PhylipSequentialWriter.new()
 531             rescue Exception => e
 532                 puts()
 533                 puts( e.to_s )
 534                 puts()
 535                 return false
 536             end
 537             return true
 538         end
 539
 540         def test_nexus_writer()
 541             begin
 542                 n = NexusWriter.new()
 543             rescue Exception => e
 544                 puts()
 545                 puts( e.to_s )
 546                 puts()
 547                 return false
 548             end
 549             return true
 550         end
 551
 552         def test_fasta_writer()
 553             begin
 554                 f = FastaWriter.new()
 555             rescue Exception => e
 556                 puts()
 557                 puts( e.to_s )
 558                 puts()
 559                 return false
 560             end
 561             return true
 562         end
 563
 564         def test_general_msa_parser( path_to_evoruby )
 565             begin
 566                 g = GeneralMsaParser.new()
 567                 f = MsaFactory.new()
 568                 sep = ""
 569                 if ( !Util::is_string_empty?( path_to_evoruby ) )
 570                     sep = Constants::FILE_SEPARATOR
 571                 end
 572                 msa = f.create_msa_from_file( path_to_evoruby +
 573                      sep +
 574                      GENERAL_MSA_FILE, g )
 575
 576                 if ( msa.get_length() != 29 )
 577                     return false
 578                 end
 579                 if ( msa.get_number_of_seqs() != 7 )
 580                     return false
 581                 end
 582
 583                 seq0 = msa.get_sequence( 0 )
 584                 seq1 = msa.get_sequence( 1 )
 585                 seq2 = msa.get_sequence( 2 )
 586                 seq3 = msa.get_sequence( 3 )
 587                 seq4 = msa.get_sequence( 4 )
 588                 seq5 = msa.get_sequence( 5 )
 589                 seq6 = msa.get_sequence( 6 )
 590
 591                 if ( seq0.get_name() != "sequence0" )
 592                     return false
 593                 end
 594                 if ( seq0.get_sequence_as_string() != "ABCDE.GHIJKLMNOPQR.TUVWabcxy0" )
 595                     return false
 596                 end
 597
 598                 if ( seq1.get_name() != "sequence1" )
 599                     return false
 600                 end
 601                 if ( seq1.get_sequence_as_string() != "abcdefghijklmnopqrstuvwabcxy1" )
 602                     return false
 603                 end
 604
 605                 if ( seq2.get_name() != "sequence2" )
 606                     return false
 607                 end
 608                 if ( seq2.get_sequence_as_string() != "abcdefghijkl---x_-*?_XXabcxy2" )
 609                     return false
 610                 end
 611
 612                 if ( seq3.get_name() != "sequence3" )
 613                     return false
 614                 end
 615                 if ( seq3.get_sequence_as_string() != "12345678901234567890123abcxy3" )
 616                     return false
 617                 end
 618
 619                 if ( seq4.get_name() != "sequence4" )
 620                     return false
 621                 end
 622                 if ( seq4.get_sequence_as_string() != "--------------------------xy4" )
 623                     return false
 624                 end
 625
 626                 if ( seq5.get_name() != "sequence5" )
 627                     return false
 628                 end
 629                 if ( seq5.get_sequence_as_string() != "a*c*ef****************wabcxy5" )
 630                     return false
 631                 end
 632
 633                 if ( seq6.get_name() != "sequence6" )
 634                     return false
 635                 end
 636                 if ( seq6.get_sequence_as_string() != "ururufhfghfgftgfhftgfttabcxy6" )
 637                     return false
 638                 end
 639
 640             rescue Exception => e
 641                 puts()
 642                 puts( e.to_s )
 643                 puts()
 644                 return false
 645             end
 646             return true
 647         end
 648
 649         def test_fasta_parser( path_to_evoruby )
 650             begin
 651                 fasta = FastaParser.new()
 652                 f = MsaFactory.new()
 653                 sep = ""
 654                 if ( !Util::is_string_empty?( path_to_evoruby ) )
 655                     sep = Constants::FILE_SEPARATOR
 656                 end
 657                 msa = f.create_msa_from_file( path_to_evoruby +
 658                      sep +
 659                      FASTA_FILE, fasta )
 660
 661                 if ( msa.get_length() != 6 )
 662                     return false
 663                 end
 664                 if ( msa.get_number_of_seqs() != 4 )
 665                     return false
 666                 end
 667
 668                 seq0 = msa.get_sequence( 0 )
 669                 seq1 = msa.get_sequence( 1 )
 670                 seq2 = msa.get_sequence( 2 )
 671                 seq3 = msa.get_sequence( 3 )
 672
 673                 if ( seq0.get_name() != "sequence 0" )
 674                     return false
 675                 end
 676                 if ( seq0.get_sequence_as_string() != "ABCDEF" )
 677                     return false
 678                 end
 679
 680                 if ( seq1.get_name() != "sequence 1" )
 681                     return false
 682                 end
 683                 if ( seq1.get_sequence_as_string() != "abcdef" )
 684                     return false
 685                 end
 686
 687                 if ( seq2.get_name() != "sequence 2" )
 688                     return false
 689                 end
 690                 if ( seq2.get_sequence_as_string() != "123456" )
 691                     return false
 692                 end
 693                 if ( seq3.get_name() != "sequence 3" )
 694                     return false
 695                 end
 696                 if ( seq3.get_sequence_as_string() != "a-c--f" )
 697                     return false
 698                 end
 699
 700             rescue Exception => e
 701                 puts()
 702                 puts( e.to_s )
 703                 puts()
 704                 return false
 705             end
 706             return true
 707         end
 708
 709         def test_ncbi_tseq_parser( path_to_evoruby )
 710             begin
 711                 parser = NcbiTSeqParser.new
 712                 f = MsaFactory.new
 713                 sep = ""
 714                 if ( !Util::is_string_empty?( path_to_evoruby ) )
 715                     sep = Constants::FILE_SEPARATOR
 716                 end
 717                 msa = f.create_msa_from_file( path_to_evoruby +
 718                      sep +
 719                      TSEQ_FILE, parser )
 720
 721                 if ( msa.get_number_of_seqs() != 9 )
 722                     return false
 723                 end
 724
 725                 seq0 = msa.get_sequence( 0 )
 726                 seq1 = msa.get_sequence( 1 )
 727                 seq8 = msa.get_sequence( 8 )
 728
 729                 if ( seq0.get_name() != "SusD [Bacteroides thetaiotaomicron VPI-5482]" )
 730                     return false
 731                 end
 732                 if ( seq0.get_sequence_as_string() != "MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK" )
 733                     return false
 734                 end
 735                 if ( seq0.get_accession != "29341016" )
 736                     return false
 737                 end
 738                 if ( seq0.get_accession_source != "gi" )
 739                     return false
 740                 end
 741                 if ( seq0.get_taxonomy.get_name != "Bacteroides thetaiotaomicron VPI-5482" )
 742                     return false
 743                 end
 744                 if ( seq0.get_taxonomy.get_id != "226186" )
 745                     return false
 746                 end
 747                 if ( seq0.get_taxonomy.get_id_source != "ncbi" )
 748                     return false
 749                 end
 750
 751
 752                 if ( seq1.get_name() != "SusD, outer membrane protein [Bacteroides thetaiotaomicron VPI-5482]" )
 753                     return false
 754                 end
 755                 if ( seq1.get_accession != "29349109" )
 756                     return false
 757                 end
 758                 if ( seq1.get_accession_source != "gi" )
 759                     return false
 760                 end
 761                 if ( seq1.get_taxonomy.get_name != "Bacteroides thetaiotaomicron VPI-5482" )
 762                     return false
 763                 end
 764                 if ( seq1.get_taxonomy.get_id != "226186" )
 765                     return false
 766                 end
 767                 if ( seq1.get_taxonomy.get_id_source != "ncbi" )
 768                     return false
 769                 end
 770
 771
 772                 if ( seq8.get_name() != "Chain A, B. Thetaiotaomicron Susd With Maltotriose" )
 773                     return false
 774                 end
 775                 if ( seq8.get_accession != "pdb|3CKB|A" )
 776                     return false
 777                 end
 778                 if ( seq8.get_accession_source != "ncbi" )
 779                     return false
 780                 end
 781                 if ( seq8.get_taxonomy.get_name != "Bacteroides thetaiotaomicron" )
 782                     return false
 783                 end
 784                 if ( seq8.get_taxonomy.get_id != "818" )
 785                     return false
 786                 end
 787                 if ( seq8.get_taxonomy.get_id_source != "ncbi" )
 788                     return false
 789                 end
 790
 791             rescue Exception => e
 792                 puts()
 793                 puts( e.to_s )
 794                 puts()
 795                 return false
 796             end
 797             return true
 798         end
 799
 800         def test_hmmsearch_domain_extractor()
 801             begin
 802                 h = Evoruby::HmmsearchDomainExtractor.new()
 803             rescue Exception => e
 804                 puts()
 805                 puts( e.to_s )
 806                 puts()
 807                 return false
 808             end
 809             return true
 810         end
 811
 812         def test_domain_sequence_extractor()
 813             begin
 814                 h = Evoruby::DomainSequenceExtractor.new()
 815             rescue Exception => e
 816                 puts()
 817                 puts( e.to_s )
 818                 puts()
 819                 return false
 820             end
 821             return true
 822         end
 823
 824         def test_hmmscan_parser()
 825             begin
 826                 h = Evoruby::HmmscanSummary.new()
 827             rescue Exception => e
 828                 puts()
 829                 puts( e.to_s )
 830                 puts()
 831                 return false
 832             end
 833             return true
 834         end
 835
 836         def test_domains_to_forester()
 837             begin
 838                 d = Evoruby::DomainsToForester.new()
 839             rescue Exception => e
 840                 puts()
 841                 puts( e.to_s )
 842                 puts()
 843                 return false
 844             end
 845             return true
 846         end
 847
 848
 849         def test_basic_table_parser()
 850             begin
 851                 b = Evoruby::BasicTableParser.new()
 852             rescue Exception => e
 853                 puts()
 854                 puts( e.to_s )
 855                 puts()
 856                 return false
 857             end
 858             return true
 859         end
 860
 861
 862         def test_cla()
 863             begin
 864                 cla = CommandLineArguments.new( Array.new )
 865             rescue Exception => e
 866                 puts()
 867                 puts( e.to_s )
 868                 puts()
 869                 return false
 870             end
 871             return true
 872         end
 873
 874         def test_tree_puzzle()
 875             begin
 876                 tp = TreePuzzle.new()
 877                 tp.run( '/home/czmasek/scratch/small.aln',
 878                     :wag,
 879                     :uniform,
 880                     200 )
 881             rescue Exception => e
 882                 puts()
 883                 puts( e.to_s )
 884                 puts()
 885                 return false
 886             end
 887             return true
 888         end
 889
 890         def test_fastme()
 891             begin
 892                 fastme = FastMe.new()
 893                 fastme.run( '/home/czmasek/scratch/outdist', 0, :GME )
 894             rescue Exception => e
 895                 puts()
 896                 puts( e.to_s )
 897                 puts()
 898                 return false
 899             end
 900             return true
 901         end
 902
 903
 904         def run()
 905
 906             t0 = Time.now
 907
 908             puts
 909             puts "ruby version " + RUBY_VERSION
 910             puts Constants::EVORUBY + " version " + Constants::EVORUBY_VERSION
 911             puts
 912
 913             path_to_evoruby = Test.get_path_to_evoruby()
 914
 915             if ( Util.is_string_empty?( path_to_evoruby ) )
 916                 path_to_evoruby = ""
 917                 puts()
 918                 puts( "Warning! Path to evoruby could not be established. Some tests will might fail." )
 919                 puts()
 920             end
 921
 922             print( "--- Taxonomy: " )
 923             if ( test_taxonomy() )
 924                 puts( "ok" )
 925                 @successes += 1
 926             else
 927                 puts( "FAILED" )
 928                 @failures += 1
 929             end
 930
 931             print( "--- Sequence: " )
 932             if ( test_sequence() )
 933                 puts( "ok" )
 934                 @successes += 1
 935             else
 936                 puts( "FAILED" )
 937                 @failures += 1
 938             end
 939
 940             print( "--- Msa: " )
 941             if ( test_msa() )
 942                 puts( "ok" )
 943                 @successes += 1
 944             else
 945                 puts( "FAILED" )
 946                 @failures += 1
 947             end
 948
 949             print( "--- MsaFactory: " )
 950             if ( test_msa_factory() )
 951                 puts( "ok" )
 952                 @successes += 1
 953             else
 954                 puts( "FAILED" )
 955                 @failures += 1
 956             end
 957
 958             print( "--- DomainStructure: " )
 959             if ( test_domain_structure() )
 960                 puts( "ok" )
 961                 @successes += 1
 962             else
 963                 puts( "FAILED" )
 964                 @failures += 1
 965             end
 966
 967             print( "--- ProteinDomain: " )
 968             if ( test_protein_domain() )
 969                 puts( "ok" )
 970                 @successes += 1
 971             else
 972                 puts( "FAILED" )
 973                 @failures += 1
 974             end
 975
 976             print( "--- BasicTable: " )
 977             if ( test_basic_table() )
 978                 puts( "ok" )
 979                 @successes += 1
 980             else
 981                 puts( "FAILED" )
 982                 @failures += 1
 983             end
 984
 985             print( "--- MsaIO: " )
 986             if ( test_msa_io )
 987                 puts( "ok" )
 988                 @successes += 1
 989             else
 990                 puts( "FAILED" )
 991                 @failures += 1
 992             end
 993
 994             print( "--- PhylipSequentialWriter: " )
 995             if ( test_phylip_sequentialwriter )
 996                 puts( "ok" )
 997                 @successes += 1
 998             else
 999                 puts( "FAILED" )
1000                 @failures += 1
1001             end
1002
1003             print( "--- FastaWriter : " )
1004             if ( test_fasta_writer )
1005                 puts( "ok" )
1006                 @successes += 1
1007             else
1008                 puts( "FAILED" )
1009                 @failures += 1
1010             end
1011
1012             print( "--- NexusWriter: " )
1013             if ( test_nexus_writer )
1014                 puts( "ok" )
1015                 @successes += 1
1016             else
1017                 puts( "FAILED" )
1018                 @failures += 1
1019             end
1020
1021             print( "--- FastaParser: " )
1022             if ( test_fasta_parser( path_to_evoruby ) )
1023                 puts( "ok" )
1024                 @successes += 1
1025             else
1026                 puts( "FAILED" )
1027                 @failures += 1
1028             end
1029
1030             print( "--- NCBI Tseq parser: " )
1031             if (  test_ncbi_tseq_parser( path_to_evoruby ) )
1032                 puts( "ok" )
1033                 @successes += 1
1034             else
1035                 puts( "FAILED" )
1036                 @failures += 1
1037             end
1038
1039             print( "--- GeneralMsaParser: " )
1040             if ( test_general_msa_parser( path_to_evoruby ) )
1041                 puts( "ok" )
1042                 @successes += 1
1043             else
1044                 puts( "FAILED" )
1045                 @failures += 1
1046             end
1047
1048
1049             print( "--- Hmmsearch domain extractor: " )
1050             if ( test_hmmsearch_domain_extractor )
1051                 puts( "ok" )
1052                 @successes += 1
1053             else
1054                 puts( "FAILED" )
1055                 @failures += 1
1056             end
1057
1058             print( "--- Domain sequence extractor: " )
1059             if ( test_domain_sequence_extractor )
1060                 puts( "ok" )
1061                 @successes += 1
1062             else
1063                 puts( "FAILED" )
1064                 @failures += 1
1065             end
1066
1067             print( "--- Hmmscan parser: " )
1068             if ( test_hmmscan_parser )
1069                 puts( "ok" )
1070                 @successes += 1
1071             else
1072                 puts( "FAILED" )
1073                 @failures += 1
1074             end
1075
1076
1077             print( "--- Domains 2 forester: " )
1078             if ( test_domains_to_forester )
1079                 puts( "ok" )
1080                 @successes += 1
1081             else
1082                 puts( "FAILED" )
1083                 @failures += 1
1084             end
1085
1086             print( "--- BasicTableParser: " )
1087             if ( test_basic_table_parser )
1088                 puts( "ok" )
1089                 @successes += 1
1090             else
1091                 puts( "FAILED" )
1092                 @failures += 1
1093             end
1094
1095             print( "--- TreePuzzle (wrapper): " )
1096             if ( test_tree_puzzle() )
1097                 puts( "ok" )
1098                 @successes += 1
1099             else
1100                 puts( "FAILED" )
1101                 @failures += 1
1102             end
1103
1104             print( "--- FastMe (wrapper): " )
1105             if ( test_fastme() )
1106                 puts( "ok" )
1107                 @successes += 1
1108             else
1109                 puts( "FAILED" )
1110                 @failures += 1
1111             end
1112
1113
1114
1115             print( "--- CLA: " )
1116             if ( test_cla() )
1117                 puts( "ok" )
1118                 @successes += 1
1119             else
1120                 puts( "FAILED" )
1121                 @failures += 1
1122             end
1123             puts
1124             puts "ruby version " + RUBY_VERSION
1125             puts Constants::EVORUBY + " version " + Constants::EVORUBY_VERSION
1126             puts
1127
1128             td = Time.at( Time.now - t0 )
1129             puts( "Time            : #{ td.sec }.#{ td.usec }s" )
1130             puts()
1131
1132             puts( "Successful tests: " + @successes.to_s )
1133             puts( "Failed tests    : " + @failures.to_s )
1134             puts()
1135             if ( @failures < 1 )
1136                 puts( "OK" )
1137             else
1138                 puts( "NOT ok" )
1139             end
1140
1141             puts()
1142         end
1143
1144         private
1145
1146         def Test.same?( n, m )
1147             return ( ( n - m ).abs < 0.000001 )
1148         end
1149
1150         def Test.get_path_to_evoruby()
1151             rubylib = ENV['RUBYLIB'].split(':')
1152             evoruby_path = nil
1153             rubylib.each do | path |
1154                 if ( path =~ /evoruby/ )
1155                     evoruby_path = path
1156                     break
1157                 end
1158             end
1159             evoruby_path
1160         end
1161
1162     end # class Test
1163
1164
1165     test = Test.new()
1166
1167     test.run()
1168
1169
1170 end # module Evoruby
1171