alg/test/test_sequence.cpp

   1 #include <boost/test/auto_unit_test.hpp>
   2 #include <boost/filesystem/path.hpp>
   3 #include <boost/filesystem/operations.hpp>
   4 namespace fs=boost::filesystem;
   5
   6 #include <boost/algorithm/string/case_conv.hpp>
   7
   8 #include <list>
   9 #include <iostream>
  10 #include <sstream>
  11
  12 #include <boost/archive/text_oarchive.hpp>
  13 #include <boost/archive/text_iarchive.hpp>
  14 #include <boost/archive/xml_oarchive.hpp>
  15 #include <boost/archive/xml_iarchive.hpp>
  16
  17 #include "alg/sequence.hpp"
  18 #include "mussa_exceptions.hpp"
  19
  20 using namespace std;
  21
  22 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  23 {
  24         Sequence s;
  25         // make sure that retrieving the sequence doesn't throw an error
  26         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  27 }
  28
  29 //! when we try to load a missing file, do we get an error?
  30 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  31 {
  32   Sequence s;
  33   // there should be errors when we try to load something that doesn't exist
  34   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  35   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  36 }
  37
  38 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  39 {
  40   string header(">Header");
  41   string line1("AAAAGGGGCCCCTTTTT");
  42   string line2("AAAAGGGGCCCCTTTTT");
  43   int seq_len = line1.size() + line2.size();
  44
  45   stringstream cr;
  46   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  47   Sequence seq_cr;
  48   seq_cr.load_fasta(cr);
  49
  50   stringstream crlf;
  51   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  52   Sequence seq_crlf;
  53   seq_crlf.load_fasta(crlf);
  54
  55   stringstream lf;
  56   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  57   Sequence seq_lf;
  58   seq_lf.load_fasta(lf);
  59
  60   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  61   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  62   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  63 }
  64
  65
  66 //! Do simple operations work correctly?
  67 BOOST_AUTO_TEST_CASE( sequence_filter )
  68 {
  69   const char *core_seq = "AATTGGCC";
  70   Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
  71   BOOST_CHECK_EQUAL(s1, core_seq);
  72
  73   Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
  74   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
  75   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
  76   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
  77   BOOST_CHECK_EQUAL(s2.size(), s2.size());
  78   //We're currently forcing sequences to uppercase
  79   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
  80
  81   Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
  82   BOOST_CHECK_EQUAL(s3, "ANNNG");
  83   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
  84
  85   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
  86   BOOST_CHECK_EQUAL(s3, "AA");
  87   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
  88   BOOST_CHECK_EQUAL( s3, "GG");
  89   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
  90   BOOST_CHECK_EQUAL( s3, "CCTT");
  91
  92   s3 = "AAGGFF";
  93   BOOST_CHECK_EQUAL(s3, "AAGGNN");
  94 }
  95
  96 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
  97 {
  98   std::string agct("AGCT");
  99   Sequence seq(agct, Sequence::nucleic_alphabet);
 100   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 101   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 102
 103   std::string bdv("BDv");
 104   Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
 105   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 106   // forcing sequence to upper case
 107   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 108                     boost::algorithm::to_upper_copy(bdv));
 109
 110 }
 111
 112 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 113 {
 114   std::string agct("AGCT");
 115   Sequence seq(agct);
 116   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 117   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 118   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 119   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 120   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 121   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 122
 123   std::string bdv("BDv");
 124   Sequence seq_bdv(bdv);
 125   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 126   // default alphabet only allows AGCTUN
 127   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 128 }
 129
 130 BOOST_AUTO_TEST_CASE( subseq_names )
 131 {
 132   Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
 133   s1.set_species("species");
 134   s1.set_fasta_header("a fasta header");
 135   Sequence s2 = s1.subseq(2,2);
 136   BOOST_CHECK_EQUAL(s2, "GG");
 137   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 138   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 139 }
 140
 141 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 142 {
 143   Sequence s1;
 144   BOOST_CHECK_EQUAL( s1.start(), 0 );
 145   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 146
 147   std::string seq_string("AAGGCCTT");
 148   Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
 149   BOOST_CHECK_EQUAL( s2.start(), 0 );
 150   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 151
 152   std::string s3seq_string = seq_string.substr(2,3);
 153   Sequence s3 = s2.subseq(2,3);
 154   BOOST_CHECK_EQUAL( s3.start(), 2);
 155   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 156   BOOST_CHECK_EQUAL( s3.size(), 3);
 157   BOOST_CHECK_EQUAL( s3, s3seq_string);
 158
 159   std::string s4seq_string = s3seq_string.substr(1,1);
 160   Sequence s4 = s3.subseq(1,1);
 161   BOOST_CHECK_EQUAL( s4.start(), 1 );
 162   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 163   BOOST_CHECK_EQUAL( s4.size(), 1);
 164   BOOST_CHECK_EQUAL( s4, s4seq_string);
 165 }
 166
 167 //! Can we load data from a file
 168 BOOST_AUTO_TEST_CASE( sequence_load )
 169 {
 170   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 171   seq_path /=  "human_mck_pro.fa";
 172   Sequence s;
 173   s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
 174   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 175   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 176   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 177                                     "muscle creatine kinase gene (CKMM), "
 178                                     "5' flank");
 179 }
 180
 181 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 182 {
 183   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 184   seq_path /= "broken.fa";
 185   bool exception_thrown = false;
 186   std::string exception_filename;
 187   Sequence s;
 188   try {
 189     s.load_fasta(seq_path);
 190   } catch(sequence_invalid_load_error e) {
 191     exception_thrown = true;
 192     size_t native_string_size = seq_path.native_file_string().size();
 193     std:string estr(e.what());
 194     BOOST_REQUIRE(estr.size() > native_string_size);
 195     std::copy(estr.begin(), estr.begin()+native_string_size,
 196               std::back_inserter(exception_filename));
 197   }
 198   BOOST_CHECK_EQUAL(exception_thrown, true);
 199   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 200 }
 201
 202 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 203 {
 204   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 205   seq_path /= "mouse_mck_pro.fa";
 206   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 207   annot_path /= "broken.annot";
 208   bool exception_thrown = false;
 209   Sequence s;
 210   s.load_fasta(seq_path);
 211
 212   std::string exception_filename;
 213   try {
 214     s.load_annot(annot_path, 0, 0);
 215   } catch(annotation_load_error e) {
 216     exception_thrown = true;
 217     std:string estr(e.what());
 218     size_t native_string_size = annot_path.native_file_string().size();
 219     BOOST_REQUIRE(estr.size() > native_string_size);
 220     std::copy(estr.begin(), estr.begin()+native_string_size,
 221               std::back_inserter(exception_filename));
 222   }
 223   BOOST_CHECK_EQUAL(exception_thrown, true);
 224   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 225 }
 226
 227 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 228 {
 229   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 230   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 231   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 232   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 233   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 234   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 235   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 236   std::stringstream garbage_fasta(garbage_string);
 237
 238   Sequence s;
 239   s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
 240   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 241                                  Sequence::reduced_dna_alphabet),
 242                     sequence_invalid_load_error);
 243   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 244                                  Sequence::reduced_dna_alphabet),
 245                     sequence_invalid_load_error);
 246   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 247                                  Sequence::reduced_dna_alphabet),
 248                     sequence_invalid_load_error);
 249
 250 }
 251
 252 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 253 {
 254   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 255   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 256   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 257   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 258   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 259   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 260   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 261   std::stringstream garbage_fasta(garbage_string);
 262
 263   Sequence s;
 264   s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
 265   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 266                                  Sequence::reduced_rna_alphabet),
 267                     sequence_invalid_load_error);
 268   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 269                                  Sequence::reduced_rna_alphabet),
 270                     sequence_invalid_load_error);
 271   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 272                                  Sequence::reduced_rna_alphabet),
 273                     sequence_invalid_load_error);
 274 }
 275
 276 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 277 {
 278   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 279   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 280   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 281   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 282   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 283   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 284   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 285   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 286   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 287   std::stringstream garbage_fasta(garbage_string);
 288
 289   Sequence s;
 290   Sequence specific;
 291   // there's two copies of reduced_rna_fasta because i didn't feel like
 292   // figuring out how to properly reset the read pointer in a stringstream
 293   s.load_fasta(reduced_rna_fasta1);
 294   specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
 295   BOOST_CHECK_EQUAL(s, specific);
 296
 297   s.load_fasta(reduced_dna_fasta1);
 298   specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
 299   BOOST_CHECK_EQUAL(s, specific);
 300
 301   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 302                     sequence_invalid_load_error);
 303   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 304                     sequence_invalid_load_error);
 305 }
 306
 307 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 308 {
 309   std::string fasta_file(
 310     ">gi|10129974|gb|AF188002.1|AF188002\n"
 311     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 312     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 313     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 314     ">gi|1621|emb|X55146.1|OCMCK1\n"
 315     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 316   );
 317   istringstream seq1_file(fasta_file);
 318   Sequence seq1;
 319   seq1.load_fasta(seq1_file, 1, 0, 0);
 320   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 321
 322   istringstream seq2_file(fasta_file);
 323   Sequence seq2;
 324   seq2.load_fasta(seq2_file, 2, 0, 0);
 325   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 326
 327   istringstream seq3_file(fasta_file);
 328   Sequence seq3;
 329   seq3.load_fasta(seq3_file, 3, 0, 0);
 330   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 331 }
 332
 333 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 334 {
 335   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 336   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 337   Sequence seqr = seq.rev_comp();
 338
 339   BOOST_CHECK( seq != seqr );
 340   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 341   // forcing sequence to upper case
 342   BOOST_CHECK_EQUAL( seq.get_sequence(),
 343                      boost::algorithm::to_upper_copy(iupac_symbols) );
 344 }
 345
 346 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 347 {
 348   std::string dna_str("AGCTN");
 349   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 350   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 351   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 352 }
 353
 354 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 355 {
 356   std::string rna_str("AGCUN");
 357   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 358   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 359   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 360 }
 361
 362 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 363 {
 364   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 365   Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
 366   Sequence subseq = seq.subseq(8,4);
 367   BOOST_CHECK_EQUAL( subseq, "AAGG");
 368   Sequence rev_subseq = subseq.rev_comp();
 369   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 370   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 371 }
 372
 373 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 374 {
 375   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 376   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 377   Sequence seq(dna_str);
 378   std::string seq_reversed(seq.rbegin(), seq.rend());
 379   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 380
 381   std::string substr = dna_str.substr(8,4);
 382   Sequence subseq = seq.subseq(8,4);
 383   BOOST_CHECK_EQUAL(substr, subseq);
 384
 385   std::string substr_reversed(substr.rbegin(), substr.rend());
 386   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 387   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 388 }
 389
 390 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 391 {
 392   // so what happens with reverse interators when we have no sequence?
 393   Sequence seq1;
 394   Sequence seq2;
 395   Sequence seq3("AGCT");
 396
 397   // all the empty sequences should have equal iterators
 398   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 399   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 400
 401   // none of the seq1 iterators should equal any of the seq3 iterators
 402   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 403   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 404   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 405   BOOST_CHECK(seq1.rend() != seq3.rend());
 406
 407   // seq3 iterators should work
 408   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 409
 410 }
 411
 412 BOOST_AUTO_TEST_CASE( annotation_load )
 413 {
 414   string annot_data = "human\n"
 415                       "0 10 name   type\n"
 416                       "10 20 myf7\n"
 417                       "20 30 myod\n"
 418                       "50\t55 anothername\n"
 419                       "60 50 backward\n"
 420                       ">ident3 asdf\n"
 421                       "GCT\n"
 422                       "gCTn\n"
 423                       "75\t90\tname2\ttype2\n"
 424                       "100 120 name-asdf type!@#$%\n"
 425                       ;
 426   string s(100, 'A');
 427   s += "GCTGCTAATT";
 428   Sequence seq(s, Sequence::reduced_dna_alphabet);
 429
 430   //istringstream annot_stream(annot_data);
 431   seq.parse_annot(annot_data, 0, 0);
 432   std::list<annot> annots_list = seq.annotations();
 433   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 434   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 435   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 436   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 437   BOOST_CHECK_EQUAL( annots[0].type, "type");
 438   BOOST_CHECK_EQUAL( annots[0].name, "name");
 439   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 440   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 441   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 442   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 443   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 444   BOOST_CHECK_EQUAL( annots[5].end, 90);
 445   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 446   BOOST_CHECK_EQUAL( annots[6].end, 120);
 447   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 448   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 449   // sequence defined annotations will always be after the
 450   // absolute positions
 451   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 452   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 453
 454   //BOOST_CHECK_EQUAL( annots
 455 }
 456
 457 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 458 {
 459   string annot_data = "human\n"
 460                       "0 10 name   type\n"
 461                       "blah60 50 backward\n"
 462                       ">ident3 asdf\n"
 463                       "GCT\n"
 464                       "gCTn\n"
 465                       ;
 466   string s(100, 'A');
 467   s += "GCTGCTAATT";
 468   Sequence seq(s, Sequence::reduced_dna_alphabet);
 469
 470   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 471   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 472   }
 473
 474 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 475 {
 476   // this actually is basically what's returned by UCSC
 477   // (well actually with some of the sequence and copies of fasta blocks
 478   // removed to make the example shorter
 479   string annot_data = "\n"
 480     "<PRE>\n"
 481     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 482     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 483     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 484     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 485     "</PRE>\n"
 486     "\n"
 487     "</BODY>\n"
 488     "</HTML>\n"
 489     ;
 490
 491   string s =
 492     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 493     "AAAAA"
 494     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 495   Sequence seq(s, Sequence::reduced_dna_alphabet);
 496   seq.parse_annot(annot_data);
 497   std::list<annot> annots = seq.annotations();
 498   BOOST_CHECK_EQUAL( annots.size(), 2);
 499 }
 500
 501 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 502 {
 503   string annot_data = "0 10 name   type\n"
 504                       "10 20 myf7\n"
 505                       "20 30 myod\n"
 506                       "50\t55 anothername\n"
 507                       "60 50 backward\n"
 508                       ">ident3 asdf\n"
 509                       "GCT\n"
 510                       "gCTn\n"
 511                       "75\t90\tname2\ttype2\n"
 512                       "100 120 name-asdf type!@#$%\n"
 513                       ;
 514   string s(100, 'A');
 515   s += "GCTGCTAATT";
 516   Sequence seq(s, Sequence::reduced_dna_alphabet);
 517
 518   //istringstream annot_stream(annot_data);
 519   seq.parse_annot(annot_data, 0, 0);
 520   std::list<annot> annots_list = seq.annotations();
 521   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 522   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 523   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 524   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 525   BOOST_CHECK_EQUAL( annots[0].type, "type");
 526 }
 527
 528 // ticket:83 when you try to load a sequence from a file that doesn't
 529 // have fasta headers it crashes.
 530 BOOST_AUTO_TEST_CASE( sequence_past_end )
 531 {
 532   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 533   seq_path /=  "misformated_seq.fa";
 534   Sequence s;
 535   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 536 }
 537
 538 BOOST_AUTO_TEST_CASE ( sequence_empty )
 539 {
 540
 541   Sequence s;
 542   BOOST_CHECK_EQUAL( s.empty(), true );
 543   s = "AAAGGG";
 544   BOOST_CHECK_EQUAL( s.empty(), false );
 545   s.clear();
 546   BOOST_CHECK_EQUAL( s.empty(), true);
 547   s = "";
 548   BOOST_CHECK_EQUAL( s.empty(), true);
 549 }
 550
 551 BOOST_AUTO_TEST_CASE ( sequence_size )
 552 {
 553
 554   Sequence s;
 555   BOOST_CHECK_EQUAL( s.size(), 0);
 556   std::string seq_string("AAAGGG");
 557   s = seq_string;
 558   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 559   s.clear();
 560   BOOST_CHECK_EQUAL( s.size(), 0);
 561   s = "";
 562   BOOST_CHECK_EQUAL( s.size(), 0);
 563 }
 564
 565 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 566 {
 567   Sequence szero("", Sequence::reduced_dna_alphabet);
 568   BOOST_CHECK_EQUAL(szero.empty(), true);
 569   BOOST_CHECK_EQUAL(szero, szero);
 570   BOOST_CHECK_EQUAL(szero, "");
 571
 572   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 573   sclear.clear();
 574   BOOST_CHECK_EQUAL(sclear.empty(), true);
 575   BOOST_CHECK_EQUAL(sclear, sclear);
 576   BOOST_CHECK_EQUAL(sclear, szero);
 577   BOOST_CHECK_EQUAL(sclear, "");
 578
 579 }
 580 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 581 {
 582   std::string seq_string = "AAGGCCTTNNTATA";
 583   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 584   const Sequence cs(s);
 585   std::string::size_type count = 0;
 586
 587   std::string::iterator str_itor;
 588   Sequence::const_iterator s_itor;
 589   Sequence::const_iterator cs_itor;
 590
 591   for( str_itor = seq_string.begin(),
 592        s_itor   = s.begin(),
 593        cs_itor  = cs.begin();
 594        str_itor != seq_string.end() and
 595        s_itor   != s.end() and
 596        cs_itor  != cs.end();
 597        ++str_itor, ++s_itor, ++cs_itor, ++count)
 598   {
 599     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 600     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 601     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 602   }
 603   BOOST_CHECK_EQUAL( seq_string.size(), count );
 604   BOOST_CHECK_EQUAL( s.size(), count );
 605   BOOST_CHECK_EQUAL( cs.size(), count );
 606 }
 607
 608 BOOST_AUTO_TEST_CASE( sequence_motifs )
 609 {
 610   string m("AAAA");
 611   string bogus("AATTGGAA");
 612   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 613
 614   list<motif>::const_iterator motif_i = s1.motifs().begin();
 615   list<motif>::const_iterator motif_end = s1.motifs().end();
 616
 617   // do our iterators work?
 618   BOOST_CHECK( motif_i == s1.motifs().begin() );
 619   BOOST_CHECK( motif_end == s1.motifs().end() );
 620   BOOST_CHECK( motif_i == motif_end );
 621
 622   // this shouldn't show up
 623   s1.add_motif(bogus);
 624   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 625   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 626
 627   s1.add_motif(m);
 628   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 629   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 630
 631   for(motif_i = s1.motifs().begin();
 632       motif_i != s1.motifs().end();
 633       ++motif_i)
 634   {
 635     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 636     BOOST_CHECK_EQUAL( motif_i->name, m);
 637     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 638   }
 639
 640   s1.clear_motifs();
 641   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 642
 643   /* FIXME: enable this when i find a way of passing storing the motif name
 644   // does our annotation travel?
 645   Sequence motif_seq(m);
 646   motif_seq.set_fasta_header("hi");
 647   s1.add_motif(motif_seq);
 648
 649   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 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, "hi");
 656     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 657   }
 658   */
 659 }
 660
 661 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 662 {
 663   // when searching for a motif on a subsequence we should
 664   // only search the subsequence ticket:199
 665   string aaaa("AAAA");
 666   string cccc("CCCC");
 667   Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
 668
 669   // this shouldn't show up
 670   s1.add_motif(cccc);
 671   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 672
 673   s1.add_motif(aaaa);
 674   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 675
 676   Sequence subseq1 = s1.subseq(4,5);
 677   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 678   subseq1.clear_motifs();
 679   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 680   // this is outside of our subsequence, and so shouldn't be found
 681   subseq1.add_motif(aaaa);
 682   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 683
 684   subseq1.add_motif(cccc);
 685   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 686   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 687   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 688   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 689   BOOST_CHECK_EQUAL(motif_i->end, 5);
 690 }
 691
 692 BOOST_AUTO_TEST_CASE( annot_test )
 693 {
 694   annot a(0, 10, "test", "thing");
 695
 696   BOOST_CHECK_EQUAL( a.begin, 0 );
 697   BOOST_CHECK_EQUAL( a.end,   10 );
 698   BOOST_CHECK_EQUAL( a.type,  "test" );
 699   BOOST_CHECK_EQUAL( a.name,  "thing" );
 700
 701   motif m(10, "AAGGCC");
 702   BOOST_CHECK_EQUAL( m.begin, 10 );
 703   BOOST_CHECK_EQUAL( m.type, "motif" );
 704   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 705   BOOST_CHECK_EQUAL( m.end,  10+6 );
 706 }
 707
 708 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 709 {
 710   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 711            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 712            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 713            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 714            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 715            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 716            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 717            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 718   string gc("GCCCCC");
 719   string gga("GGACACCTC");
 720   Sequence seq(s, Sequence::reduced_dna_alphabet);
 721
 722   std::list<Sequence> query_list;
 723   std::list<string> string_list;
 724   query_list.push_back(Sequence(gc));
 725   string_list.push_back(gc);
 726   query_list.push_back(Sequence(gga));
 727   string_list.push_back(gga);
 728
 729   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 730   seq.find_sequences(query_list.begin(), query_list.end());
 731
 732   int count = 0;
 733   for(list<string>::iterator string_i = string_list.begin();
 734       string_i != string_list.end();
 735       ++string_i)
 736   {
 737     string::size_type pos=0;
 738     while(pos != string::npos) {
 739       pos = s.find(*string_i, pos);
 740       if (pos != string::npos) {
 741         ++count;
 742         ++pos;
 743       }
 744     }
 745   }
 746   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 747   const std::list<annot> &a = seq.annotations();
 748   for (std::list<annot>::const_iterator annot_i = a.begin();
 749        annot_i != a.end();
 750        ++annot_i)
 751   {
 752     int count = annot_i->end - annot_i->begin ;
 753   }
 754 }
 755
 756 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 757 {
 758   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 759            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 760            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 761            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 762            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 763            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 764            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 765            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 766   Sequence seq(s, Sequence::reduced_dna_alphabet);
 767
 768
 769   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 770   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 771   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 772   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 773   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 774
 775   Sequence subseq = seq.subseq(5, 10);
 776   const list<annot> annots = subseq.annotations();
 777   // generate some ground truth
 778   list<annot> correct;
 779   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 780   correct.push_back(annot(5,10, "10-20", "10-20"));
 781   correct.push_back(annot(0,10, "0-20",  "0-20"));
 782   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 783   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 784
 785   list<annot>::iterator correct_i = correct.begin();
 786   list<annot>::const_iterator annot_i = annots.begin();
 787   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 788   {
 789     BOOST_CHECK( *annot_i == *correct_i );
 790   }
 791 }
 792
 793 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 794 {
 795   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 796            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 797            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 798            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 799            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 800            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 801            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 802            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 803   Sequence seq(s, Sequence::reduced_dna_alphabet);
 804
 805   // starting conditions
 806   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 807   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 808   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 809   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 810   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 811   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 812   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 813   seq.add_motif("CCGTCCC");
 814   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 815   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 816   seq.clear_motifs();
 817   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 818   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 819 }
 820
 821 BOOST_AUTO_TEST_CASE( out_operator )
 822 {
 823   string s("AAGGCCTT");
 824   Sequence seq(s, Sequence::reduced_dna_alphabet);
 825
 826   ostringstream buf;
 827   buf << s;
 828   BOOST_CHECK_EQUAL( s, buf.str() );
 829 }
 830
 831 BOOST_AUTO_TEST_CASE( get_name )
 832 {
 833   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 834
 835   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 836   seq.set_species("hooman"); // anyone remember tradewars?
 837   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 838   seq.set_fasta_header("fasta human");
 839   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 840 }
 841
 842 BOOST_AUTO_TEST_CASE( serialize_simple )
 843 {
 844   std::string seq_string = "AAGGCCTT";
 845   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 846   seq.set_species("ribbet");
 847   std::ostringstream oss;
 848   // allocate/deallocate serialization components
 849   {
 850     boost::archive::text_oarchive oarchive(oss);
 851     const Sequence& const_seq(seq);
 852     BOOST_CHECK_EQUAL(seq, const_seq);
 853     oarchive << const_seq;
 854   }
 855   Sequence seq_loaded;
 856   {
 857     std::istringstream iss(oss.str());
 858     boost::archive::text_iarchive iarchive(iss);
 859     iarchive >> seq_loaded;
 860   }
 861   BOOST_CHECK_EQUAL(seq_loaded, seq);
 862   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 863 }
 864
 865 BOOST_AUTO_TEST_CASE( serialize_tree )
 866 {
 867   std::string seq_string = "AAGGCCTT";
 868   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 869   seq.set_species("ribbet");
 870   seq.add_motif("AA");
 871   seq.add_motif("GC");
 872   annot a1(6,7,"t","t");
 873   seq.add_annotation(a1);
 874
 875   std::ostringstream oss;
 876   // allocate/deallocate serialization components
 877   {
 878     boost::archive::text_oarchive oarchive(oss);
 879     const Sequence& const_seq(seq);
 880     BOOST_CHECK_EQUAL(seq, const_seq);
 881     oarchive << const_seq;
 882   }
 883
 884   Sequence seq_loaded;
 885   {
 886     std::istringstream iss(oss.str());
 887     boost::archive::text_iarchive iarchive(iss);
 888     iarchive >> seq_loaded;
 889   }
 890   BOOST_CHECK_EQUAL(seq_loaded, seq);
 891 }
 892
 893 // this writes out an "old" style annotated sequence
 894 // with annotations attached as "motifs" and "annots"
 895 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 896 {
 897   std::string seq_string = "AAGGCCTT";
 898   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 899   seq.set_species("ribbet");
 900   seq.add_motif("AA");
 901   seq.add_motif("GC");
 902   annot a1(6,7,"t","t");
 903   seq.add_annotation(a1);
 904
 905   std::ostringstream oss;
 906   // allocate/deallocate serialization components
 907   {
 908     boost::archive::xml_oarchive oarchive(oss);
 909     const Sequence& const_seq(seq);
 910     BOOST_CHECK_EQUAL(seq, const_seq);
 911     oarchive << boost::serialization::make_nvp("root", const_seq);
 912   }
 913   Sequence seq_loaded;
 914   {
 915     std::istringstream iss(oss.str());
 916     boost::archive::xml_iarchive iarchive(iss);
 917     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 918   }
 919   BOOST_CHECK_EQUAL(seq_loaded, seq);
 920 }
 921
 922 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 923 {
 924   std::string seq_string = "AAGGCCTT";
 925   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 926   Sequence seq2(seq1);
 927
 928   std::ostringstream oss;
 929   // allocate/deallocate serialization components
 930   {
 931     boost::archive::xml_oarchive oarchive(oss);
 932     const Sequence& const_seq1(seq1);
 933     const Sequence& const_seq2(seq2);
 934     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 935     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 936   }
 937   //std::cout << "xml: " << oss.str() << std::endl;
 938   Sequence seq1_loaded;
 939   Sequence seq2_loaded;
 940   {
 941     std::istringstream iss(oss.str());
 942     boost::archive::xml_iarchive iarchive(iss);
 943     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 944     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 945   }
 946   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 947   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 948   // test if our pointers are the same
 949   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 950 }