alg/test/test_sequence.cpp

   1 #include <boost/test/auto_unit_test.hpp>
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 namespace fs=boost::filesystem;
   5
   6 #include <list>
   7 #include <iostream>
   8 #include <sstream>
   9
  10 #include <boost/archive/text_oarchive.hpp>
  11 #include <boost/archive/text_iarchive.hpp>
  12 #include <boost/archive/xml_oarchive.hpp>
  13 #include <boost/archive/xml_iarchive.hpp>
  14
  15 #include "alg/sequence.hpp"
  16 #include "mussa_exceptions.hpp"
  17
  18 using namespace std;
  19
  20 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  21 {
  22         Sequence s;
  23         // make sure that retrieving the sequence doesn't throw an error
  24         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  25 }
  26
  27 //! when we try to load a missing file, do we get an error?
  28 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  29 {
  30   Sequence s;
  31   // there should be errors when we try to load something that doesn't exist
  32   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  33   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  34 }
  35
  36 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  37 {
  38   string header(">Header");
  39   string line1("AAAAGGGGCCCCTTTTT");
  40   string line2("AAAAGGGGCCCCTTTTT");
  41   int seq_len = line1.size() + line2.size();
  42
  43   stringstream cr;
  44   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  45   Sequence seq_cr;
  46   seq_cr.load_fasta(cr);
  47
  48   stringstream crlf;
  49   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  50   Sequence seq_crlf;
  51   seq_crlf.load_fasta(crlf);
  52
  53   stringstream lf;
  54   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  55   Sequence seq_lf;
  56   seq_lf.load_fasta(lf);
  57
  58   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  59   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  60   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  61 }
  62
  63
  64 //! Do simple operations work correctly?
  65 BOOST_AUTO_TEST_CASE( sequence_filter )
  66 {
  67   const char *core_seq = "AATTGGCC";
  68   Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
  69   BOOST_CHECK_EQUAL(s1, core_seq);
  70
  71   Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
  72   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
  73   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
  74   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
  75   BOOST_CHECK_EQUAL(s2.size(), s2.size());
  76   BOOST_CHECK_EQUAL(s2.get_sequence(), "aattggcc");
  77
  78   Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
  79   BOOST_CHECK_EQUAL(s3, "ANNNG");
  80   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
  81
  82   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
  83   BOOST_CHECK_EQUAL(s3, "AA");
  84   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
  85   BOOST_CHECK_EQUAL( s3, "GG");
  86   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
  87   BOOST_CHECK_EQUAL( s3, "CCTT");
  88
  89   s3 = "AAGGFF";
  90   BOOST_CHECK_EQUAL(s3, "AAGGNN");
  91 }
  92
  93 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
  94 {
  95   std::string agct("AGCT");
  96   Sequence seq(agct, Sequence::nucleic_alphabet);
  97   BOOST_CHECK_EQUAL(seq.size(), agct.size());
  98   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
  99
 100   std::string bdv("BDv");
 101   Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
 102   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 103   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), bdv);
 104
 105 }
 106
 107 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 108 {
 109   std::string agct("AGCT");
 110   Sequence seq(agct);
 111   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 112   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 113   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 114   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 115   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 116   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 117
 118   std::string bdv("BDv");
 119   Sequence seq_bdv(bdv);
 120   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 121   // default alphabet only allows AGCTUN
 122   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 123 }
 124
 125 BOOST_AUTO_TEST_CASE( subseq_names )
 126 {
 127   Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
 128   s1.set_species("species");
 129   s1.set_fasta_header("a fasta header");
 130   Sequence s2 = s1.subseq(2,2);
 131   BOOST_CHECK_EQUAL(s2, "GG");
 132   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 133   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 134 }
 135
 136 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 137 {
 138   Sequence s1;
 139   BOOST_CHECK_EQUAL( s1.start(), 0 );
 140   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 141
 142   std::string seq_string("AAGGCCTT");
 143   Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
 144   BOOST_CHECK_EQUAL( s2.start(), 0 );
 145   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 146
 147   std::string s3seq_string = seq_string.substr(2,3);
 148   Sequence s3 = s2.subseq(2,3);
 149   BOOST_CHECK_EQUAL( s3.start(), 2);
 150   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 151   BOOST_CHECK_EQUAL( s3.size(), 3);
 152   BOOST_CHECK_EQUAL( s3, s3seq_string);
 153
 154   std::string s4seq_string = s3seq_string.substr(1,1);
 155   Sequence s4 = s3.subseq(1,1);
 156   BOOST_CHECK_EQUAL( s4.start(), 1 );
 157   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 158   BOOST_CHECK_EQUAL( s4.size(), 1);
 159   BOOST_CHECK_EQUAL( s4, s4seq_string);
 160 }
 161
 162 //! Can we load data from a file
 163 BOOST_AUTO_TEST_CASE( sequence_load )
 164 {
 165   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 166   seq_path /=  "human_mck_pro.fa";
 167   Sequence s;
 168   s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
 169   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 170   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 171   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 172                                     "muscle creatine kinase gene (CKMM), "
 173                                     "5' flank");
 174 }
 175
 176 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 177 {
 178   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 179   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 180   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 181   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 182   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 183   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 184   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 185   std::stringstream garbage_fasta(garbage_string);
 186
 187   Sequence s;
 188   s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
 189   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 190                                  Sequence::reduced_dna_alphabet),
 191                     sequence_invalid_load_error);
 192   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 193                                  Sequence::reduced_dna_alphabet),
 194                     sequence_invalid_load_error);
 195   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 196                                  Sequence::reduced_dna_alphabet),
 197                     sequence_invalid_load_error);
 198
 199 }
 200
 201 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 202 {
 203   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 204   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 205   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 206   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 207   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 208   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 209   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 210   std::stringstream garbage_fasta(garbage_string);
 211
 212   Sequence s;
 213   s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
 214   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 215                                  Sequence::reduced_rna_alphabet),
 216                     sequence_invalid_load_error);
 217   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 218                                  Sequence::reduced_rna_alphabet),
 219                     sequence_invalid_load_error);
 220   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 221                                  Sequence::reduced_rna_alphabet),
 222                     sequence_invalid_load_error);
 223 }
 224
 225 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 226 {
 227   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 228   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 229   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 230   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 231   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 232   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 233   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 234   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 235   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 236   std::stringstream garbage_fasta(garbage_string);
 237
 238   Sequence s;
 239   Sequence specific;
 240   // there's two copies of reduced_rna_fasta because i didn't feel like
 241   // figuring out how to properly reset the read pointer in a stringstream
 242   s.load_fasta(reduced_rna_fasta1);
 243   specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
 244   BOOST_CHECK_EQUAL(s, specific);
 245
 246   s.load_fasta(reduced_dna_fasta1);
 247   specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
 248   BOOST_CHECK_EQUAL(s, specific);
 249
 250   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 251                     sequence_invalid_load_error);
 252   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 253                     sequence_invalid_load_error);
 254 }
 255
 256 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 257 {
 258   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 259   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 260   Sequence seqr = seq.rev_comp();
 261
 262   BOOST_CHECK( seq != seqr );
 263   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 264   BOOST_CHECK_EQUAL( seq.get_sequence(), iupac_symbols );
 265 }
 266
 267 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 268 {
 269   std::string dna_str("AGCTN");
 270   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 271   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 272   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 273 }
 274
 275 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 276 {
 277   std::string rna_str("AGCUN");
 278   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 279   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 280   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 281 }
 282
 283 BOOST_AUTO_TEST_CASE( annotation_load )
 284 {
 285   string annot_data = "human\n"
 286                       "0 10 name   type\n"
 287                       "10 20 myf7\n"
 288                       "20 30 myod\n"
 289                       "50\t55 anothername\n"
 290                       "60 50 backward\n"
 291                       ">ident3 asdf\n"
 292                       "GCT\n"
 293                       "gCTn\n"
 294                       "75\t90\tname2\ttype2\n"
 295                       "100 120 name-asdf type!@#$%\n"
 296                       ;
 297   string s(100, 'A');
 298   s += "GCTGCTAATT";
 299   Sequence seq(s, Sequence::reduced_dna_alphabet);
 300
 301   //istringstream annot_stream(annot_data);
 302   seq.parse_annot(annot_data, 0, 0);
 303   std::list<annot> annots_list = seq.annotations();
 304   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 305   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 306   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 307   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 308   BOOST_CHECK_EQUAL( annots[0].type, "type");
 309   BOOST_CHECK_EQUAL( annots[0].name, "name");
 310   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 311   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 312   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 313   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 314   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 315   BOOST_CHECK_EQUAL( annots[5].end, 90);
 316   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 317   BOOST_CHECK_EQUAL( annots[6].end, 120);
 318   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 319   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 320   // sequence defined annotations will always be after the
 321   // absolute positions
 322   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 323   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 324
 325   //BOOST_CHECK_EQUAL( annots
 326 }
 327
 328
 329 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 330 {
 331   // this actually is basically what's returned by UCSC
 332   // (well actually with some of the sequence and copies of fasta blocks
 333   // removed to make the example shorter
 334   string annot_data = "\n"
 335     "<PRE>\n"
 336     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 337     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 338     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 339     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 340     "</PRE>\n"
 341     "\n"
 342     "</BODY>\n"
 343     "</HTML>\n"
 344     ;
 345
 346   string s =
 347     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 348     "AAAAA"
 349     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 350   Sequence seq(s, Sequence::reduced_dna_alphabet);
 351   seq.parse_annot(annot_data);
 352   std::list<annot> annots = seq.annotations();
 353   BOOST_CHECK_EQUAL( annots.size(), 2);
 354 }
 355
 356 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 357 {
 358   string annot_data = "0 10 name   type\n"
 359                       "10 20 myf7\n"
 360                       "20 30 myod\n"
 361                       "50\t55 anothername\n"
 362                       "60 50 backward\n"
 363                       ">ident3 asdf\n"
 364                       "GCT\n"
 365                       "gCTn\n"
 366                       "75\t90\tname2\ttype2\n"
 367                       "100 120 name-asdf type!@#$%\n"
 368                       ;
 369   string s(100, 'A');
 370   s += "GCTGCTAATT";
 371   Sequence seq(s, Sequence::reduced_dna_alphabet);
 372
 373   //istringstream annot_stream(annot_data);
 374   seq.parse_annot(annot_data, 0, 0);
 375   std::list<annot> annots_list = seq.annotations();
 376   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 377   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 378   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 379   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 380   BOOST_CHECK_EQUAL( annots[0].type, "type");
 381 }
 382
 383 // ticket:83 when you try to load a sequence from a file that doesn't
 384 // have fasta headers it crashes.
 385 BOOST_AUTO_TEST_CASE( sequence_past_end )
 386 {
 387   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 388   seq_path /=  "misformated_seq.fa";
 389   Sequence s;
 390   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 391 }
 392
 393 BOOST_AUTO_TEST_CASE ( sequence_empty )
 394 {
 395
 396   Sequence s;
 397   BOOST_CHECK_EQUAL( s.empty(), true );
 398   s = "AAAGGG";
 399   BOOST_CHECK_EQUAL( s.empty(), false );
 400   s.clear();
 401   BOOST_CHECK_EQUAL( s.empty(), true);
 402   s = "";
 403   BOOST_CHECK_EQUAL( s.empty(), true);
 404 }
 405
 406 BOOST_AUTO_TEST_CASE ( sequence_size )
 407 {
 408
 409   Sequence s;
 410   BOOST_CHECK_EQUAL( s.size(), 0);
 411   std::string seq_string("AAAGGG");
 412   s = seq_string;
 413   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 414   s.clear();
 415   BOOST_CHECK_EQUAL( s.size(), 0);
 416   s = "";
 417   BOOST_CHECK_EQUAL( s.size(), 0);
 418 }
 419
 420 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 421 {
 422   Sequence szero("", Sequence::reduced_dna_alphabet);
 423   BOOST_CHECK_EQUAL(szero.empty(), true);
 424   BOOST_CHECK_EQUAL(szero, szero);
 425   BOOST_CHECK_EQUAL(szero, "");
 426
 427   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 428   sclear.clear();
 429   BOOST_CHECK_EQUAL(sclear.empty(), true);
 430   BOOST_CHECK_EQUAL(sclear, sclear);
 431   BOOST_CHECK_EQUAL(sclear, szero);
 432   BOOST_CHECK_EQUAL(sclear, "");
 433
 434 }
 435 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 436 {
 437   std::string seq_string = "AAGGCCTTNNTATA";
 438   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 439   const Sequence cs(s);
 440   std::string::size_type count = 0;
 441
 442   std::string::iterator str_itor;
 443   Sequence::const_iterator s_itor;
 444   Sequence::const_iterator cs_itor;
 445
 446   for( str_itor = seq_string.begin(),
 447        s_itor   = s.begin(),
 448        cs_itor  = cs.begin();
 449        str_itor != seq_string.end() and
 450        s_itor   != s.end() and
 451        cs_itor  != cs.end();
 452        ++str_itor, ++s_itor, ++cs_itor, ++count)
 453   {
 454     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 455     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 456     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 457   }
 458   BOOST_CHECK_EQUAL( seq_string.size(), count );
 459   BOOST_CHECK_EQUAL( s.size(), count );
 460   BOOST_CHECK_EQUAL( cs.size(), count );
 461 }
 462
 463 BOOST_AUTO_TEST_CASE( sequence_motifs )
 464 {
 465   string m("AAAA");
 466   string bogus("AATTGGAA");
 467   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 468
 469   list<motif>::const_iterator motif_i = s1.motifs().begin();
 470   list<motif>::const_iterator motif_end = s1.motifs().end();
 471
 472   // do our iterators work?
 473   BOOST_CHECK( motif_i == s1.motifs().begin() );
 474   BOOST_CHECK( motif_end == s1.motifs().end() );
 475   BOOST_CHECK( motif_i == motif_end );
 476
 477   // this shouldn't show up
 478   s1.add_motif(bogus);
 479   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 480   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 481
 482   s1.add_motif(m);
 483   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 484   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 485
 486   for(motif_i = s1.motifs().begin();
 487       motif_i != s1.motifs().end();
 488       ++motif_i)
 489   {
 490     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 491     BOOST_CHECK_EQUAL( motif_i->name, m);
 492     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 493   }
 494
 495   s1.clear_motifs();
 496   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 497
 498   /* FIXME: enable this when i find a way of passing storing the motif name
 499   // does our annotation travel?
 500   Sequence motif_seq(m);
 501   motif_seq.set_fasta_header("hi");
 502   s1.add_motif(motif_seq);
 503
 504   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 505   for(motif_i = s1.motifs().begin();
 506       motif_i != s1.motifs().end();
 507       ++motif_i)
 508   {
 509     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 510     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 511     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 512   }
 513   */
 514 }
 515
 516 BOOST_AUTO_TEST_CASE( annot_test )
 517 {
 518   annot a(0, 10, "test", "thing");
 519
 520   BOOST_CHECK_EQUAL( a.begin, 0 );
 521   BOOST_CHECK_EQUAL( a.end,   10 );
 522   BOOST_CHECK_EQUAL( a.type,  "test" );
 523   BOOST_CHECK_EQUAL( a.name,  "thing" );
 524
 525   motif m(10, "AAGGCC");
 526   BOOST_CHECK_EQUAL( m.begin, 10 );
 527   BOOST_CHECK_EQUAL( m.type, "motif" );
 528   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 529   BOOST_CHECK_EQUAL( m.end,  10+6 );
 530 }
 531
 532 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 533 {
 534   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 535            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 536            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 537            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 538            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 539            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 540            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 541            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 542   string gc("GCCCCC");
 543   string gga("GGACACCTC");
 544   Sequence seq(s, Sequence::reduced_dna_alphabet);
 545
 546   std::list<Sequence> query_list;
 547   std::list<string> string_list;
 548   query_list.push_back(Sequence(gc));
 549   string_list.push_back(gc);
 550   query_list.push_back(Sequence(gga));
 551   string_list.push_back(gga);
 552
 553   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 554   seq.find_sequences(query_list.begin(), query_list.end());
 555
 556   int count = 0;
 557   for(list<string>::iterator string_i = string_list.begin();
 558       string_i != string_list.end();
 559       ++string_i)
 560   {
 561     string::size_type pos=0;
 562     while(pos != string::npos) {
 563       pos = s.find(*string_i, pos);
 564       if (pos != string::npos) {
 565         ++count;
 566         ++pos;
 567       }
 568     }
 569   }
 570   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 571   const std::list<annot> &a = seq.annotations();
 572   for (std::list<annot>::const_iterator annot_i = a.begin();
 573        annot_i != a.end();
 574        ++annot_i)
 575   {
 576     int count = annot_i->end - annot_i->begin ;
 577   }
 578 }
 579
 580 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 581 {
 582   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 583            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 584            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 585            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 586            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 587            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 588            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 589            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 590   Sequence seq(s, Sequence::reduced_dna_alphabet);
 591
 592
 593   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 594   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 595   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 596   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 597   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 598
 599   Sequence subseq = seq.subseq(5, 10);
 600   const list<annot> annots = subseq.annotations();
 601   // generate some ground truth
 602   list<annot> correct;
 603   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 604   correct.push_back(annot(5,10, "10-20", "10-20"));
 605   correct.push_back(annot(0,10, "0-20",  "0-20"));
 606   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 607   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 608
 609   list<annot>::iterator correct_i = correct.begin();
 610   list<annot>::const_iterator annot_i = annots.begin();
 611   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 612   {
 613     BOOST_CHECK( *annot_i == *correct_i );
 614   }
 615 }
 616
 617 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 618 {
 619   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 620            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 621            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 622            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 623            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 624            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 625            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 626            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 627   Sequence seq(s, Sequence::reduced_dna_alphabet);
 628
 629   // starting conditions
 630   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 631   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 632   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 633   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 634   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 635   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 636   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 637   seq.add_motif("CCGTCCC");
 638   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 639   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 640   seq.clear_motifs();
 641   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 642   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 643 }
 644
 645 BOOST_AUTO_TEST_CASE( out_operator )
 646 {
 647   string s("AAGGCCTT");
 648   Sequence seq(s, Sequence::reduced_dna_alphabet);
 649
 650   ostringstream buf;
 651   buf << s;
 652   BOOST_CHECK_EQUAL( s, buf.str() );
 653 }
 654
 655 BOOST_AUTO_TEST_CASE( get_name )
 656 {
 657   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 658
 659   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 660   seq.set_species("hooman"); // anyone remember tradewars?
 661   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 662   seq.set_fasta_header("fasta human");
 663   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 664 }
 665
 666 BOOST_AUTO_TEST_CASE( serialize_simple )
 667 {
 668   std::string seq_string = "AAGGCCTT";
 669   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 670   seq.set_species("ribbet");
 671   std::ostringstream oss;
 672   // allocate/deallocate serialization components
 673   {
 674     boost::archive::text_oarchive oarchive(oss);
 675     const Sequence& const_seq(seq);
 676     BOOST_CHECK_EQUAL(seq, const_seq);
 677     oarchive << const_seq;
 678   }
 679   Sequence seq_loaded;
 680   {
 681     std::istringstream iss(oss.str());
 682     boost::archive::text_iarchive iarchive(iss);
 683     iarchive >> seq_loaded;
 684   }
 685   BOOST_CHECK_EQUAL(seq_loaded, seq);
 686   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 687 }
 688
 689 BOOST_AUTO_TEST_CASE( serialize_tree )
 690 {
 691   std::string seq_string = "AAGGCCTT";
 692   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 693   seq.set_species("ribbet");
 694   seq.add_motif("AA");
 695   seq.add_motif("GC");
 696   annot a1(6,7,"t","t");
 697   seq.add_annotation(a1);
 698
 699   std::ostringstream oss;
 700   // allocate/deallocate serialization components
 701   {
 702     boost::archive::text_oarchive oarchive(oss);
 703     const Sequence& const_seq(seq);
 704     BOOST_CHECK_EQUAL(seq, const_seq);
 705     oarchive << const_seq;
 706   }
 707
 708   Sequence seq_loaded;
 709   {
 710     std::istringstream iss(oss.str());
 711     boost::archive::text_iarchive iarchive(iss);
 712     iarchive >> seq_loaded;
 713   }
 714   BOOST_CHECK_EQUAL(seq_loaded, seq);
 715 }
 716
 717 // this writes out an "old" style annotated sequence
 718 // with annotations attached as "motifs" and "annots"
 719 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 720 {
 721   std::string seq_string = "AAGGCCTT";
 722   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 723   seq.set_species("ribbet");
 724   seq.add_motif("AA");
 725   seq.add_motif("GC");
 726   annot a1(6,7,"t","t");
 727   seq.add_annotation(a1);
 728
 729   std::ostringstream oss;
 730   // allocate/deallocate serialization components
 731   {
 732     boost::archive::xml_oarchive oarchive(oss);
 733     const Sequence& const_seq(seq);
 734     BOOST_CHECK_EQUAL(seq, const_seq);
 735     oarchive << boost::serialization::make_nvp("root", const_seq);
 736   }
 737   Sequence seq_loaded;
 738   {
 739     std::istringstream iss(oss.str());
 740     boost::archive::xml_iarchive iarchive(iss);
 741     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 742   }
 743   BOOST_CHECK_EQUAL(seq_loaded, seq);
 744 }
 745
 746 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 747 {
 748   std::string seq_string = "AAGGCCTT";
 749   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 750   Sequence seq2(seq1);
 751
 752   std::ostringstream oss;
 753   // allocate/deallocate serialization components
 754   {
 755     boost::archive::xml_oarchive oarchive(oss);
 756     const Sequence& const_seq1(seq1);
 757     const Sequence& const_seq2(seq2);
 758     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 759     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 760   }
 761   //std::cout << "xml: " << oss.str() << std::endl;
 762   Sequence seq1_loaded;
 763   Sequence seq2_loaded;
 764   {
 765     std::istringstream iss(oss.str());
 766     boost::archive::xml_iarchive iarchive(iss);
 767     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 768     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 769   }
 770   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 771   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 772   // test if our pointers are the same
 773   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 774 }