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_get_sequence )
  24 {
  25         Sequence s;
  26         // make sure that retrieving the sequence doesn't throw an error
  27         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  28 }
  29
  30 BOOST_AUTO_TEST_CASE( sequence_from_string )
  31 {
  32   std::string str1("AAAT");
  33   Sequence seq1(str1);
  34   BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
  35 }
  36
  37 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  38 {
  39   std::string str1("AAAAT");
  40   Sequence seq1(str1);
  41   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  42
  43   std::string str2("AATTGGCC");
  44   Sequence seq2(str2);
  45   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  46 }
  47
  48 //! when we try to load a missing file, do we get an error?
  49 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  50 {
  51   Sequence s;
  52   // there should be errors when we try to load something that doesn't exist
  53   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  54   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  55 }
  56
  57 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  58 {
  59   string header(">Header");
  60   string line1("AAAAGGGGCCCCTTTTT");
  61   string line2("AAAAGGGGCCCCTTTTT");
  62   int seq_len = line1.size() + line2.size();
  63
  64   stringstream cr;
  65   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  66   Sequence seq_cr;
  67   seq_cr.load_fasta(cr);
  68
  69   stringstream crlf;
  70   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  71   Sequence seq_crlf;
  72   seq_crlf.load_fasta(crlf);
  73
  74   stringstream lf;
  75   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  76   Sequence seq_lf;
  77   seq_lf.load_fasta(lf);
  78
  79   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  80   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  81   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  82 }
  83
  84
  85 //! Do simple operations work correctly?
  86 BOOST_AUTO_TEST_CASE( sequence_filter )
  87 {
  88   const char *core_seq = "AATTGGCC";
  89   Sequence s1(core_seq, reduced_dna_alphabet);
  90   BOOST_CHECK_EQUAL(s1, core_seq);
  91
  92   Sequence s2("aattggcc", reduced_dna_alphabet);
  93   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
  94   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
  95   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
  96   BOOST_CHECK_EQUAL(s2.size(), s2.size());
  97   //We're currently forcing sequences to uppercase
  98   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
  99
 100   Sequence s3("asdfg", reduced_dna_alphabet);
 101   BOOST_CHECK_EQUAL(s3, "ANNNG");
 102   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 103
 104   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
 105   BOOST_CHECK_EQUAL(s3, "AA");
 106   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
 107   BOOST_CHECK_EQUAL( s3, "GG");
 108   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
 109   BOOST_CHECK_EQUAL( s3, "CCTT");
 110
 111   s3 = "AAGGFF";
 112   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 113 }
 114
 115 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 116 {
 117   std::string agct("AGCT");
 118   Sequence seq(agct, nucleic_alphabet);
 119   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 120   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 121
 122   std::string bdv("BDv");
 123   Sequence seq_bdv(bdv, nucleic_alphabet);
 124   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 125   // forcing sequence to upper case
 126   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 127                     boost::algorithm::to_upper_copy(bdv));
 128
 129 }
 130
 131 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 132 {
 133   std::string agct("AGCT");
 134   Sequence seq(agct);
 135   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 136   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 137   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 138   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 139   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 140   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 141
 142   std::string bdv("BDv");
 143   Sequence seq_bdv(bdv);
 144   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 145   // default alphabet only allows AGCTUN
 146   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 147 }
 148
 149 BOOST_AUTO_TEST_CASE( subseq_names )
 150 {
 151   Sequence s1("AAGGCCTT", reduced_dna_alphabet);
 152   s1.set_species("species");
 153   s1.set_fasta_header("a fasta header");
 154   Sequence s2 = s1.subseq(2,2);
 155   BOOST_CHECK_EQUAL(s2, "GG");
 156   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 157   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 158 }
 159
 160 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 161 {
 162   Sequence s1;
 163   BOOST_CHECK_EQUAL( s1.start(), 0 );
 164   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 165
 166   std::string seq_string("AAGGCCTT");
 167   Sequence s2(seq_string, reduced_dna_alphabet);
 168   BOOST_CHECK_EQUAL( s2.start(), 0 );
 169   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 170
 171   std::string s3seq_string = seq_string.substr(2,3);
 172   Sequence s3 = s2.subseq(2,3);
 173   BOOST_CHECK_EQUAL( s3.start(), 2);
 174   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 175   BOOST_CHECK_EQUAL( s3.size(), 3);
 176   BOOST_CHECK_EQUAL( s3, s3seq_string);
 177
 178   std::string s4seq_string = s3seq_string.substr(1,1);
 179   Sequence s4 = s3.subseq(1,1);
 180   BOOST_CHECK_EQUAL( s4.start(), 1 );
 181   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 182   BOOST_CHECK_EQUAL( s4.size(), 1);
 183   BOOST_CHECK_EQUAL( s4, s4seq_string);
 184 }
 185
 186 //! Can we load data from a file
 187 BOOST_AUTO_TEST_CASE( sequence_load )
 188 {
 189   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 190   seq_path /=  "human_mck_pro.fa";
 191   Sequence s;
 192   s.load_fasta(seq_path, reduced_dna_alphabet);
 193   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 194   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 195   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 196                                     "muscle creatine kinase gene (CKMM), "
 197                                     "5' flank");
 198 }
 199
 200 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 201 {
 202   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 203   seq_path /= "broken.fa";
 204   bool exception_thrown = false;
 205   std::string exception_filename;
 206   Sequence s;
 207   try {
 208     s.load_fasta(seq_path);
 209   } catch(sequence_invalid_load_error e) {
 210     exception_thrown = true;
 211     size_t native_string_size = seq_path.native_file_string().size();
 212     std:string estr(e.what());
 213     BOOST_REQUIRE(estr.size() > native_string_size);
 214     std::copy(estr.begin(), estr.begin()+native_string_size,
 215               std::back_inserter(exception_filename));
 216   }
 217   BOOST_CHECK_EQUAL(exception_thrown, true);
 218   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 219 }
 220
 221 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 222 {
 223   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 224   seq_path /= "mouse_mck_pro.fa";
 225   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 226   annot_path /= "broken.annot";
 227   bool exception_thrown = false;
 228   Sequence s;
 229   s.load_fasta(seq_path);
 230
 231   std::string exception_filename;
 232   try {
 233     s.load_annot(annot_path, 0, 0);
 234   } catch(annotation_load_error e) {
 235     exception_thrown = true;
 236     std:string estr(e.what());
 237     size_t native_string_size = annot_path.native_file_string().size();
 238     BOOST_REQUIRE(estr.size() > native_string_size);
 239     std::copy(estr.begin(), estr.begin()+native_string_size,
 240               std::back_inserter(exception_filename));
 241   }
 242   BOOST_CHECK_EQUAL(exception_thrown, true);
 243   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 244 }
 245
 246 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 247 {
 248   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 249   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 250   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 251   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 252   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 253   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 254   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 255   std::stringstream garbage_fasta(garbage_string);
 256
 257   Sequence s;
 258   s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
 259   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 260                                  reduced_dna_alphabet),
 261                     sequence_invalid_load_error);
 262   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 263                                  reduced_dna_alphabet),
 264                     sequence_invalid_load_error);
 265   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 266                                  reduced_dna_alphabet),
 267                     sequence_invalid_load_error);
 268
 269 }
 270
 271 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 272 {
 273   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 274   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 275   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 276   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 277   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 278   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 279   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 280   std::stringstream garbage_fasta(garbage_string);
 281
 282   Sequence s;
 283   s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
 284   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 285                                  reduced_rna_alphabet),
 286                     sequence_invalid_load_error);
 287   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 288                                  reduced_rna_alphabet),
 289                     sequence_invalid_load_error);
 290   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 291                                  reduced_rna_alphabet),
 292                     sequence_invalid_load_error);
 293 }
 294
 295 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 296 {
 297   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 298   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 299   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 300   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 301   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 302   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 303   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 304   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 305   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 306   std::stringstream garbage_fasta(garbage_string);
 307
 308   Sequence s;
 309   Sequence specific;
 310   // there's two copies of reduced_rna_fasta because i didn't feel like
 311   // figuring out how to properly reset the read pointer in a stringstream
 312   s.load_fasta(reduced_rna_fasta1);
 313   specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
 314   BOOST_CHECK_EQUAL(s, specific);
 315
 316   s.load_fasta(reduced_dna_fasta1);
 317   specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
 318   BOOST_CHECK_EQUAL(s, specific);
 319
 320   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 321                     sequence_invalid_load_error);
 322   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 323                     sequence_invalid_load_error);
 324 }
 325
 326 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 327 {
 328   std::string fasta_file(
 329     ">gi|10129974|gb|AF188002.1|AF188002\n"
 330     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 331     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 332     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 333     ">gi|1621|emb|X55146.1|OCMCK1\n"
 334     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 335   );
 336   istringstream seq1_file(fasta_file);
 337   Sequence seq1;
 338   seq1.load_fasta(seq1_file, 1, 0, 0);
 339   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 340
 341   istringstream seq2_file(fasta_file);
 342   Sequence seq2;
 343   seq2.load_fasta(seq2_file, 2, 0, 0);
 344   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 345
 346   istringstream seq3_file(fasta_file);
 347   Sequence seq3;
 348   seq3.load_fasta(seq3_file, 3, 0, 0);
 349   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 350 }
 351
 352 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 353 {
 354   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 355   Sequence seq(iupac_symbols, nucleic_alphabet);
 356   Sequence seqr = seq.rev_comp();
 357
 358   BOOST_CHECK( seq != seqr );
 359   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 360   // forcing sequence to upper case
 361   BOOST_CHECK_EQUAL( seq.get_sequence(),
 362                      boost::algorithm::to_upper_copy(iupac_symbols) );
 363 }
 364
 365 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 366 {
 367   std::string dna_str("AGCTN");
 368   Sequence dna_seq(dna_str, reduced_dna_alphabet);
 369   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 370   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 371 }
 372
 373 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 374 {
 375   std::string rna_str("AGCUN");
 376   Sequence rna_seq(rna_str, reduced_rna_alphabet);
 377   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 378   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 379 }
 380
 381 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 382 {
 383   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 384   Sequence seq(dna_str, reduced_dna_alphabet);
 385   Sequence subseq = seq.subseq(8,4);
 386   BOOST_CHECK_EQUAL( subseq, "AAGG");
 387   Sequence rev_subseq = subseq.rev_comp();
 388   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 389   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 390 }
 391
 392 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 393 {
 394   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 395   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 396   Sequence seq(dna_str);
 397   std::string seq_reversed(seq.rbegin(), seq.rend());
 398   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 399
 400   std::string substr = dna_str.substr(8,4);
 401   Sequence subseq = seq.subseq(8,4);
 402   BOOST_CHECK_EQUAL(substr, subseq);
 403
 404   std::string substr_reversed(substr.rbegin(), substr.rend());
 405   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 406   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 407 }
 408
 409 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 410 {
 411   // so what happens with reverse interators when we have no sequence?
 412   Sequence seq1;
 413   Sequence seq2;
 414   Sequence seq3("AGCT");
 415
 416   // all the empty sequences should have equal iterators
 417   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 418   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 419
 420   // none of the seq1 iterators should equal any of the seq3 iterators
 421   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 422   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 423   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 424   BOOST_CHECK(seq1.rend() != seq3.rend());
 425
 426   // seq3 iterators should work
 427   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 428
 429 }
 430
 431 BOOST_AUTO_TEST_CASE( annotation_load )
 432 {
 433   string annot_data = "human\n"
 434                       "0 10 name   type\n"
 435                       "10 20 myf7\n"
 436                       "20 30 myod\n"
 437                       "50\t55 anothername\n"
 438                       "60 50 backward\n"
 439                       ">ident3 asdf\n"
 440                       "GCT\n"
 441                       "gCTn\n"
 442                       "75\t90\tname2\ttype2\n"
 443                       "100 120 name-asdf type!@#$%\n"
 444                       ;
 445   string s(100, 'A');
 446   s += "GCTGCTAATT";
 447   Sequence seq(s, reduced_dna_alphabet);
 448
 449   //istringstream annot_stream(annot_data);
 450   seq.parse_annot(annot_data, 0, 0);
 451   std::list<annot> annots_list = seq.annotations();
 452   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 453   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 454   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 455   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 456   BOOST_CHECK_EQUAL( annots[0].type, "type");
 457   BOOST_CHECK_EQUAL( annots[0].name, "name");
 458   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 459   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 460   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 461   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 462   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 463   BOOST_CHECK_EQUAL( annots[5].end, 90);
 464   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 465   BOOST_CHECK_EQUAL( annots[6].end, 120);
 466   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 467   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 468   // sequence defined annotations will always be after the
 469   // absolute positions
 470   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 471   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 472
 473   //BOOST_CHECK_EQUAL( annots
 474 }
 475
 476 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 477 {
 478   string annot_data = "human\n"
 479                       "0 10 name   type\n"
 480                       "blah60 50 backward\n"
 481                       ">ident3 asdf\n"
 482                       "GCT\n"
 483                       "gCTn\n"
 484                       ;
 485   string s(100, 'A');
 486   s += "GCTGCTAATT";
 487   Sequence seq(s, reduced_dna_alphabet);
 488
 489   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 490   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 491   }
 492
 493 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 494 {
 495   // this actually is basically what's returned by UCSC
 496   // (well actually with some of the sequence and copies of fasta blocks
 497   // removed to make the example shorter
 498   string annot_data = "\n"
 499     "<PRE>\n"
 500     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 501     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 502     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 503     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 504     "</PRE>\n"
 505     "\n"
 506     "</BODY>\n"
 507     "</HTML>\n"
 508     ;
 509
 510   string s =
 511     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 512     "AAAAA"
 513     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 514   Sequence seq(s, reduced_dna_alphabet);
 515   seq.parse_annot(annot_data);
 516   std::list<annot> annots = seq.annotations();
 517   BOOST_CHECK_EQUAL( annots.size(), 2);
 518 }
 519
 520 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 521 {
 522   string annot_data = "0 10 name   type\n"
 523                       "10 20 myf7\n"
 524                       "20 30 myod\n"
 525                       "50\t55 anothername\n"
 526                       "60 50 backward\n"
 527                       ">ident3 asdf\n"
 528                       "GCT\n"
 529                       "gCTn\n"
 530                       "75\t90\tname2\ttype2\n"
 531                       "100 120 name-asdf type!@#$%\n"
 532                       ;
 533   string s(100, 'A');
 534   s += "GCTGCTAATT";
 535   Sequence seq(s, reduced_dna_alphabet);
 536
 537   //istringstream annot_stream(annot_data);
 538   seq.parse_annot(annot_data, 0, 0);
 539   std::list<annot> annots_list = seq.annotations();
 540   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 541   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 542   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 543   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 544   BOOST_CHECK_EQUAL( annots[0].type, "type");
 545 }
 546
 547 // ticket:83 when you try to load a sequence from a file that doesn't
 548 // have fasta headers it crashes.
 549 BOOST_AUTO_TEST_CASE( sequence_past_end )
 550 {
 551   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 552   seq_path /=  "misformated_seq.fa";
 553   Sequence s;
 554   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 555 }
 556
 557 BOOST_AUTO_TEST_CASE ( sequence_empty )
 558 {
 559
 560   Sequence s;
 561   BOOST_CHECK_EQUAL( s.empty(), true );
 562   s = "AAAGGG";
 563   BOOST_CHECK_EQUAL( s.empty(), false );
 564   s.clear();
 565   BOOST_CHECK_EQUAL( s.empty(), true);
 566   s = "";
 567   BOOST_CHECK_EQUAL( s.empty(), true);
 568 }
 569
 570 BOOST_AUTO_TEST_CASE ( sequence_size )
 571 {
 572
 573   Sequence s;
 574   BOOST_CHECK_EQUAL( s.size(), 0);
 575   std::string seq_string("AAAGGG");
 576   s = seq_string;
 577   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 578   s.clear();
 579   BOOST_CHECK_EQUAL( s.size(), 0);
 580   s = "";
 581   BOOST_CHECK_EQUAL( s.size(), 0);
 582 }
 583
 584 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 585 {
 586   Sequence szero("", reduced_dna_alphabet);
 587   BOOST_CHECK_EQUAL(szero.empty(), true);
 588   BOOST_CHECK_EQUAL(szero, szero);
 589   BOOST_CHECK_EQUAL(szero, "");
 590
 591   Sequence sclear("AGCT", reduced_dna_alphabet);
 592   sclear.clear();
 593   BOOST_CHECK_EQUAL(sclear.empty(), true);
 594   BOOST_CHECK_EQUAL(sclear, sclear);
 595   BOOST_CHECK_EQUAL(sclear, szero);
 596   BOOST_CHECK_EQUAL(sclear, "");
 597
 598 }
 599 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 600 {
 601   std::string seq_string = "AAGGCCTTNNTATA";
 602   Sequence s(seq_string, reduced_dna_alphabet);
 603   const Sequence cs(s);
 604   std::string::size_type count = 0;
 605
 606   std::string::iterator str_itor;
 607   Sequence::const_iterator s_itor;
 608   Sequence::const_iterator cs_itor;
 609
 610   for( str_itor = seq_string.begin(),
 611        s_itor   = s.begin(),
 612        cs_itor  = cs.begin();
 613        str_itor != seq_string.end() and
 614        s_itor   != s.end() and
 615        cs_itor  != cs.end();
 616        ++str_itor, ++s_itor, ++cs_itor, ++count)
 617   {
 618     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 619     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 620     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 621   }
 622   BOOST_CHECK_EQUAL( seq_string.size(), count );
 623   BOOST_CHECK_EQUAL( s.size(), count );
 624   BOOST_CHECK_EQUAL( cs.size(), count );
 625 }
 626
 627 BOOST_AUTO_TEST_CASE( sequence_motifs )
 628 {
 629   string m("AAAA");
 630   string bogus("AATTGGAA");
 631   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 632
 633   list<motif>::const_iterator motif_i = s1.motifs().begin();
 634   list<motif>::const_iterator motif_end = s1.motifs().end();
 635
 636   // do our iterators work?
 637   BOOST_CHECK( motif_i == s1.motifs().begin() );
 638   BOOST_CHECK( motif_end == s1.motifs().end() );
 639   BOOST_CHECK( motif_i == motif_end );
 640
 641   // this shouldn't show up
 642   s1.add_motif(bogus);
 643   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 644   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 645
 646   s1.add_motif(m);
 647   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 648   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 649
 650   for(motif_i = s1.motifs().begin();
 651       motif_i != s1.motifs().end();
 652       ++motif_i)
 653   {
 654     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 655     BOOST_CHECK_EQUAL( motif_i->name, m);
 656     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 657   }
 658
 659   s1.clear_motifs();
 660   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 661
 662   /* FIXME: enable this when i find a way of passing storing the motif name
 663   // does our annotation travel?
 664   Sequence motif_seq(m);
 665   motif_seq.set_fasta_header("hi");
 666   s1.add_motif(motif_seq);
 667
 668   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 669   for(motif_i = s1.motifs().begin();
 670       motif_i != s1.motifs().end();
 671       ++motif_i)
 672   {
 673     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 674     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 675     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 676   }
 677   */
 678 }
 679
 680 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 681 {
 682   // when searching for a motif on a subsequence we should
 683   // only search the subsequence ticket:199
 684   string aaaa("AAAA");
 685   string cccc("CCCC");
 686   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 687
 688   // this shouldn't show up
 689   s1.add_motif(cccc);
 690   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 691
 692   s1.add_motif(aaaa);
 693   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 694
 695   Sequence subseq1 = s1.subseq(4,5);
 696   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 697   subseq1.clear_motifs();
 698   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 699   // this is outside of our subsequence, and so shouldn't be found
 700   subseq1.add_motif(aaaa);
 701   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 702
 703   subseq1.add_motif(cccc);
 704   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 705   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 706   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 707   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 708   BOOST_CHECK_EQUAL(motif_i->end, 5);
 709 }
 710
 711 BOOST_AUTO_TEST_CASE( annot_test )
 712 {
 713   annot a(0, 10, "test", "thing");
 714
 715   BOOST_CHECK_EQUAL( a.begin, 0 );
 716   BOOST_CHECK_EQUAL( a.end,   10 );
 717   BOOST_CHECK_EQUAL( a.type,  "test" );
 718   BOOST_CHECK_EQUAL( a.name,  "thing" );
 719
 720   motif m(10, "AAGGCC");
 721   BOOST_CHECK_EQUAL( m.begin, 10 );
 722   BOOST_CHECK_EQUAL( m.type, "motif" );
 723   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 724   BOOST_CHECK_EQUAL( m.end,  10+6 );
 725 }
 726
 727 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 728 {
 729   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 730            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 731            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 732            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 733            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 734            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 735            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 736            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 737   string gc("GCCCCC");
 738   string gga("GGACACCTC");
 739   Sequence seq(s, reduced_dna_alphabet);
 740
 741   std::list<Sequence> query_list;
 742   std::list<string> string_list;
 743   query_list.push_back(Sequence(gc));
 744   string_list.push_back(gc);
 745   query_list.push_back(Sequence(gga));
 746   string_list.push_back(gga);
 747
 748   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 749   seq.find_sequences(query_list.begin(), query_list.end());
 750
 751   int count = 0;
 752   for(list<string>::iterator string_i = string_list.begin();
 753       string_i != string_list.end();
 754       ++string_i)
 755   {
 756     string::size_type pos=0;
 757     while(pos != string::npos) {
 758       pos = s.find(*string_i, pos);
 759       if (pos != string::npos) {
 760         ++count;
 761         ++pos;
 762       }
 763     }
 764   }
 765   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 766   const std::list<annot> &a = seq.annotations();
 767   for (std::list<annot>::const_iterator annot_i = a.begin();
 768        annot_i != a.end();
 769        ++annot_i)
 770   {
 771     int count = annot_i->end - annot_i->begin ;
 772   }
 773 }
 774
 775 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 776 {
 777   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 778            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 779            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 780            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 781            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 782            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 783            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 784            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 785   Sequence seq(s, reduced_dna_alphabet);
 786
 787
 788   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 789   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 790   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 791   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 792   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 793
 794   Sequence subseq = seq.subseq(5, 10);
 795   const list<annot> annots = subseq.annotations();
 796   // generate some ground truth
 797   list<annot> correct;
 798   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 799   correct.push_back(annot(5,10, "10-20", "10-20"));
 800   correct.push_back(annot(0,10, "0-20",  "0-20"));
 801   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 802   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 803
 804   list<annot>::iterator correct_i = correct.begin();
 805   list<annot>::const_iterator annot_i = annots.begin();
 806   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 807   {
 808     BOOST_CHECK( *annot_i == *correct_i );
 809   }
 810 }
 811
 812 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 813 {
 814   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 815            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 816            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 817            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 818            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 819            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 820            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 821            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 822   Sequence seq(s, reduced_dna_alphabet);
 823
 824   // starting conditions
 825   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 826   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 827   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 828   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 829   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 830   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 831   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 832   seq.add_motif("CCGTCCC");
 833   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 834   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 835   seq.clear_motifs();
 836   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 837   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 838 }
 839
 840 BOOST_AUTO_TEST_CASE( out_operator )
 841 {
 842   string s("AAGGCCTT");
 843   Sequence seq(s, reduced_dna_alphabet);
 844
 845   ostringstream buf;
 846   buf << s;
 847   BOOST_CHECK_EQUAL( s, buf.str() );
 848 }
 849
 850 BOOST_AUTO_TEST_CASE( get_name )
 851 {
 852   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 853
 854   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 855   seq.set_species("hooman"); // anyone remember tradewars?
 856   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 857   seq.set_fasta_header("fasta human");
 858   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 859 }
 860
 861 BOOST_AUTO_TEST_CASE( serialize_simple )
 862 {
 863   std::string seq_string = "AAGGCCTT";
 864   Sequence seq(seq_string, reduced_dna_alphabet);
 865   seq.set_species("ribbet");
 866   std::ostringstream oss;
 867   // allocate/deallocate serialization components
 868   {
 869     boost::archive::text_oarchive oarchive(oss);
 870     const Sequence& const_seq(seq);
 871     BOOST_CHECK_EQUAL(seq, const_seq);
 872     oarchive << const_seq;
 873   }
 874   Sequence seq_loaded;
 875   {
 876     std::istringstream iss(oss.str());
 877     boost::archive::text_iarchive iarchive(iss);
 878     iarchive >> seq_loaded;
 879   }
 880   BOOST_CHECK_EQUAL(seq_loaded, seq);
 881   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 882 }
 883
 884 BOOST_AUTO_TEST_CASE( serialize_tree )
 885 {
 886   std::string seq_string = "AAGGCCTT";
 887   Sequence seq(seq_string, reduced_dna_alphabet);
 888   seq.set_species("ribbet");
 889   seq.add_motif("AA");
 890   seq.add_motif("GC");
 891   annot a1(6,7,"t","t");
 892   seq.add_annotation(a1);
 893
 894   std::ostringstream oss;
 895   // allocate/deallocate serialization components
 896   {
 897     boost::archive::text_oarchive oarchive(oss);
 898     const Sequence& const_seq(seq);
 899     BOOST_CHECK_EQUAL(seq, const_seq);
 900     oarchive << const_seq;
 901   }
 902
 903   Sequence seq_loaded;
 904   {
 905     std::istringstream iss(oss.str());
 906     boost::archive::text_iarchive iarchive(iss);
 907     iarchive >> seq_loaded;
 908   }
 909   BOOST_CHECK_EQUAL(seq_loaded, seq);
 910 }
 911
 912 // this writes out an "old" style annotated sequence
 913 // with annotations attached as "motifs" and "annots"
 914 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 915 {
 916   std::string seq_string = "AAGGCCTT";
 917   Sequence seq(seq_string, reduced_dna_alphabet);
 918   seq.set_species("ribbet");
 919   seq.add_motif("AA");
 920   seq.add_motif("GC");
 921   annot a1(6,7,"t","t");
 922   seq.add_annotation(a1);
 923
 924   std::ostringstream oss;
 925   // allocate/deallocate serialization components
 926   {
 927     boost::archive::xml_oarchive oarchive(oss);
 928     const Sequence& const_seq(seq);
 929     BOOST_CHECK_EQUAL(seq, const_seq);
 930     oarchive << boost::serialization::make_nvp("root", const_seq);
 931   }
 932   Sequence seq_loaded;
 933   {
 934     std::istringstream iss(oss.str());
 935     boost::archive::xml_iarchive iarchive(iss);
 936     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 937   }
 938   BOOST_CHECK_EQUAL(seq_loaded, seq);
 939 }
 940
 941 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 942 {
 943   std::string seq_string = "AAGGCCTT";
 944   Sequence seq1(seq_string, reduced_dna_alphabet);
 945   Sequence seq2(seq1);
 946
 947   std::ostringstream oss;
 948   // allocate/deallocate serialization components
 949   {
 950     boost::archive::xml_oarchive oarchive(oss);
 951     const Sequence& const_seq1(seq1);
 952     const Sequence& const_seq2(seq2);
 953     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 954     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 955   }
 956   //std::cout << "xml: " << oss.str() << std::endl;
 957   Sequence seq1_loaded;
 958   Sequence seq2_loaded;
 959   {
 960     std::istringstream iss(oss.str());
 961     boost::archive::xml_iarchive iarchive(iss);
 962     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 963     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 964   }
 965   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 966   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 967   // test if our pointers are the same
 968   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
 969 }