alg/test/test_sequence.cpp

   1 #define BOOST_AUTO_TEST_MAIN
   2 #include <boost/test/auto_unit_test.hpp>
   3 #include <boost/filesystem/path.hpp>
   4 #include <boost/filesystem/operations.hpp>
   5 namespace fs=boost::filesystem;
   6
   7 #include <boost/algorithm/string/case_conv.hpp>
   8
   9 #include <list>
  10 #include <iostream>
  11 #include <sstream>
  12
  13 #include <boost/archive/text_oarchive.hpp>
  14 #include <boost/archive/text_iarchive.hpp>
  15 #include <boost/archive/xml_oarchive.hpp>
  16 #include <boost/archive/xml_iarchive.hpp>
  17
  18 #include "alg/sequence.hpp"
  19 #include "mussa_exceptions.hpp"
  20
  21 using namespace std;
  22
  23 BOOST_AUTO_TEST_CASE( sequence_copy_constructor )
  24 {
  25   SequenceRef s(new Sequence("AAAAGGGG"));
  26   s->set_species("foo");
  27   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  28
  29   SequenceRef c(new Sequence(s));
  30   BOOST_CHECK_EQUAL(c->get_species(), "foo");
  31
  32   c->set_species("bar");
  33   BOOST_CHECK_EQUAL(s->get_species(), "foo");
  34   BOOST_CHECK_EQUAL(c->get_species(), "bar");
  35 }
  36
  37 BOOST_AUTO_TEST_CASE( sequence_copy_constructor_copy_motifs )
  38 {
  39   SequenceRef s(new Sequence("AAAAGGGGAAAA"));
  40   s->add_motif("AAGG");
  41   BOOST_CHECK_EQUAL(s->motifs().size(), 1);
  42
  43   SequenceRef c(new Sequence(s->subseq()));
  44   BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  45
  46   s->clear_motifs();
  47   BOOST_CHECK_EQUAL(s->motifs().size(), 0);
  48   // FIXME: Technically c shouldn't lose its motifs.
  49   // FIXME: getting that to work is hard.
  50   // BOOST_CHECK_EQUAL(c->motifs().size(), 1);
  51   BOOST_CHECK_EQUAL(c->motifs().size(), 0);
  52 }
  53
  54 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  55 {
  56         Sequence s;
  57         // make sure that retrieving the sequence doesn't throw an error
  58         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  59 }
  60
  61 BOOST_AUTO_TEST_CASE( sequence_from_string )
  62 {
  63   std::string str1("AAAT");
  64   Sequence seq1(str1);
  65   BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
  66 }
  67
  68 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  69 {
  70   std::string str1("AAAAT");
  71   Sequence seq1(str1);
  72   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  73
  74   std::string str2("AATTGGCC");
  75   Sequence seq2(str2);
  76   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  77 }
  78
  79 //! when we try to load a missing file, do we get an error?
  80 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  81 {
  82   Sequence s;
  83   // there should be errors when we try to load something that doesn't exist
  84   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  85   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  86 }
  87
  88 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  89 {
  90   string header(">Header");
  91   string line1("AAAAGGGGCCCCTTTTT");
  92   string line2("AAAAGGGGCCCCTTTTT");
  93   int seq_len = line1.size() + line2.size();
  94
  95   stringstream cr;
  96   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  97   Sequence seq_cr;
  98   seq_cr.load_fasta(cr);
  99
 100   stringstream crlf;
 101   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
 102   Sequence seq_crlf;
 103   seq_crlf.load_fasta(crlf);
 104
 105   stringstream lf;
 106   lf << header << "\012" << line1 << "\012" << line2 << "\012";
 107   Sequence seq_lf;
 108   seq_lf.load_fasta(lf);
 109
 110   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 111   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
 112   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
 113 }
 114
 115
 116 //! Do simple operations work correctly?
 117 BOOST_AUTO_TEST_CASE( sequence_filter )
 118 {
 119   const char *core_seq = "AATTGGCC";
 120   Sequence s1(core_seq, reduced_dna_alphabet);
 121   BOOST_CHECK_EQUAL(s1, core_seq);
 122
 123   Sequence s2("aattggcc", reduced_dna_alphabet);
 124   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
 125   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
 126   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
 127   BOOST_CHECK_EQUAL(s2.size(), s2.size());
 128   //We're currently forcing sequences to uppercase
 129   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
 130
 131   Sequence s3("asdfg", reduced_dna_alphabet);
 132   BOOST_CHECK_EQUAL(s3, "ANNNG");
 133   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 134
 135   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
 136   BOOST_CHECK_EQUAL(s3, "AA");
 137   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
 138   BOOST_CHECK_EQUAL( s3, "GG");
 139   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
 140   BOOST_CHECK_EQUAL( s3, "CCTT");
 141
 142   s3 = "AAGGFF";
 143   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 144 }
 145
 146 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 147 {
 148   std::string agct("AGCT");
 149   Sequence seq(agct, nucleic_alphabet);
 150   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 151   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 152
 153   std::string bdv("BDv");
 154   Sequence seq_bdv(bdv, nucleic_alphabet);
 155   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 156   // forcing sequence to upper case
 157   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 158                     boost::algorithm::to_upper_copy(bdv));
 159
 160 }
 161
 162 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 163 {
 164   std::string agct("AGCT");
 165   Sequence seq(agct);
 166   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 167   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 168   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 169   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 170   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 171   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 172
 173   std::string bdv("BDv");
 174   Sequence seq_bdv(bdv);
 175   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 176   // default alphabet only allows AGCTUN
 177   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 178 }
 179
 180 BOOST_AUTO_TEST_CASE( subseq_names )
 181 {
 182   Sequence s1("AAGGCCTT", reduced_dna_alphabet);
 183   s1.set_species("species");
 184   s1.set_fasta_header("a fasta header");
 185   Sequence s2 = s1.subseq(2,2);
 186   BOOST_CHECK_EQUAL(s2, "GG");
 187   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 188   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 189 }
 190
 191 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 192 {
 193   Sequence s1;
 194   BOOST_CHECK_EQUAL( s1.start(), 0 );
 195   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 196
 197   std::string seq_string("AAGGCCTT");
 198   Sequence s2(seq_string, reduced_dna_alphabet);
 199   BOOST_CHECK_EQUAL( s2.start(), 0 );
 200   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 201
 202   std::string s3seq_string = seq_string.substr(2,3);
 203   Sequence s3 = s2.subseq(2,3);
 204   BOOST_CHECK_EQUAL( s3.start(), 2);
 205   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 206   BOOST_CHECK_EQUAL( s3.size(), 3);
 207   BOOST_CHECK_EQUAL( s3, s3seq_string);
 208
 209   std::string s4seq_string = s3seq_string.substr(1,1);
 210   Sequence s4 = s3.subseq(1,1);
 211   BOOST_CHECK_EQUAL( s4.start(), 1 );
 212   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 213   BOOST_CHECK_EQUAL( s4.size(), 1);
 214   BOOST_CHECK_EQUAL( s4, s4seq_string);
 215 }
 216
 217 //! Can we load data from a file
 218 BOOST_AUTO_TEST_CASE( sequence_load )
 219 {
 220   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 221   seq_path /=  "human_mck_pro.fa";
 222   Sequence s;
 223   s.load_fasta(seq_path, reduced_dna_alphabet);
 224   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 225   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 226   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 227                                     "muscle creatine kinase gene (CKMM), "
 228                                     "5' flank");
 229 }
 230
 231 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 232 {
 233   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 234   seq_path /= "broken.fa";
 235   bool exception_thrown = false;
 236   std::string exception_filename;
 237   Sequence s;
 238   try {
 239     s.load_fasta(seq_path);
 240   } catch(sequence_invalid_load_error e) {
 241     exception_thrown = true;
 242     size_t native_string_size = seq_path.native_file_string().size();
 243     std:string estr(e.what());
 244     BOOST_REQUIRE(estr.size() > native_string_size);
 245     std::copy(estr.begin(), estr.begin()+native_string_size,
 246               std::back_inserter(exception_filename));
 247   }
 248   BOOST_CHECK_EQUAL(exception_thrown, true);
 249   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 250 }
 251
 252 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 253 {
 254   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 255   seq_path /= "mouse_mck_pro.fa";
 256   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 257   annot_path /= "broken.annot";
 258   bool exception_thrown = false;
 259   Sequence s;
 260   s.load_fasta(seq_path);
 261
 262   std::string exception_filename;
 263   try {
 264     s.load_annot(annot_path, 0, 0);
 265   } catch(annotation_load_error e) {
 266     exception_thrown = true;
 267     std:string estr(e.what());
 268     size_t native_string_size = annot_path.native_file_string().size();
 269     BOOST_REQUIRE(estr.size() > native_string_size);
 270     std::copy(estr.begin(), estr.begin()+native_string_size,
 271               std::back_inserter(exception_filename));
 272   }
 273   BOOST_CHECK_EQUAL(exception_thrown, true);
 274   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 275 }
 276
 277 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 278 {
 279   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 280   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 281   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 282   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 283   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 284   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 285   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 286   std::stringstream garbage_fasta(garbage_string);
 287
 288   Sequence s;
 289   s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
 290   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 291                                  reduced_dna_alphabet),
 292                     sequence_invalid_load_error);
 293   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 294                                  reduced_dna_alphabet),
 295                     sequence_invalid_load_error);
 296   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 297                                  reduced_dna_alphabet),
 298                     sequence_invalid_load_error);
 299
 300 }
 301
 302 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 303 {
 304   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 305   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 306   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 307   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 308   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 309   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 310   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 311   std::stringstream garbage_fasta(garbage_string);
 312
 313   Sequence s;
 314   s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
 315   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 316                                  reduced_rna_alphabet),
 317                     sequence_invalid_load_error);
 318   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 319                                  reduced_rna_alphabet),
 320                     sequence_invalid_load_error);
 321   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 322                                  reduced_rna_alphabet),
 323                     sequence_invalid_load_error);
 324 }
 325
 326 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 327 {
 328   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 329   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 330   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 331   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 332   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 333   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 334   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 335   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 336   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 337   std::stringstream garbage_fasta(garbage_string);
 338
 339   Sequence s;
 340   Sequence specific;
 341   // there's two copies of reduced_rna_fasta because i didn't feel like
 342   // figuring out how to properly reset the read pointer in a stringstream
 343   s.load_fasta(reduced_rna_fasta1);
 344   specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
 345   BOOST_CHECK_EQUAL(s, specific);
 346
 347   s.load_fasta(reduced_dna_fasta1);
 348   specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
 349   BOOST_CHECK_EQUAL(s, specific);
 350
 351   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 352                     sequence_invalid_load_error);
 353   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 354                     sequence_invalid_load_error);
 355 }
 356
 357 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 358 {
 359   std::string fasta_file(
 360     ">gi|10129974|gb|AF188002.1|AF188002\n"
 361     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 362     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 363     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 364     ">gi|1621|emb|X55146.1|OCMCK1\n"
 365     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 366   );
 367   istringstream seq1_file(fasta_file);
 368   Sequence seq1;
 369   seq1.load_fasta(seq1_file, 1, 0, 0);
 370   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 371
 372   istringstream seq2_file(fasta_file);
 373   Sequence seq2;
 374   seq2.load_fasta(seq2_file, 2, 0, 0);
 375   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 376
 377   istringstream seq3_file(fasta_file);
 378   Sequence seq3;
 379   seq3.load_fasta(seq3_file, 3, 0, 0);
 380   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 381 }
 382
 383 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 384 {
 385   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 386   Sequence seq(iupac_symbols, nucleic_alphabet);
 387   Sequence seqr = seq.rev_comp();
 388
 389   BOOST_CHECK( seq != seqr );
 390   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 391   // forcing sequence to upper case
 392   BOOST_CHECK_EQUAL( seq.get_sequence(),
 393                      boost::algorithm::to_upper_copy(iupac_symbols) );
 394 }
 395
 396 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 397 {
 398   std::string dna_str("AGCTN");
 399   Sequence dna_seq(dna_str, reduced_dna_alphabet);
 400   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 401   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 402 }
 403
 404 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 405 {
 406   std::string rna_str("AGCUN");
 407   Sequence rna_seq(rna_str, reduced_rna_alphabet);
 408   BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
 409   BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
 410                     rna_seq.rev_comp().rev_comp().get_sequence());
 411 }
 412
 413 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 414 {
 415   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 416   Sequence seq(dna_str, reduced_dna_alphabet);
 417   Sequence subseq = seq.subseq(8,4);
 418   BOOST_CHECK_EQUAL( subseq, "AAGG");
 419   Sequence rev_subseq = subseq.rev_comp();
 420   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 421   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 422 }
 423
 424 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 425 {
 426   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 427   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 428   Sequence seq(dna_str);
 429   std::string seq_reversed(seq.rbegin(), seq.rend());
 430   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 431
 432   std::string substr = dna_str.substr(8,4);
 433   Sequence subseq = seq.subseq(8,4);
 434   BOOST_CHECK_EQUAL(substr, subseq);
 435
 436   std::string substr_reversed(substr.rbegin(), substr.rend());
 437   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 438   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 439 }
 440
 441 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 442 {
 443   // so what happens with reverse interators when we have no sequence?
 444   Sequence seq1;
 445   Sequence seq2;
 446   Sequence seq3("AGCT");
 447
 448   // all the empty sequences should have equal iterators
 449   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 450   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 451
 452   // none of the seq1 iterators should equal any of the seq3 iterators
 453   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 454   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 455   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 456   BOOST_CHECK(seq1.rend() != seq3.rend());
 457
 458   // seq3 iterators should work
 459   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 460
 461 }
 462
 463 BOOST_AUTO_TEST_CASE( annotation_load )
 464 {
 465   string annot_data = "human\n"
 466                       "0 10 name   type\n"     //0
 467                       "10 20 myf7\n"           //1
 468                       "20 30 myod\n"           //2
 469                       "50\t55 anothername\n"   //3
 470                       "60 50 backward\n"       //4
 471                       ">ident3 asdf\n"         //7 (as these are added last)
 472                       "GCT\n"
 473                       "gCTn\n"
 474                       "75\t90\tname2\ttype2\n" //5
 475                       "100 120 name-asdf type!@#$%\n" //6
 476                       ;
 477   string s(100, 'A');
 478   s += "GCTGCTAATT";
 479   Sequence seq(s, reduced_dna_alphabet);
 480
 481   //istringstream annot_stream(annot_data);
 482   seq.parse_annot(annot_data, 0, 0);
 483   SeqSpanRefList annots_list(seq.annotations());
 484   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 485   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 486   BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
 487   BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
 488   BOOST_REQUIRE( annots[0]->annotations() );
 489   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 490   BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
 491   BOOST_REQUIRE( annots[1]->annotations() );
 492   BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
 493   BOOST_REQUIRE( annots[2]->annotations() );
 494   BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
 495   BOOST_REQUIRE( annots[3]->annotations() );
 496   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
 497   BOOST_REQUIRE( annots[4]->annotations() );
 498   BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
 499   BOOST_REQUIRE( annots[5]->annotations() );
 500   BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
 501   BOOST_CHECK_EQUAL( annots[5]->start(), 75);
 502   BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
 503   BOOST_CHECK_EQUAL( annots[6]->start(), 100);
 504   BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
 505   BOOST_REQUIRE( annots[6]->annotations() );
 506   BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
 507   BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
 508   // sequence defined annotations will always be after the
 509   // absolute positions
 510   BOOST_REQUIRE( annots[7]->annotations() );
 511   BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
 512   BOOST_CHECK_EQUAL( annots[7]->start(), 100);
 513   BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
 514
 515   //BOOST_CHECK_EQUAL( annots
 516 }
 517
 518 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 519 {
 520   string annot_data = "human\n"
 521                       "0 10 name   type\n"
 522                       "blah60 50 backward\n"
 523                       ">ident3 asdf\n"
 524                       "GCT\n"
 525                       "gCTn\n"
 526                       ;
 527   string s(100, 'A');
 528   s += "GCTGCTAATT";
 529   Sequence seq(s, reduced_dna_alphabet);
 530
 531   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 532   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 533   }
 534
 535 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 536 {
 537   // this actually is basically what's returned by UCSC
 538   // (well actually with some of the sequence and copies of fasta blocks
 539   // removed to make the example shorter
 540   string annot_data = "\n"
 541     "<PRE>\n"
 542     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 543     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 544     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 545     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 546     "</PRE>\n"
 547     "\n"
 548     "</BODY>\n"
 549     "</HTML>\n"
 550     ;
 551
 552   string s =
 553     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 554     "AAAAA"
 555     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 556   Sequence seq(s, reduced_dna_alphabet);
 557   seq.parse_annot(annot_data);
 558   SeqSpanRefList annots(seq.annotations());
 559   BOOST_CHECK_EQUAL( annots.size(), 2);
 560 }
 561
 562 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 563 {
 564   string annot_data = "0 10 name   type\n"
 565                       "10 20 myf7\n"
 566                       "20 30 myod\n"
 567                       "50\t55 anothername\n"
 568                       "60 50 backward\n"
 569                       ">ident3 asdf\n"
 570                       "GCT\n"
 571                       "gCTn\n"
 572                       "75\t90\tname2\ttype2\n"
 573                       "100 120 name-asdf type!@#$%\n"
 574                       ;
 575   string s(100, 'A');
 576   s += "GCTGCTAATT";
 577   Sequence seq(s, reduced_dna_alphabet);
 578
 579   //istringstream annot_stream(annot_data);
 580   seq.parse_annot(annot_data, 0, 0);
 581   SeqSpanRefList annots_list(seq.annotations());
 582   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 583   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 584   BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
 585   BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
 586   BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
 587 }
 588
 589 // when we do a subsequence (or something that calls copy_children)
 590 // the annotations need to be updated to have the right parent
 591 BOOST_AUTO_TEST_CASE( update_annotations_seqref )
 592 {
 593   Sequence s1("AAAAGGGG");
 594   s1.add_annotation("A", "A", 0, 4);
 595   BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
 596   BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
 597
 598   Sequence subseq1(s1.subseq(2,4));
 599   BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
 600   BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
 601   BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
 602   BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
 603 }
 604
 605 // ticket:83 when you try to load a sequence from a file that doesn't
 606 // have fasta headers it crashes.
 607 BOOST_AUTO_TEST_CASE( sequence_past_end )
 608 {
 609   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 610   seq_path /=  "misformated_seq.fa";
 611   Sequence s;
 612   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 613 }
 614
 615 BOOST_AUTO_TEST_CASE ( sequence_empty )
 616 {
 617
 618   Sequence s;
 619   BOOST_CHECK_EQUAL( s.empty(), true );
 620   s = "AAAGGG";
 621   BOOST_CHECK_EQUAL( s.empty(), false );
 622   s.clear();
 623   BOOST_CHECK_EQUAL( s.empty(), true);
 624   s = "";
 625   BOOST_CHECK_EQUAL( s.empty(), true);
 626 }
 627
 628 BOOST_AUTO_TEST_CASE ( sequence_size )
 629 {
 630
 631   Sequence s;
 632   BOOST_CHECK_EQUAL( s.size(), 0);
 633   std::string seq_string("AAAGGG");
 634   s = seq_string;
 635   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 636   s.clear();
 637   BOOST_CHECK_EQUAL( s.size(), 0);
 638   s = "";
 639   BOOST_CHECK_EQUAL( s.size(), 0);
 640 }
 641
 642 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 643 {
 644   Sequence szero("", reduced_dna_alphabet);
 645   BOOST_CHECK_EQUAL(szero.empty(), true);
 646   BOOST_CHECK_EQUAL(szero, szero);
 647   BOOST_CHECK_EQUAL(szero, "");
 648
 649   Sequence sclear("AGCT", reduced_dna_alphabet);
 650   sclear.clear();
 651   BOOST_CHECK_EQUAL(sclear.empty(), true);
 652   BOOST_CHECK_EQUAL(sclear, sclear);
 653   BOOST_CHECK_EQUAL(sclear, szero);
 654   BOOST_CHECK_EQUAL(sclear, "");
 655
 656 }
 657 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 658 {
 659   std::string seq_string = "AAGGCCTTNNTATA";
 660   Sequence s(seq_string, reduced_dna_alphabet);
 661   const Sequence cs(s);
 662   std::string::size_type count = 0;
 663
 664   std::string::iterator str_itor;
 665   Sequence::const_iterator s_itor;
 666   Sequence::const_iterator cs_itor;
 667
 668   for( str_itor = seq_string.begin(),
 669        s_itor   = s.begin(),
 670        cs_itor  = cs.begin();
 671        str_itor != seq_string.end() and
 672        s_itor   != s.end() and
 673        cs_itor  != cs.end();
 674        ++str_itor, ++s_itor, ++cs_itor, ++count)
 675   {
 676     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 677     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 678     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 679   }
 680   BOOST_CHECK_EQUAL( seq_string.size(), count );
 681   BOOST_CHECK_EQUAL( s.size(), count );
 682   BOOST_CHECK_EQUAL( cs.size(), count );
 683 }
 684
 685 BOOST_AUTO_TEST_CASE( sequence_motifs )
 686 {
 687   string m("AAAA");
 688   string bogus("AATTGGAA");
 689   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 690
 691   list<motif>::const_iterator motif_i = s1.motifs().begin();
 692   list<motif>::const_iterator motif_end = s1.motifs().end();
 693
 694   // do our iterators work?
 695   BOOST_CHECK( motif_i == s1.motifs().begin() );
 696   BOOST_CHECK( motif_end == s1.motifs().end() );
 697   BOOST_CHECK( motif_i == motif_end );
 698
 699   // this shouldn't show up
 700   s1.add_motif(bogus);
 701   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 702   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 703
 704   s1.add_motif(m);
 705   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 706   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 707
 708   for(motif_i = s1.motifs().begin();
 709       motif_i != s1.motifs().end();
 710       ++motif_i)
 711   {
 712     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 713     BOOST_CHECK_EQUAL( motif_i->name, m);
 714     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 715   }
 716
 717   s1.clear_motifs();
 718   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 719
 720   /* FIXME: enable this when i find a way of passing storing the motif name
 721   // does our annotation travel?
 722   Sequence motif_seq(m);
 723   motif_seq.set_fasta_header("hi");
 724   s1.add_motif(motif_seq);
 725
 726   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 727   for(motif_i = s1.motifs().begin();
 728       motif_i != s1.motifs().end();
 729       ++motif_i)
 730   {
 731     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 732     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 733     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 734   }
 735   */
 736 }
 737
 738 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 739 {
 740   // when searching for a motif on a subsequence we should
 741   // only search the subsequence ticket:199
 742   string aaaa("AAAA");
 743   string cccc("CCCC");
 744   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 745
 746   // this shouldn't show up
 747   s1.add_motif(cccc);
 748   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 749
 750   s1.add_motif(aaaa);
 751   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 752
 753   Sequence subseq1 = s1.subseq(4,5);
 754   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 755   subseq1.clear_motifs();
 756   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 757   // this is outside of our subsequence, and so shouldn't be found
 758   subseq1.add_motif(aaaa);
 759   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 760
 761   subseq1.add_motif(cccc);
 762   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 763   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 764   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 765   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 766   BOOST_CHECK_EQUAL(motif_i->end, 5);
 767 }
 768
 769 BOOST_AUTO_TEST_CASE( annot_test )
 770 {
 771   Sequence s("AAAAAAAAAA");
 772   s.add_annotation("test", "thing", 0, 10);
 773   SeqSpanRef a(s.annotations().front());
 774
 775   BOOST_CHECK_EQUAL( a->start(), 0 );
 776   BOOST_CHECK_EQUAL( a->stop(),   10 );
 777   BOOST_CHECK_EQUAL( a->annotations()->get("name"),  "test" );
 778   BOOST_CHECK_EQUAL( a->annotations()->get("type"),  "thing" );
 779
 780   motif m(10, "AAGGCC");
 781   BOOST_CHECK_EQUAL( m.begin, 10 );
 782   BOOST_CHECK_EQUAL( m.type, "motif" );
 783   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 784   BOOST_CHECK_EQUAL( m.end,  10+6 );
 785 }
 786
 787 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 788 {
 789   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 790            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 791            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 792            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 793            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 794            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 795            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 796            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 797   string gc("GCCCCC");
 798   string gga("GGACACCTC");
 799   Sequence seq(s, reduced_dna_alphabet);
 800
 801   std::list<Sequence> query_list;
 802   std::list<string> string_list;
 803   query_list.push_back(Sequence(gc));
 804   string_list.push_back(gc);
 805   query_list.push_back(Sequence(gga));
 806   string_list.push_back(gga);
 807
 808   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 809   seq.find_sequences(query_list.begin(), query_list.end());
 810
 811   int count = 0;
 812   for(list<string>::iterator string_i = string_list.begin();
 813       string_i != string_list.end();
 814       ++string_i)
 815   {
 816     string::size_type pos=0;
 817     while(pos != string::npos) {
 818       pos = s.find(*string_i, pos);
 819       if (pos != string::npos) {
 820         ++count;
 821         ++pos;
 822       }
 823     }
 824   }
 825   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 826   const SeqSpanRefList& a = seq.annotations();
 827   for (SeqSpanRefList::const_iterator annot_i = a.begin();
 828        annot_i != a.end();
 829        ++annot_i)
 830   {
 831     //FIXME: was I doing something here?
 832     int count = (*annot_i)->stop() - (*annot_i)->start();
 833   }
 834 }
 835
 836 BOOST_AUTO_TEST_CASE( sequence_no_trailing_newline )
 837 {
 838   // sorry about the long string...
 839   string s = "AATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTT";
 840   std::string species = "HumanHXA5\n";
 841   std::string header0 = ">hg18_knownGene_NM_019102_0\n";
 842   std::string str0 = "GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG";
 843   std::string header1 = ">hg18_knownGene_NM_019102_1\n";
 844   std::string str1 = "ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT";
 845   stringstream annot;
 846   annot << species
 847         << header0
 848         << str0 << std::endl
 849         << std::endl
 850         << header1
 851         << str1;
 852   // need to convert strings to sequences for reverse complementing
 853   Sequence seq0(str0, reduced_dna_alphabet);
 854   Sequence seq1(str1, reduced_dna_alphabet);
 855
 856   Sequence annotated_seq(s, reduced_dna_alphabet);
 857   annotated_seq.load_annot(annot, 0, 0);
 858
 859   SeqSpanRefList annots_list = annotated_seq.annotations();
 860   // both sequences were found
 861   BOOST_REQUIRE_EQUAL( annots_list.size(),  2 );
 862
 863   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 864   // are they the same sequence?
 865   BOOST_CHECK_EQUAL( annots[0]->size(),  seq0.size());
 866   BOOST_CHECK_EQUAL( annots[0]->sequence(), seq0.rev_comp() );
 867   // this should hopefully catch the case when my hack in
 868   // sequence.cpp::push_back_seq::operator() is no longer needed.
 869   // spirit (or my grammar was duplicating the last char,
 870   // the hack removes the duplicate. but if what ever's causing
 871   // the dup gets fixed actual meaningful data will be being removed.
 872   // see mussa ticket:265 for more information
 873   BOOST_CHECK_EQUAL( annots[1]->size(),  seq1.size());
 874   BOOST_CHECK_EQUAL( annots[1]->sequence(), seq1.rev_comp() );
 875
 876 }
 877
 878 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 879 {
 880   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 881            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 882            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 883            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 884            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 885            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 886            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 887            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 888   Sequence seq(s, reduced_dna_alphabet);
 889
 890   seq.add_annotation("0-10", "0-10", 0, 10);
 891   seq.add_annotation("10-20", "10-20", 10, 20);
 892   seq.add_annotation("0-20", "0-20", 0, 20);
 893   seq.add_annotation("8-12", "8-12", 8, 12);
 894   seq.add_annotation("100-5000", "100-5000", 100, 5000);
 895
 896   Sequence subseq = seq.subseq(5, 10);
 897   SeqSpanRefList annots_list = subseq.annotations();
 898   BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
 899
 900   std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
 901   BOOST_CHECK_EQUAL( annots[0]->parentStart(),  0);
 902   BOOST_CHECK_EQUAL( annots[0]->size(),  5);
 903   BOOST_REQUIRE( annots[0]->annotations() );
 904   BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
 905
 906   BOOST_CHECK_EQUAL( annots[1]->parentStart(), 5);
 907   BOOST_CHECK_EQUAL( annots[1]->size(), 5);
 908   BOOST_REQUIRE( annots[1]->annotations() );
 909   BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
 910
 911   BOOST_CHECK_EQUAL( annots[2]->parentStart(), 0);
 912   BOOST_CHECK_EQUAL( annots[2]->size(), 10);
 913   BOOST_REQUIRE( annots[2]->annotations() );
 914   BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
 915
 916   BOOST_CHECK_EQUAL( annots[3]->parentStart(), 3);
 917   BOOST_CHECK_EQUAL( annots[3]->size(),  7);
 918   BOOST_REQUIRE( annots[3]->annotations() );
 919   BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
 920 }
 921
 922 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 923 {
 924   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 925            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 926            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 927            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 928            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 929            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 930            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 931            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 932   Sequence seq(s, reduced_dna_alphabet);
 933
 934   // starting conditions
 935   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 936   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 937   seq.add_annotation("0-10", "0-10", 0, 10);
 938   seq.add_annotation("10-20", "10-20", 10, 20);
 939   seq.add_annotation("0-20", "0-20", 0, 20);
 940   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 941   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 942   seq.add_motif("CCGTCCC");
 943   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 944   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 945   seq.clear_motifs();
 946   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 947   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 948 }
 949
 950 BOOST_AUTO_TEST_CASE( out_operator )
 951 {
 952   string s("AAGGCCTT");
 953   Sequence seq(s, reduced_dna_alphabet);
 954
 955   ostringstream buf;
 956   buf << s;
 957   BOOST_CHECK_EQUAL( s, buf.str() );
 958 }
 959
 960 BOOST_AUTO_TEST_CASE( get_name )
 961 {
 962   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 963
 964   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 965   seq.set_species("hooman"); // anyone remember tradewars?
 966   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 967   seq.set_fasta_header("fasta human");
 968   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 969 }
 970 /*
 971 BOOST_AUTO_TEST_CASE( serialize_simple )
 972 {
 973   std::string seq_string = "AAGGCCTT";
 974   Sequence seq(seq_string, reduced_dna_alphabet);
 975   seq.set_species("ribbet");
 976   std::ostringstream oss;
 977   // allocate/deallocate serialization components
 978   {
 979     boost::archive::text_oarchive oarchive(oss);
 980     const Sequence& const_seq(seq);
 981     BOOST_CHECK_EQUAL(seq, const_seq);
 982     oarchive << const_seq;
 983   }
 984   Sequence seq_loaded;
 985   {
 986     std::istringstream iss(oss.str());
 987     boost::archive::text_iarchive iarchive(iss);
 988     iarchive >> seq_loaded;
 989   }
 990   BOOST_CHECK_EQUAL(seq_loaded, seq);
 991   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 992 }
 993
 994 BOOST_AUTO_TEST_CASE( serialize_tree )
 995 {
 996   std::string seq_string = "AAGGCCTT";
 997   Sequence seq(seq_string, reduced_dna_alphabet);
 998   seq.set_species("ribbet");
 999   seq.add_motif("AA");
1000   seq.add_motif("GC");
1001   seq.add_annotation("t", "t", 6, 7);
1002
1003   std::ostringstream oss;
1004   // allocate/deallocate serialization components
1005   {
1006     boost::archive::text_oarchive oarchive(oss);
1007     const Sequence& const_seq(seq);
1008     BOOST_CHECK_EQUAL(seq, const_seq);
1009     oarchive << const_seq;
1010   }
1011
1012   Sequence seq_loaded;
1013   {
1014     std::istringstream iss(oss.str());
1015     boost::archive::text_iarchive iarchive(iss);
1016     iarchive >> seq_loaded;
1017   }
1018   BOOST_CHECK_EQUAL(seq_loaded, seq);
1019 }
1020
1021 // this writes out an "old" style annotated sequence
1022 // with annotations attached as "motifs" and "annots"
1023 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
1024 {
1025   std::string seq_string = "AAGGCCTT";
1026   Sequence seq(seq_string, reduced_dna_alphabet);
1027   seq.set_species("ribbet");
1028   seq.add_motif("AA");
1029   seq.add_motif("GC");
1030   seq.add_annotation("t", "t", 6, 7);
1031
1032   std::ostringstream oss;
1033   // allocate/deallocate serialization components
1034   {
1035     boost::archive::xml_oarchive oarchive(oss);
1036     const Sequence& const_seq(seq);
1037     BOOST_CHECK_EQUAL(seq, const_seq);
1038     oarchive << boost::serialization::make_nvp("root", const_seq);
1039   }
1040   Sequence seq_loaded;
1041   {
1042     std::istringstream iss(oss.str());
1043     boost::archive::xml_iarchive iarchive(iss);
1044     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
1045   }
1046   BOOST_CHECK_EQUAL(seq_loaded, seq);
1047 }
1048
1049 BOOST_AUTO_TEST_CASE( serialize_xml_two )
1050 {
1051   std::string seq_string = "AAGGCCTT";
1052   Sequence seq1(seq_string, reduced_dna_alphabet);
1053   Sequence seq2(seq1);
1054
1055   std::ostringstream oss;
1056   // allocate/deallocate serialization components
1057   {
1058     boost::archive::xml_oarchive oarchive(oss);
1059     const Sequence& const_seq1(seq1);
1060     const Sequence& const_seq2(seq2);
1061     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
1062     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
1063   }
1064   //std::cout << "xml: " << oss.str() << std::endl;
1065   Sequence seq1_loaded;
1066   Sequence seq2_loaded;
1067   {
1068     std::istringstream iss(oss.str());
1069     boost::archive::xml_iarchive iarchive(iss);
1070     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
1071     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
1072   }
1073   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
1074   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
1075   // test if our pointers are the same
1076   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
1077 }
1078 */