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().get_sequence(), "NAGCU");
 378   BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
 379                     rna_seq.rev_comp().rev_comp().get_sequence());
 380 }
 381
 382 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 383 {
 384   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 385   Sequence seq(dna_str, reduced_dna_alphabet);
 386   Sequence subseq = seq.subseq(8,4);
 387   BOOST_CHECK_EQUAL( subseq, "AAGG");
 388   Sequence rev_subseq = subseq.rev_comp();
 389   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 390   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 391 }
 392
 393 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 394 {
 395   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 396   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 397   Sequence seq(dna_str);
 398   std::string seq_reversed(seq.rbegin(), seq.rend());
 399   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 400
 401   std::string substr = dna_str.substr(8,4);
 402   Sequence subseq = seq.subseq(8,4);
 403   BOOST_CHECK_EQUAL(substr, subseq);
 404
 405   std::string substr_reversed(substr.rbegin(), substr.rend());
 406   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 407   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 408 }
 409
 410 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 411 {
 412   // so what happens with reverse interators when we have no sequence?
 413   Sequence seq1;
 414   Sequence seq2;
 415   Sequence seq3("AGCT");
 416
 417   // all the empty sequences should have equal iterators
 418   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 419   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 420
 421   // none of the seq1 iterators should equal any of the seq3 iterators
 422   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 423   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 424   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 425   BOOST_CHECK(seq1.rend() != seq3.rend());
 426
 427   // seq3 iterators should work
 428   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 429
 430 }
 431
 432 BOOST_AUTO_TEST_CASE( annotation_load )
 433 {
 434   string annot_data = "human\n"
 435                       "0 10 name   type\n"
 436                       "10 20 myf7\n"
 437                       "20 30 myod\n"
 438                       "50\t55 anothername\n"
 439                       "60 50 backward\n"
 440                       ">ident3 asdf\n"
 441                       "GCT\n"
 442                       "gCTn\n"
 443                       "75\t90\tname2\ttype2\n"
 444                       "100 120 name-asdf type!@#$%\n"
 445                       ;
 446   string s(100, 'A');
 447   s += "GCTGCTAATT";
 448   Sequence seq(s, reduced_dna_alphabet);
 449
 450   //istringstream annot_stream(annot_data);
 451   seq.parse_annot(annot_data, 0, 0);
 452   std::list<annot> annots_list = seq.annotations();
 453   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 454   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 455   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 456   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 457   BOOST_CHECK_EQUAL( annots[0].type, "type");
 458   BOOST_CHECK_EQUAL( annots[0].name, "name");
 459   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 460   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 461   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 462   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 463   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 464   BOOST_CHECK_EQUAL( annots[5].end, 90);
 465   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 466   BOOST_CHECK_EQUAL( annots[6].end, 120);
 467   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 468   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 469   // sequence defined annotations will always be after the
 470   // absolute positions
 471   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 472   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 473
 474   //BOOST_CHECK_EQUAL( annots
 475 }
 476
 477 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 478 {
 479   string annot_data = "human\n"
 480                       "0 10 name   type\n"
 481                       "blah60 50 backward\n"
 482                       ">ident3 asdf\n"
 483                       "GCT\n"
 484                       "gCTn\n"
 485                       ;
 486   string s(100, 'A');
 487   s += "GCTGCTAATT";
 488   Sequence seq(s, reduced_dna_alphabet);
 489
 490   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 491   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 492   }
 493
 494 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 495 {
 496   // this actually is basically what's returned by UCSC
 497   // (well actually with some of the sequence and copies of fasta blocks
 498   // removed to make the example shorter
 499   string annot_data = "\n"
 500     "<PRE>\n"
 501     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 502     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 503     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 504     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 505     "</PRE>\n"
 506     "\n"
 507     "</BODY>\n"
 508     "</HTML>\n"
 509     ;
 510
 511   string s =
 512     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 513     "AAAAA"
 514     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 515   Sequence seq(s, reduced_dna_alphabet);
 516   seq.parse_annot(annot_data);
 517   std::list<annot> annots = seq.annotations();
 518   BOOST_CHECK_EQUAL( annots.size(), 2);
 519 }
 520
 521 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 522 {
 523   string annot_data = "0 10 name   type\n"
 524                       "10 20 myf7\n"
 525                       "20 30 myod\n"
 526                       "50\t55 anothername\n"
 527                       "60 50 backward\n"
 528                       ">ident3 asdf\n"
 529                       "GCT\n"
 530                       "gCTn\n"
 531                       "75\t90\tname2\ttype2\n"
 532                       "100 120 name-asdf type!@#$%\n"
 533                       ;
 534   string s(100, 'A');
 535   s += "GCTGCTAATT";
 536   Sequence seq(s, reduced_dna_alphabet);
 537
 538   //istringstream annot_stream(annot_data);
 539   seq.parse_annot(annot_data, 0, 0);
 540   std::list<annot> annots_list = seq.annotations();
 541   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 542   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 543   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 544   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 545   BOOST_CHECK_EQUAL( annots[0].type, "type");
 546 }
 547
 548 // ticket:83 when you try to load a sequence from a file that doesn't
 549 // have fasta headers it crashes.
 550 BOOST_AUTO_TEST_CASE( sequence_past_end )
 551 {
 552   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 553   seq_path /=  "misformated_seq.fa";
 554   Sequence s;
 555   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 556 }
 557
 558 BOOST_AUTO_TEST_CASE ( sequence_empty )
 559 {
 560
 561   Sequence s;
 562   BOOST_CHECK_EQUAL( s.empty(), true );
 563   s = "AAAGGG";
 564   BOOST_CHECK_EQUAL( s.empty(), false );
 565   s.clear();
 566   BOOST_CHECK_EQUAL( s.empty(), true);
 567   s = "";
 568   BOOST_CHECK_EQUAL( s.empty(), true);
 569 }
 570
 571 BOOST_AUTO_TEST_CASE ( sequence_size )
 572 {
 573
 574   Sequence s;
 575   BOOST_CHECK_EQUAL( s.size(), 0);
 576   std::string seq_string("AAAGGG");
 577   s = seq_string;
 578   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 579   s.clear();
 580   BOOST_CHECK_EQUAL( s.size(), 0);
 581   s = "";
 582   BOOST_CHECK_EQUAL( s.size(), 0);
 583 }
 584
 585 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 586 {
 587   Sequence szero("", reduced_dna_alphabet);
 588   BOOST_CHECK_EQUAL(szero.empty(), true);
 589   BOOST_CHECK_EQUAL(szero, szero);
 590   BOOST_CHECK_EQUAL(szero, "");
 591
 592   Sequence sclear("AGCT", reduced_dna_alphabet);
 593   sclear.clear();
 594   BOOST_CHECK_EQUAL(sclear.empty(), true);
 595   BOOST_CHECK_EQUAL(sclear, sclear);
 596   BOOST_CHECK_EQUAL(sclear, szero);
 597   BOOST_CHECK_EQUAL(sclear, "");
 598
 599 }
 600 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 601 {
 602   std::string seq_string = "AAGGCCTTNNTATA";
 603   Sequence s(seq_string, reduced_dna_alphabet);
 604   const Sequence cs(s);
 605   std::string::size_type count = 0;
 606
 607   std::string::iterator str_itor;
 608   Sequence::const_iterator s_itor;
 609   Sequence::const_iterator cs_itor;
 610
 611   for( str_itor = seq_string.begin(),
 612        s_itor   = s.begin(),
 613        cs_itor  = cs.begin();
 614        str_itor != seq_string.end() and
 615        s_itor   != s.end() and
 616        cs_itor  != cs.end();
 617        ++str_itor, ++s_itor, ++cs_itor, ++count)
 618   {
 619     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 620     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 621     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 622   }
 623   BOOST_CHECK_EQUAL( seq_string.size(), count );
 624   BOOST_CHECK_EQUAL( s.size(), count );
 625   BOOST_CHECK_EQUAL( cs.size(), count );
 626 }
 627
 628 BOOST_AUTO_TEST_CASE( sequence_motifs )
 629 {
 630   string m("AAAA");
 631   string bogus("AATTGGAA");
 632   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 633
 634   list<motif>::const_iterator motif_i = s1.motifs().begin();
 635   list<motif>::const_iterator motif_end = s1.motifs().end();
 636
 637   // do our iterators work?
 638   BOOST_CHECK( motif_i == s1.motifs().begin() );
 639   BOOST_CHECK( motif_end == s1.motifs().end() );
 640   BOOST_CHECK( motif_i == motif_end );
 641
 642   // this shouldn't show up
 643   s1.add_motif(bogus);
 644   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 645   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 646
 647   s1.add_motif(m);
 648   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 649   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 650
 651   for(motif_i = s1.motifs().begin();
 652       motif_i != s1.motifs().end();
 653       ++motif_i)
 654   {
 655     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 656     BOOST_CHECK_EQUAL( motif_i->name, m);
 657     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 658   }
 659
 660   s1.clear_motifs();
 661   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 662
 663   /* FIXME: enable this when i find a way of passing storing the motif name
 664   // does our annotation travel?
 665   Sequence motif_seq(m);
 666   motif_seq.set_fasta_header("hi");
 667   s1.add_motif(motif_seq);
 668
 669   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 670   for(motif_i = s1.motifs().begin();
 671       motif_i != s1.motifs().end();
 672       ++motif_i)
 673   {
 674     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 675     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 676     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 677   }
 678   */
 679 }
 680
 681 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 682 {
 683   // when searching for a motif on a subsequence we should
 684   // only search the subsequence ticket:199
 685   string aaaa("AAAA");
 686   string cccc("CCCC");
 687   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 688
 689   // this shouldn't show up
 690   s1.add_motif(cccc);
 691   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 692
 693   s1.add_motif(aaaa);
 694   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 695
 696   Sequence subseq1 = s1.subseq(4,5);
 697   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 698   subseq1.clear_motifs();
 699   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 700   // this is outside of our subsequence, and so shouldn't be found
 701   subseq1.add_motif(aaaa);
 702   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 703
 704   subseq1.add_motif(cccc);
 705   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 706   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 707   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 708   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 709   BOOST_CHECK_EQUAL(motif_i->end, 5);
 710 }
 711
 712 BOOST_AUTO_TEST_CASE( annot_test )
 713 {
 714   annot a(0, 10, "test", "thing");
 715
 716   BOOST_CHECK_EQUAL( a.begin, 0 );
 717   BOOST_CHECK_EQUAL( a.end,   10 );
 718   BOOST_CHECK_EQUAL( a.type,  "test" );
 719   BOOST_CHECK_EQUAL( a.name,  "thing" );
 720
 721   motif m(10, "AAGGCC");
 722   BOOST_CHECK_EQUAL( m.begin, 10 );
 723   BOOST_CHECK_EQUAL( m.type, "motif" );
 724   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 725   BOOST_CHECK_EQUAL( m.end,  10+6 );
 726 }
 727
 728 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 729 {
 730   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 731            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 732            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 733            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 734            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 735            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 736            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 737            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 738   string gc("GCCCCC");
 739   string gga("GGACACCTC");
 740   Sequence seq(s, reduced_dna_alphabet);
 741
 742   std::list<Sequence> query_list;
 743   std::list<string> string_list;
 744   query_list.push_back(Sequence(gc));
 745   string_list.push_back(gc);
 746   query_list.push_back(Sequence(gga));
 747   string_list.push_back(gga);
 748
 749   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 750   seq.find_sequences(query_list.begin(), query_list.end());
 751
 752   int count = 0;
 753   for(list<string>::iterator string_i = string_list.begin();
 754       string_i != string_list.end();
 755       ++string_i)
 756   {
 757     string::size_type pos=0;
 758     while(pos != string::npos) {
 759       pos = s.find(*string_i, pos);
 760       if (pos != string::npos) {
 761         ++count;
 762         ++pos;
 763       }
 764     }
 765   }
 766   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 767   const std::list<annot> &a = seq.annotations();
 768   for (std::list<annot>::const_iterator annot_i = a.begin();
 769        annot_i != a.end();
 770        ++annot_i)
 771   {
 772     int count = annot_i->end - annot_i->begin ;
 773   }
 774 }
 775
 776 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 777 {
 778   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 779            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 780            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 781            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 782            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 783            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 784            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 785            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 786   Sequence seq(s, reduced_dna_alphabet);
 787
 788
 789   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 790   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 791   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 792   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 793   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 794
 795   Sequence subseq = seq.subseq(5, 10);
 796   const list<annot> annots = subseq.annotations();
 797   // generate some ground truth
 798   list<annot> correct;
 799   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 800   correct.push_back(annot(5,10, "10-20", "10-20"));
 801   correct.push_back(annot(0,10, "0-20",  "0-20"));
 802   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 803   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 804
 805   list<annot>::iterator correct_i = correct.begin();
 806   list<annot>::const_iterator annot_i = annots.begin();
 807   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 808   {
 809     BOOST_CHECK( *annot_i == *correct_i );
 810   }
 811 }
 812
 813 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 814 {
 815   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 816            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 817            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 818            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 819            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 820            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 821            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 822            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 823   Sequence seq(s, reduced_dna_alphabet);
 824
 825   // starting conditions
 826   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 827   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 828   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 829   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 830   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 831   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 832   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 833   seq.add_motif("CCGTCCC");
 834   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 835   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 836   seq.clear_motifs();
 837   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 838   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 839 }
 840
 841 BOOST_AUTO_TEST_CASE( out_operator )
 842 {
 843   string s("AAGGCCTT");
 844   Sequence seq(s, reduced_dna_alphabet);
 845
 846   ostringstream buf;
 847   buf << s;
 848   BOOST_CHECK_EQUAL( s, buf.str() );
 849 }
 850
 851 BOOST_AUTO_TEST_CASE( get_name )
 852 {
 853   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 854
 855   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 856   seq.set_species("hooman"); // anyone remember tradewars?
 857   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 858   seq.set_fasta_header("fasta human");
 859   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 860 }
 861
 862 BOOST_AUTO_TEST_CASE( serialize_simple )
 863 {
 864   std::string seq_string = "AAGGCCTT";
 865   Sequence seq(seq_string, reduced_dna_alphabet);
 866   seq.set_species("ribbet");
 867   std::ostringstream oss;
 868   // allocate/deallocate serialization components
 869   {
 870     boost::archive::text_oarchive oarchive(oss);
 871     const Sequence& const_seq(seq);
 872     BOOST_CHECK_EQUAL(seq, const_seq);
 873     oarchive << const_seq;
 874   }
 875   Sequence seq_loaded;
 876   {
 877     std::istringstream iss(oss.str());
 878     boost::archive::text_iarchive iarchive(iss);
 879     iarchive >> seq_loaded;
 880   }
 881   BOOST_CHECK_EQUAL(seq_loaded, seq);
 882   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 883 }
 884
 885 BOOST_AUTO_TEST_CASE( serialize_tree )
 886 {
 887   std::string seq_string = "AAGGCCTT";
 888   Sequence seq(seq_string, reduced_dna_alphabet);
 889   seq.set_species("ribbet");
 890   seq.add_motif("AA");
 891   seq.add_motif("GC");
 892   annot a1(6,7,"t","t");
 893   seq.add_annotation(a1);
 894
 895   std::ostringstream oss;
 896   // allocate/deallocate serialization components
 897   {
 898     boost::archive::text_oarchive oarchive(oss);
 899     const Sequence& const_seq(seq);
 900     BOOST_CHECK_EQUAL(seq, const_seq);
 901     oarchive << const_seq;
 902   }
 903
 904   Sequence seq_loaded;
 905   {
 906     std::istringstream iss(oss.str());
 907     boost::archive::text_iarchive iarchive(iss);
 908     iarchive >> seq_loaded;
 909   }
 910   BOOST_CHECK_EQUAL(seq_loaded, seq);
 911 }
 912
 913 // this writes out an "old" style annotated sequence
 914 // with annotations attached as "motifs" and "annots"
 915 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 916 {
 917   std::string seq_string = "AAGGCCTT";
 918   Sequence seq(seq_string, reduced_dna_alphabet);
 919   seq.set_species("ribbet");
 920   seq.add_motif("AA");
 921   seq.add_motif("GC");
 922   annot a1(6,7,"t","t");
 923   seq.add_annotation(a1);
 924
 925   std::ostringstream oss;
 926   // allocate/deallocate serialization components
 927   {
 928     boost::archive::xml_oarchive oarchive(oss);
 929     const Sequence& const_seq(seq);
 930     BOOST_CHECK_EQUAL(seq, const_seq);
 931     oarchive << boost::serialization::make_nvp("root", const_seq);
 932   }
 933   Sequence seq_loaded;
 934   {
 935     std::istringstream iss(oss.str());
 936     boost::archive::xml_iarchive iarchive(iss);
 937     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 938   }
 939   BOOST_CHECK_EQUAL(seq_loaded, seq);
 940 }
 941
 942 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 943 {
 944   std::string seq_string = "AAGGCCTT";
 945   Sequence seq1(seq_string, reduced_dna_alphabet);
 946   Sequence seq2(seq1);
 947
 948   std::ostringstream oss;
 949   // allocate/deallocate serialization components
 950   {
 951     boost::archive::xml_oarchive oarchive(oss);
 952     const Sequence& const_seq1(seq1);
 953     const Sequence& const_seq2(seq2);
 954     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 955     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 956   }
 957   //std::cout << "xml: " << oss.str() << std::endl;
 958   Sequence seq1_loaded;
 959   Sequence seq2_loaded;
 960   {
 961     std::istringstream iss(oss.str());
 962     boost::archive::xml_iarchive iarchive(iss);
 963     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 964     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 965   }
 966   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 967   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 968   // test if our pointers are the same
 969   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
 970 }