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 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  37 {
  38         Sequence s;
  39         // make sure that retrieving the sequence doesn't throw an error
  40         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  41 }
  42
  43 BOOST_AUTO_TEST_CASE( sequence_from_string )
  44 {
  45   std::string str1("AAAT");
  46   Sequence seq1(str1);
  47   BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
  48 }
  49
  50 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  51 {
  52   std::string str1("AAAAT");
  53   Sequence seq1(str1);
  54   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  55
  56   std::string str2("AATTGGCC");
  57   Sequence seq2(str2);
  58   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  59 }
  60
  61 //! when we try to load a missing file, do we get an error?
  62 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  63 {
  64   Sequence s;
  65   // there should be errors when we try to load something that doesn't exist
  66   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  67   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  68 }
  69
  70 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  71 {
  72   string header(">Header");
  73   string line1("AAAAGGGGCCCCTTTTT");
  74   string line2("AAAAGGGGCCCCTTTTT");
  75   int seq_len = line1.size() + line2.size();
  76
  77   stringstream cr;
  78   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  79   Sequence seq_cr;
  80   seq_cr.load_fasta(cr);
  81
  82   stringstream crlf;
  83   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  84   Sequence seq_crlf;
  85   seq_crlf.load_fasta(crlf);
  86
  87   stringstream lf;
  88   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  89   Sequence seq_lf;
  90   seq_lf.load_fasta(lf);
  91
  92   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  93   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  94   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  95 }
  96
  97
  98 //! Do simple operations work correctly?
  99 BOOST_AUTO_TEST_CASE( sequence_filter )
 100 {
 101   const char *core_seq = "AATTGGCC";
 102   Sequence s1(core_seq, reduced_dna_alphabet);
 103   BOOST_CHECK_EQUAL(s1, core_seq);
 104
 105   Sequence s2("aattggcc", reduced_dna_alphabet);
 106   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
 107   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
 108   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
 109   BOOST_CHECK_EQUAL(s2.size(), s2.size());
 110   //We're currently forcing sequences to uppercase
 111   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
 112
 113   Sequence s3("asdfg", reduced_dna_alphabet);
 114   BOOST_CHECK_EQUAL(s3, "ANNNG");
 115   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
 116
 117   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
 118   BOOST_CHECK_EQUAL(s3, "AA");
 119   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
 120   BOOST_CHECK_EQUAL( s3, "GG");
 121   s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
 122   BOOST_CHECK_EQUAL( s3, "CCTT");
 123
 124   s3 = "AAGGFF";
 125   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 126 }
 127
 128 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 129 {
 130   std::string agct("AGCT");
 131   Sequence seq(agct, nucleic_alphabet);
 132   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 133   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 134
 135   std::string bdv("BDv");
 136   Sequence seq_bdv(bdv, nucleic_alphabet);
 137   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 138   // forcing sequence to upper case
 139   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 140                     boost::algorithm::to_upper_copy(bdv));
 141
 142 }
 143
 144 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 145 {
 146   std::string agct("AGCT");
 147   Sequence seq(agct);
 148   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 149   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 150   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 151   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 152   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 153   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 154
 155   std::string bdv("BDv");
 156   Sequence seq_bdv(bdv);
 157   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 158   // default alphabet only allows AGCTUN
 159   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 160 }
 161
 162 BOOST_AUTO_TEST_CASE( subseq_names )
 163 {
 164   Sequence s1("AAGGCCTT", reduced_dna_alphabet);
 165   s1.set_species("species");
 166   s1.set_fasta_header("a fasta header");
 167   Sequence s2 = s1.subseq(2,2);
 168   BOOST_CHECK_EQUAL(s2, "GG");
 169   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 170   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 171 }
 172
 173 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 174 {
 175   Sequence s1;
 176   BOOST_CHECK_EQUAL( s1.start(), 0 );
 177   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 178
 179   std::string seq_string("AAGGCCTT");
 180   Sequence s2(seq_string, reduced_dna_alphabet);
 181   BOOST_CHECK_EQUAL( s2.start(), 0 );
 182   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 183
 184   std::string s3seq_string = seq_string.substr(2,3);
 185   Sequence s3 = s2.subseq(2,3);
 186   BOOST_CHECK_EQUAL( s3.start(), 2);
 187   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 188   BOOST_CHECK_EQUAL( s3.size(), 3);
 189   BOOST_CHECK_EQUAL( s3, s3seq_string);
 190
 191   std::string s4seq_string = s3seq_string.substr(1,1);
 192   Sequence s4 = s3.subseq(1,1);
 193   BOOST_CHECK_EQUAL( s4.start(), 1 );
 194   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 195   BOOST_CHECK_EQUAL( s4.size(), 1);
 196   BOOST_CHECK_EQUAL( s4, s4seq_string);
 197 }
 198
 199 //! Can we load data from a file
 200 BOOST_AUTO_TEST_CASE( sequence_load )
 201 {
 202   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 203   seq_path /=  "human_mck_pro.fa";
 204   Sequence s;
 205   s.load_fasta(seq_path, reduced_dna_alphabet);
 206   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 207   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 208   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 209                                     "muscle creatine kinase gene (CKMM), "
 210                                     "5' flank");
 211 }
 212
 213 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 214 {
 215   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 216   seq_path /= "broken.fa";
 217   bool exception_thrown = false;
 218   std::string exception_filename;
 219   Sequence s;
 220   try {
 221     s.load_fasta(seq_path);
 222   } catch(sequence_invalid_load_error e) {
 223     exception_thrown = true;
 224     size_t native_string_size = seq_path.native_file_string().size();
 225     std:string estr(e.what());
 226     BOOST_REQUIRE(estr.size() > native_string_size);
 227     std::copy(estr.begin(), estr.begin()+native_string_size,
 228               std::back_inserter(exception_filename));
 229   }
 230   BOOST_CHECK_EQUAL(exception_thrown, true);
 231   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 232 }
 233
 234 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 235 {
 236   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 237   seq_path /= "mouse_mck_pro.fa";
 238   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 239   annot_path /= "broken.annot";
 240   bool exception_thrown = false;
 241   Sequence s;
 242   s.load_fasta(seq_path);
 243
 244   std::string exception_filename;
 245   try {
 246     s.load_annot(annot_path, 0, 0);
 247   } catch(annotation_load_error e) {
 248     exception_thrown = true;
 249     std:string estr(e.what());
 250     size_t native_string_size = annot_path.native_file_string().size();
 251     BOOST_REQUIRE(estr.size() > native_string_size);
 252     std::copy(estr.begin(), estr.begin()+native_string_size,
 253               std::back_inserter(exception_filename));
 254   }
 255   BOOST_CHECK_EQUAL(exception_thrown, true);
 256   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 257 }
 258
 259 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 260 {
 261   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 262   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 263   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 264   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 265   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 266   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 267   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 268   std::stringstream garbage_fasta(garbage_string);
 269
 270   Sequence s;
 271   s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
 272   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 273                                  reduced_dna_alphabet),
 274                     sequence_invalid_load_error);
 275   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 276                                  reduced_dna_alphabet),
 277                     sequence_invalid_load_error);
 278   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 279                                  reduced_dna_alphabet),
 280                     sequence_invalid_load_error);
 281
 282 }
 283
 284 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 285 {
 286   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 287   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 288   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 289   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 290   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 291   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 292   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 293   std::stringstream garbage_fasta(garbage_string);
 294
 295   Sequence s;
 296   s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
 297   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 298                                  reduced_rna_alphabet),
 299                     sequence_invalid_load_error);
 300   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 301                                  reduced_rna_alphabet),
 302                     sequence_invalid_load_error);
 303   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 304                                  reduced_rna_alphabet),
 305                     sequence_invalid_load_error);
 306 }
 307
 308 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 309 {
 310   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 311   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 312   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 313   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 314   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 315   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 316   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 317   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 318   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 319   std::stringstream garbage_fasta(garbage_string);
 320
 321   Sequence s;
 322   Sequence specific;
 323   // there's two copies of reduced_rna_fasta because i didn't feel like
 324   // figuring out how to properly reset the read pointer in a stringstream
 325   s.load_fasta(reduced_rna_fasta1);
 326   specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
 327   BOOST_CHECK_EQUAL(s, specific);
 328
 329   s.load_fasta(reduced_dna_fasta1);
 330   specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
 331   BOOST_CHECK_EQUAL(s, specific);
 332
 333   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 334                     sequence_invalid_load_error);
 335   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 336                     sequence_invalid_load_error);
 337 }
 338
 339 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 340 {
 341   std::string fasta_file(
 342     ">gi|10129974|gb|AF188002.1|AF188002\n"
 343     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 344     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 345     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 346     ">gi|1621|emb|X55146.1|OCMCK1\n"
 347     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 348   );
 349   istringstream seq1_file(fasta_file);
 350   Sequence seq1;
 351   seq1.load_fasta(seq1_file, 1, 0, 0);
 352   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 353
 354   istringstream seq2_file(fasta_file);
 355   Sequence seq2;
 356   seq2.load_fasta(seq2_file, 2, 0, 0);
 357   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 358
 359   istringstream seq3_file(fasta_file);
 360   Sequence seq3;
 361   seq3.load_fasta(seq3_file, 3, 0, 0);
 362   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 363 }
 364
 365 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 366 {
 367   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 368   Sequence seq(iupac_symbols, nucleic_alphabet);
 369   Sequence seqr = seq.rev_comp();
 370
 371   BOOST_CHECK( seq != seqr );
 372   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 373   // forcing sequence to upper case
 374   BOOST_CHECK_EQUAL( seq.get_sequence(),
 375                      boost::algorithm::to_upper_copy(iupac_symbols) );
 376 }
 377
 378 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 379 {
 380   std::string dna_str("AGCTN");
 381   Sequence dna_seq(dna_str, reduced_dna_alphabet);
 382   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 383   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 384 }
 385
 386 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 387 {
 388   std::string rna_str("AGCUN");
 389   Sequence rna_seq(rna_str, reduced_rna_alphabet);
 390   BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
 391   BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
 392                     rna_seq.rev_comp().rev_comp().get_sequence());
 393 }
 394
 395 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 396 {
 397   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 398   Sequence seq(dna_str, reduced_dna_alphabet);
 399   Sequence subseq = seq.subseq(8,4);
 400   BOOST_CHECK_EQUAL( subseq, "AAGG");
 401   Sequence rev_subseq = subseq.rev_comp();
 402   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 403   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 404 }
 405
 406 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 407 {
 408   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 409   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 410   Sequence seq(dna_str);
 411   std::string seq_reversed(seq.rbegin(), seq.rend());
 412   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 413
 414   std::string substr = dna_str.substr(8,4);
 415   Sequence subseq = seq.subseq(8,4);
 416   BOOST_CHECK_EQUAL(substr, subseq);
 417
 418   std::string substr_reversed(substr.rbegin(), substr.rend());
 419   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 420   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 421 }
 422
 423 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 424 {
 425   // so what happens with reverse interators when we have no sequence?
 426   Sequence seq1;
 427   Sequence seq2;
 428   Sequence seq3("AGCT");
 429
 430   // all the empty sequences should have equal iterators
 431   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 432   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 433
 434   // none of the seq1 iterators should equal any of the seq3 iterators
 435   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 436   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 437   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 438   BOOST_CHECK(seq1.rend() != seq3.rend());
 439
 440   // seq3 iterators should work
 441   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 442
 443 }
 444
 445 BOOST_AUTO_TEST_CASE( annotation_load )
 446 {
 447   string annot_data = "human\n"
 448                       "0 10 name   type\n"
 449                       "10 20 myf7\n"
 450                       "20 30 myod\n"
 451                       "50\t55 anothername\n"
 452                       "60 50 backward\n"
 453                       ">ident3 asdf\n"
 454                       "GCT\n"
 455                       "gCTn\n"
 456                       "75\t90\tname2\ttype2\n"
 457                       "100 120 name-asdf type!@#$%\n"
 458                       ;
 459   string s(100, 'A');
 460   s += "GCTGCTAATT";
 461   Sequence seq(s, reduced_dna_alphabet);
 462
 463   //istringstream annot_stream(annot_data);
 464   seq.parse_annot(annot_data, 0, 0);
 465   std::list<annot> annots_list = seq.annotations();
 466   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 467   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 468   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 469   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 470   BOOST_CHECK_EQUAL( annots[0].type, "type");
 471   BOOST_CHECK_EQUAL( annots[0].name, "name");
 472   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 473   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 474   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 475   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 476   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 477   BOOST_CHECK_EQUAL( annots[5].end, 90);
 478   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 479   BOOST_CHECK_EQUAL( annots[6].end, 120);
 480   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 481   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 482   // sequence defined annotations will always be after the
 483   // absolute positions
 484   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 485   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 486
 487   //BOOST_CHECK_EQUAL( annots
 488 }
 489
 490 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 491 {
 492   string annot_data = "human\n"
 493                       "0 10 name   type\n"
 494                       "blah60 50 backward\n"
 495                       ">ident3 asdf\n"
 496                       "GCT\n"
 497                       "gCTn\n"
 498                       ;
 499   string s(100, 'A');
 500   s += "GCTGCTAATT";
 501   Sequence seq(s, reduced_dna_alphabet);
 502
 503   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 504   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 505   }
 506
 507 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 508 {
 509   // this actually is basically what's returned by UCSC
 510   // (well actually with some of the sequence and copies of fasta blocks
 511   // removed to make the example shorter
 512   string annot_data = "\n"
 513     "<PRE>\n"
 514     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 515     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 516     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 517     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 518     "</PRE>\n"
 519     "\n"
 520     "</BODY>\n"
 521     "</HTML>\n"
 522     ;
 523
 524   string s =
 525     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 526     "AAAAA"
 527     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 528   Sequence seq(s, reduced_dna_alphabet);
 529   seq.parse_annot(annot_data);
 530   std::list<annot> annots = seq.annotations();
 531   BOOST_CHECK_EQUAL( annots.size(), 2);
 532 }
 533
 534 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 535 {
 536   string annot_data = "0 10 name   type\n"
 537                       "10 20 myf7\n"
 538                       "20 30 myod\n"
 539                       "50\t55 anothername\n"
 540                       "60 50 backward\n"
 541                       ">ident3 asdf\n"
 542                       "GCT\n"
 543                       "gCTn\n"
 544                       "75\t90\tname2\ttype2\n"
 545                       "100 120 name-asdf type!@#$%\n"
 546                       ;
 547   string s(100, 'A');
 548   s += "GCTGCTAATT";
 549   Sequence seq(s, reduced_dna_alphabet);
 550
 551   //istringstream annot_stream(annot_data);
 552   seq.parse_annot(annot_data, 0, 0);
 553   std::list<annot> annots_list = seq.annotations();
 554   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 555   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 556   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 557   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 558   BOOST_CHECK_EQUAL( annots[0].type, "type");
 559 }
 560
 561 // ticket:83 when you try to load a sequence from a file that doesn't
 562 // have fasta headers it crashes.
 563 BOOST_AUTO_TEST_CASE( sequence_past_end )
 564 {
 565   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 566   seq_path /=  "misformated_seq.fa";
 567   Sequence s;
 568   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 569 }
 570
 571 BOOST_AUTO_TEST_CASE ( sequence_empty )
 572 {
 573
 574   Sequence s;
 575   BOOST_CHECK_EQUAL( s.empty(), true );
 576   s = "AAAGGG";
 577   BOOST_CHECK_EQUAL( s.empty(), false );
 578   s.clear();
 579   BOOST_CHECK_EQUAL( s.empty(), true);
 580   s = "";
 581   BOOST_CHECK_EQUAL( s.empty(), true);
 582 }
 583
 584 BOOST_AUTO_TEST_CASE ( sequence_size )
 585 {
 586
 587   Sequence s;
 588   BOOST_CHECK_EQUAL( s.size(), 0);
 589   std::string seq_string("AAAGGG");
 590   s = seq_string;
 591   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 592   s.clear();
 593   BOOST_CHECK_EQUAL( s.size(), 0);
 594   s = "";
 595   BOOST_CHECK_EQUAL( s.size(), 0);
 596 }
 597
 598 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 599 {
 600   Sequence szero("", reduced_dna_alphabet);
 601   BOOST_CHECK_EQUAL(szero.empty(), true);
 602   BOOST_CHECK_EQUAL(szero, szero);
 603   BOOST_CHECK_EQUAL(szero, "");
 604
 605   Sequence sclear("AGCT", reduced_dna_alphabet);
 606   sclear.clear();
 607   BOOST_CHECK_EQUAL(sclear.empty(), true);
 608   BOOST_CHECK_EQUAL(sclear, sclear);
 609   BOOST_CHECK_EQUAL(sclear, szero);
 610   BOOST_CHECK_EQUAL(sclear, "");
 611
 612 }
 613 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 614 {
 615   std::string seq_string = "AAGGCCTTNNTATA";
 616   Sequence s(seq_string, reduced_dna_alphabet);
 617   const Sequence cs(s);
 618   std::string::size_type count = 0;
 619
 620   std::string::iterator str_itor;
 621   Sequence::const_iterator s_itor;
 622   Sequence::const_iterator cs_itor;
 623
 624   for( str_itor = seq_string.begin(),
 625        s_itor   = s.begin(),
 626        cs_itor  = cs.begin();
 627        str_itor != seq_string.end() and
 628        s_itor   != s.end() and
 629        cs_itor  != cs.end();
 630        ++str_itor, ++s_itor, ++cs_itor, ++count)
 631   {
 632     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 633     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 634     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 635   }
 636   BOOST_CHECK_EQUAL( seq_string.size(), count );
 637   BOOST_CHECK_EQUAL( s.size(), count );
 638   BOOST_CHECK_EQUAL( cs.size(), count );
 639 }
 640
 641 BOOST_AUTO_TEST_CASE( sequence_motifs )
 642 {
 643   string m("AAAA");
 644   string bogus("AATTGGAA");
 645   Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
 646
 647   list<motif>::const_iterator motif_i = s1.motifs().begin();
 648   list<motif>::const_iterator motif_end = s1.motifs().end();
 649
 650   // do our iterators work?
 651   BOOST_CHECK( motif_i == s1.motifs().begin() );
 652   BOOST_CHECK( motif_end == s1.motifs().end() );
 653   BOOST_CHECK( motif_i == motif_end );
 654
 655   // this shouldn't show up
 656   s1.add_motif(bogus);
 657   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 658   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 659
 660   s1.add_motif(m);
 661   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 662   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 663
 664   for(motif_i = s1.motifs().begin();
 665       motif_i != s1.motifs().end();
 666       ++motif_i)
 667   {
 668     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 669     BOOST_CHECK_EQUAL( motif_i->name, m);
 670     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 671   }
 672
 673   s1.clear_motifs();
 674   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 675
 676   /* FIXME: enable this when i find a way of passing storing the motif name
 677   // does our annotation travel?
 678   Sequence motif_seq(m);
 679   motif_seq.set_fasta_header("hi");
 680   s1.add_motif(motif_seq);
 681
 682   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 683   for(motif_i = s1.motifs().begin();
 684       motif_i != s1.motifs().end();
 685       ++motif_i)
 686   {
 687     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 688     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 689     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 690   }
 691   */
 692 }
 693
 694 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 695 {
 696   // when searching for a motif on a subsequence we should
 697   // only search the subsequence ticket:199
 698   string aaaa("AAAA");
 699   string cccc("CCCC");
 700   Sequence s1("AAAANCCCC", reduced_dna_alphabet);
 701
 702   // this shouldn't show up
 703   s1.add_motif(cccc);
 704   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 705
 706   s1.add_motif(aaaa);
 707   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 708
 709   Sequence subseq1 = s1.subseq(4,5);
 710   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 711   subseq1.clear_motifs();
 712   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 713   // this is outside of our subsequence, and so shouldn't be found
 714   subseq1.add_motif(aaaa);
 715   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 716
 717   subseq1.add_motif(cccc);
 718   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 719   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 720   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 721   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 722   BOOST_CHECK_EQUAL(motif_i->end, 5);
 723 }
 724
 725 BOOST_AUTO_TEST_CASE( annot_test )
 726 {
 727   annot a(0, 10, "test", "thing");
 728
 729   BOOST_CHECK_EQUAL( a.begin, 0 );
 730   BOOST_CHECK_EQUAL( a.end,   10 );
 731   BOOST_CHECK_EQUAL( a.type,  "test" );
 732   BOOST_CHECK_EQUAL( a.name,  "thing" );
 733
 734   motif m(10, "AAGGCC");
 735   BOOST_CHECK_EQUAL( m.begin, 10 );
 736   BOOST_CHECK_EQUAL( m.type, "motif" );
 737   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 738   BOOST_CHECK_EQUAL( m.end,  10+6 );
 739 }
 740
 741 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 742 {
 743   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 744            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 745            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 746            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 747            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 748            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 749            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 750            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 751   string gc("GCCCCC");
 752   string gga("GGACACCTC");
 753   Sequence seq(s, reduced_dna_alphabet);
 754
 755   std::list<Sequence> query_list;
 756   std::list<string> string_list;
 757   query_list.push_back(Sequence(gc));
 758   string_list.push_back(gc);
 759   query_list.push_back(Sequence(gga));
 760   string_list.push_back(gga);
 761
 762   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 763   seq.find_sequences(query_list.begin(), query_list.end());
 764
 765   int count = 0;
 766   for(list<string>::iterator string_i = string_list.begin();
 767       string_i != string_list.end();
 768       ++string_i)
 769   {
 770     string::size_type pos=0;
 771     while(pos != string::npos) {
 772       pos = s.find(*string_i, pos);
 773       if (pos != string::npos) {
 774         ++count;
 775         ++pos;
 776       }
 777     }
 778   }
 779   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 780   const std::list<annot> &a = seq.annotations();
 781   for (std::list<annot>::const_iterator annot_i = a.begin();
 782        annot_i != a.end();
 783        ++annot_i)
 784   {
 785     int count = annot_i->end - annot_i->begin ;
 786   }
 787 }
 788
 789 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 790 {
 791   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 792            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 793            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 794            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 795            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 796            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 797            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 798            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 799   Sequence seq(s, reduced_dna_alphabet);
 800
 801
 802   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 803   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 804   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 805   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 806   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 807
 808   Sequence subseq = seq.subseq(5, 10);
 809   const list<annot> annots = subseq.annotations();
 810   // generate some ground truth
 811   list<annot> correct;
 812   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 813   correct.push_back(annot(5,10, "10-20", "10-20"));
 814   correct.push_back(annot(0,10, "0-20",  "0-20"));
 815   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 816   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 817
 818   list<annot>::iterator correct_i = correct.begin();
 819   list<annot>::const_iterator annot_i = annots.begin();
 820   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 821   {
 822     BOOST_CHECK( *annot_i == *correct_i );
 823   }
 824 }
 825
 826 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 827 {
 828   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 829            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 830            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 831            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 832            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 833            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 834            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 835            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 836   Sequence seq(s, reduced_dna_alphabet);
 837
 838   // starting conditions
 839   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 840   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 841   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 842   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 843   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 844   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 845   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 846   seq.add_motif("CCGTCCC");
 847   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 848   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 849   seq.clear_motifs();
 850   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 851   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 852 }
 853
 854 BOOST_AUTO_TEST_CASE( out_operator )
 855 {
 856   string s("AAGGCCTT");
 857   Sequence seq(s, reduced_dna_alphabet);
 858
 859   ostringstream buf;
 860   buf << s;
 861   BOOST_CHECK_EQUAL( s, buf.str() );
 862 }
 863
 864 BOOST_AUTO_TEST_CASE( get_name )
 865 {
 866   Sequence seq("AAGGCCTT", reduced_dna_alphabet);
 867
 868   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 869   seq.set_species("hooman"); // anyone remember tradewars?
 870   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 871   seq.set_fasta_header("fasta human");
 872   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 873 }
 874
 875 BOOST_AUTO_TEST_CASE( serialize_simple )
 876 {
 877   std::string seq_string = "AAGGCCTT";
 878   Sequence seq(seq_string, reduced_dna_alphabet);
 879   seq.set_species("ribbet");
 880   std::ostringstream oss;
 881   // allocate/deallocate serialization components
 882   {
 883     boost::archive::text_oarchive oarchive(oss);
 884     const Sequence& const_seq(seq);
 885     BOOST_CHECK_EQUAL(seq, const_seq);
 886     oarchive << const_seq;
 887   }
 888   Sequence seq_loaded;
 889   {
 890     std::istringstream iss(oss.str());
 891     boost::archive::text_iarchive iarchive(iss);
 892     iarchive >> seq_loaded;
 893   }
 894   BOOST_CHECK_EQUAL(seq_loaded, seq);
 895   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 896 }
 897
 898 BOOST_AUTO_TEST_CASE( serialize_tree )
 899 {
 900   std::string seq_string = "AAGGCCTT";
 901   Sequence seq(seq_string, reduced_dna_alphabet);
 902   seq.set_species("ribbet");
 903   seq.add_motif("AA");
 904   seq.add_motif("GC");
 905   annot a1(6,7,"t","t");
 906   seq.add_annotation(a1);
 907
 908   std::ostringstream oss;
 909   // allocate/deallocate serialization components
 910   {
 911     boost::archive::text_oarchive oarchive(oss);
 912     const Sequence& const_seq(seq);
 913     BOOST_CHECK_EQUAL(seq, const_seq);
 914     oarchive << const_seq;
 915   }
 916
 917   Sequence seq_loaded;
 918   {
 919     std::istringstream iss(oss.str());
 920     boost::archive::text_iarchive iarchive(iss);
 921     iarchive >> seq_loaded;
 922   }
 923   BOOST_CHECK_EQUAL(seq_loaded, seq);
 924 }
 925
 926 // this writes out an "old" style annotated sequence
 927 // with annotations attached as "motifs" and "annots"
 928 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 929 {
 930   std::string seq_string = "AAGGCCTT";
 931   Sequence seq(seq_string, reduced_dna_alphabet);
 932   seq.set_species("ribbet");
 933   seq.add_motif("AA");
 934   seq.add_motif("GC");
 935   annot a1(6,7,"t","t");
 936   seq.add_annotation(a1);
 937
 938   std::ostringstream oss;
 939   // allocate/deallocate serialization components
 940   {
 941     boost::archive::xml_oarchive oarchive(oss);
 942     const Sequence& const_seq(seq);
 943     BOOST_CHECK_EQUAL(seq, const_seq);
 944     oarchive << boost::serialization::make_nvp("root", const_seq);
 945   }
 946   Sequence seq_loaded;
 947   {
 948     std::istringstream iss(oss.str());
 949     boost::archive::xml_iarchive iarchive(iss);
 950     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 951   }
 952   BOOST_CHECK_EQUAL(seq_loaded, seq);
 953 }
 954
 955 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 956 {
 957   std::string seq_string = "AAGGCCTT";
 958   Sequence seq1(seq_string, reduced_dna_alphabet);
 959   Sequence seq2(seq1);
 960
 961   std::ostringstream oss;
 962   // allocate/deallocate serialization components
 963   {
 964     boost::archive::xml_oarchive oarchive(oss);
 965     const Sequence& const_seq1(seq1);
 966     const Sequence& const_seq2(seq2);
 967     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 968     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 969   }
 970   //std::cout << "xml: " << oss.str() << std::endl;
 971   Sequence seq1_loaded;
 972   Sequence seq2_loaded;
 973   {
 974     std::istringstream iss(oss.str());
 975     boost::archive::xml_iarchive iarchive(iss);
 976     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 977     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 978   }
 979   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 980   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 981   // test if our pointers are the same
 982   BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());
 983 }