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_dna_reduced )
 182 {
 183   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 184   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 185   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 186   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 187   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 188   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 189   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 190   std::stringstream garbage_fasta(garbage_string);
 191
 192   Sequence s;
 193   s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
 194   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 195                                  Sequence::reduced_dna_alphabet),
 196                     sequence_invalid_load_error);
 197   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 198                                  Sequence::reduced_dna_alphabet),
 199                     sequence_invalid_load_error);
 200   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 201                                  Sequence::reduced_dna_alphabet),
 202                     sequence_invalid_load_error);
 203
 204 }
 205
 206 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 207 {
 208   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 209   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 210   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 211   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 212   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 213   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 214   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 215   std::stringstream garbage_fasta(garbage_string);
 216
 217   Sequence s;
 218   s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
 219   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 220                                  Sequence::reduced_rna_alphabet),
 221                     sequence_invalid_load_error);
 222   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 223                                  Sequence::reduced_rna_alphabet),
 224                     sequence_invalid_load_error);
 225   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 226                                  Sequence::reduced_rna_alphabet),
 227                     sequence_invalid_load_error);
 228 }
 229
 230 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 231 {
 232   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 233   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 234   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 235   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 236   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 237   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 238   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 239   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 240   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 241   std::stringstream garbage_fasta(garbage_string);
 242
 243   Sequence s;
 244   Sequence specific;
 245   // there's two copies of reduced_rna_fasta because i didn't feel like
 246   // figuring out how to properly reset the read pointer in a stringstream
 247   s.load_fasta(reduced_rna_fasta1);
 248   specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
 249   BOOST_CHECK_EQUAL(s, specific);
 250
 251   s.load_fasta(reduced_dna_fasta1);
 252   specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
 253   BOOST_CHECK_EQUAL(s, specific);
 254
 255   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 256                     sequence_invalid_load_error);
 257   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 258                     sequence_invalid_load_error);
 259 }
 260
 261 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 262 {
 263   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 264   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 265   Sequence seqr = seq.rev_comp();
 266
 267   BOOST_CHECK( seq != seqr );
 268   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 269   // forcing sequence to upper case
 270   BOOST_CHECK_EQUAL( seq.get_sequence(),
 271                      boost::algorithm::to_upper_copy(iupac_symbols) );
 272 }
 273
 274 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 275 {
 276   std::string dna_str("AGCTN");
 277   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 278   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 279   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 280 }
 281
 282 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 283 {
 284   std::string rna_str("AGCUN");
 285   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 286   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 287   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 288 }
 289
 290 BOOST_AUTO_TEST_CASE( annotation_load )
 291 {
 292   string annot_data = "human\n"
 293                       "0 10 name   type\n"
 294                       "10 20 myf7\n"
 295                       "20 30 myod\n"
 296                       "50\t55 anothername\n"
 297                       "60 50 backward\n"
 298                       ">ident3 asdf\n"
 299                       "GCT\n"
 300                       "gCTn\n"
 301                       "75\t90\tname2\ttype2\n"
 302                       "100 120 name-asdf type!@#$%\n"
 303                       ;
 304   string s(100, 'A');
 305   s += "GCTGCTAATT";
 306   Sequence seq(s, Sequence::reduced_dna_alphabet);
 307
 308   //istringstream annot_stream(annot_data);
 309   seq.parse_annot(annot_data, 0, 0);
 310   std::list<annot> annots_list = seq.annotations();
 311   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 312   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 313   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 314   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 315   BOOST_CHECK_EQUAL( annots[0].type, "type");
 316   BOOST_CHECK_EQUAL( annots[0].name, "name");
 317   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 318   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 319   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 320   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 321   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 322   BOOST_CHECK_EQUAL( annots[5].end, 90);
 323   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 324   BOOST_CHECK_EQUAL( annots[6].end, 120);
 325   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 326   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 327   // sequence defined annotations will always be after the
 328   // absolute positions
 329   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 330   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 331
 332   //BOOST_CHECK_EQUAL( annots
 333 }
 334
 335 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 336 {
 337   string annot_data = "human\n"
 338                       "0 10 name   type\n"
 339                       "blah60 50 backward\n"
 340                       ">ident3 asdf\n"
 341                       "GCT\n"
 342                       "gCTn\n"
 343                       ;
 344   string s(100, 'A');
 345   s += "GCTGCTAATT";
 346   Sequence seq(s, Sequence::reduced_dna_alphabet);
 347
 348   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 349   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 350   }
 351
 352 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 353 {
 354   // this actually is basically what's returned by UCSC
 355   // (well actually with some of the sequence and copies of fasta blocks
 356   // removed to make the example shorter
 357   string annot_data = "\n"
 358     "<PRE>\n"
 359     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 360     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 361     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 362     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 363     "</PRE>\n"
 364     "\n"
 365     "</BODY>\n"
 366     "</HTML>\n"
 367     ;
 368
 369   string s =
 370     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 371     "AAAAA"
 372     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 373   Sequence seq(s, Sequence::reduced_dna_alphabet);
 374   seq.parse_annot(annot_data);
 375   std::list<annot> annots = seq.annotations();
 376   BOOST_CHECK_EQUAL( annots.size(), 2);
 377 }
 378
 379 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 380 {
 381   string annot_data = "0 10 name   type\n"
 382                       "10 20 myf7\n"
 383                       "20 30 myod\n"
 384                       "50\t55 anothername\n"
 385                       "60 50 backward\n"
 386                       ">ident3 asdf\n"
 387                       "GCT\n"
 388                       "gCTn\n"
 389                       "75\t90\tname2\ttype2\n"
 390                       "100 120 name-asdf type!@#$%\n"
 391                       ;
 392   string s(100, 'A');
 393   s += "GCTGCTAATT";
 394   Sequence seq(s, Sequence::reduced_dna_alphabet);
 395
 396   //istringstream annot_stream(annot_data);
 397   seq.parse_annot(annot_data, 0, 0);
 398   std::list<annot> annots_list = seq.annotations();
 399   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 400   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 401   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 402   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 403   BOOST_CHECK_EQUAL( annots[0].type, "type");
 404 }
 405
 406 // ticket:83 when you try to load a sequence from a file that doesn't
 407 // have fasta headers it crashes.
 408 BOOST_AUTO_TEST_CASE( sequence_past_end )
 409 {
 410   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 411   seq_path /=  "misformated_seq.fa";
 412   Sequence s;
 413   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 414 }
 415
 416 BOOST_AUTO_TEST_CASE ( sequence_empty )
 417 {
 418
 419   Sequence s;
 420   BOOST_CHECK_EQUAL( s.empty(), true );
 421   s = "AAAGGG";
 422   BOOST_CHECK_EQUAL( s.empty(), false );
 423   s.clear();
 424   BOOST_CHECK_EQUAL( s.empty(), true);
 425   s = "";
 426   BOOST_CHECK_EQUAL( s.empty(), true);
 427 }
 428
 429 BOOST_AUTO_TEST_CASE ( sequence_size )
 430 {
 431
 432   Sequence s;
 433   BOOST_CHECK_EQUAL( s.size(), 0);
 434   std::string seq_string("AAAGGG");
 435   s = seq_string;
 436   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 437   s.clear();
 438   BOOST_CHECK_EQUAL( s.size(), 0);
 439   s = "";
 440   BOOST_CHECK_EQUAL( s.size(), 0);
 441 }
 442
 443 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 444 {
 445   Sequence szero("", Sequence::reduced_dna_alphabet);
 446   BOOST_CHECK_EQUAL(szero.empty(), true);
 447   BOOST_CHECK_EQUAL(szero, szero);
 448   BOOST_CHECK_EQUAL(szero, "");
 449
 450   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 451   sclear.clear();
 452   BOOST_CHECK_EQUAL(sclear.empty(), true);
 453   BOOST_CHECK_EQUAL(sclear, sclear);
 454   BOOST_CHECK_EQUAL(sclear, szero);
 455   BOOST_CHECK_EQUAL(sclear, "");
 456
 457 }
 458 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 459 {
 460   std::string seq_string = "AAGGCCTTNNTATA";
 461   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 462   const Sequence cs(s);
 463   std::string::size_type count = 0;
 464
 465   std::string::iterator str_itor;
 466   Sequence::const_iterator s_itor;
 467   Sequence::const_iterator cs_itor;
 468
 469   for( str_itor = seq_string.begin(),
 470        s_itor   = s.begin(),
 471        cs_itor  = cs.begin();
 472        str_itor != seq_string.end() and
 473        s_itor   != s.end() and
 474        cs_itor  != cs.end();
 475        ++str_itor, ++s_itor, ++cs_itor, ++count)
 476   {
 477     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 478     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 479     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 480   }
 481   BOOST_CHECK_EQUAL( seq_string.size(), count );
 482   BOOST_CHECK_EQUAL( s.size(), count );
 483   BOOST_CHECK_EQUAL( cs.size(), count );
 484 }
 485
 486 BOOST_AUTO_TEST_CASE( sequence_motifs )
 487 {
 488   string m("AAAA");
 489   string bogus("AATTGGAA");
 490   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 491
 492   list<motif>::const_iterator motif_i = s1.motifs().begin();
 493   list<motif>::const_iterator motif_end = s1.motifs().end();
 494
 495   // do our iterators work?
 496   BOOST_CHECK( motif_i == s1.motifs().begin() );
 497   BOOST_CHECK( motif_end == s1.motifs().end() );
 498   BOOST_CHECK( motif_i == motif_end );
 499
 500   // this shouldn't show up
 501   s1.add_motif(bogus);
 502   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 503   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 504
 505   s1.add_motif(m);
 506   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 507   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 508
 509   for(motif_i = s1.motifs().begin();
 510       motif_i != s1.motifs().end();
 511       ++motif_i)
 512   {
 513     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 514     BOOST_CHECK_EQUAL( motif_i->name, m);
 515     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 516   }
 517
 518   s1.clear_motifs();
 519   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 520
 521   /* FIXME: enable this when i find a way of passing storing the motif name
 522   // does our annotation travel?
 523   Sequence motif_seq(m);
 524   motif_seq.set_fasta_header("hi");
 525   s1.add_motif(motif_seq);
 526
 527   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 528   for(motif_i = s1.motifs().begin();
 529       motif_i != s1.motifs().end();
 530       ++motif_i)
 531   {
 532     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 533     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 534     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 535   }
 536   */
 537 }
 538
 539 BOOST_AUTO_TEST_CASE( annot_test )
 540 {
 541   annot a(0, 10, "test", "thing");
 542
 543   BOOST_CHECK_EQUAL( a.begin, 0 );
 544   BOOST_CHECK_EQUAL( a.end,   10 );
 545   BOOST_CHECK_EQUAL( a.type,  "test" );
 546   BOOST_CHECK_EQUAL( a.name,  "thing" );
 547
 548   motif m(10, "AAGGCC");
 549   BOOST_CHECK_EQUAL( m.begin, 10 );
 550   BOOST_CHECK_EQUAL( m.type, "motif" );
 551   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 552   BOOST_CHECK_EQUAL( m.end,  10+6 );
 553 }
 554
 555 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 556 {
 557   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 558            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 559            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 560            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 561            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 562            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 563            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 564            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 565   string gc("GCCCCC");
 566   string gga("GGACACCTC");
 567   Sequence seq(s, Sequence::reduced_dna_alphabet);
 568
 569   std::list<Sequence> query_list;
 570   std::list<string> string_list;
 571   query_list.push_back(Sequence(gc));
 572   string_list.push_back(gc);
 573   query_list.push_back(Sequence(gga));
 574   string_list.push_back(gga);
 575
 576   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 577   seq.find_sequences(query_list.begin(), query_list.end());
 578
 579   int count = 0;
 580   for(list<string>::iterator string_i = string_list.begin();
 581       string_i != string_list.end();
 582       ++string_i)
 583   {
 584     string::size_type pos=0;
 585     while(pos != string::npos) {
 586       pos = s.find(*string_i, pos);
 587       if (pos != string::npos) {
 588         ++count;
 589         ++pos;
 590       }
 591     }
 592   }
 593   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 594   const std::list<annot> &a = seq.annotations();
 595   for (std::list<annot>::const_iterator annot_i = a.begin();
 596        annot_i != a.end();
 597        ++annot_i)
 598   {
 599     int count = annot_i->end - annot_i->begin ;
 600   }
 601 }
 602
 603 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 604 {
 605   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 606            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 607            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 608            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 609            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 610            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 611            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 612            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 613   Sequence seq(s, Sequence::reduced_dna_alphabet);
 614
 615
 616   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 617   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 618   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 619   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 620   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 621
 622   Sequence subseq = seq.subseq(5, 10);
 623   const list<annot> annots = subseq.annotations();
 624   // generate some ground truth
 625   list<annot> correct;
 626   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 627   correct.push_back(annot(5,10, "10-20", "10-20"));
 628   correct.push_back(annot(0,10, "0-20",  "0-20"));
 629   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 630   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 631
 632   list<annot>::iterator correct_i = correct.begin();
 633   list<annot>::const_iterator annot_i = annots.begin();
 634   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 635   {
 636     BOOST_CHECK( *annot_i == *correct_i );
 637   }
 638 }
 639
 640 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 641 {
 642   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 643            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 644            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 645            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 646            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 647            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 648            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 649            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 650   Sequence seq(s, Sequence::reduced_dna_alphabet);
 651
 652   // starting conditions
 653   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 654   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 655   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 656   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 657   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 658   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 659   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 660   seq.add_motif("CCGTCCC");
 661   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 662   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 663   seq.clear_motifs();
 664   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 665   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 666 }
 667
 668 BOOST_AUTO_TEST_CASE( out_operator )
 669 {
 670   string s("AAGGCCTT");
 671   Sequence seq(s, Sequence::reduced_dna_alphabet);
 672
 673   ostringstream buf;
 674   buf << s;
 675   BOOST_CHECK_EQUAL( s, buf.str() );
 676 }
 677
 678 BOOST_AUTO_TEST_CASE( get_name )
 679 {
 680   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 681
 682   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 683   seq.set_species("hooman"); // anyone remember tradewars?
 684   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 685   seq.set_fasta_header("fasta human");
 686   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 687 }
 688
 689 BOOST_AUTO_TEST_CASE( serialize_simple )
 690 {
 691   std::string seq_string = "AAGGCCTT";
 692   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 693   seq.set_species("ribbet");
 694   std::ostringstream oss;
 695   // allocate/deallocate serialization components
 696   {
 697     boost::archive::text_oarchive oarchive(oss);
 698     const Sequence& const_seq(seq);
 699     BOOST_CHECK_EQUAL(seq, const_seq);
 700     oarchive << const_seq;
 701   }
 702   Sequence seq_loaded;
 703   {
 704     std::istringstream iss(oss.str());
 705     boost::archive::text_iarchive iarchive(iss);
 706     iarchive >> seq_loaded;
 707   }
 708   BOOST_CHECK_EQUAL(seq_loaded, seq);
 709   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 710 }
 711
 712 BOOST_AUTO_TEST_CASE( serialize_tree )
 713 {
 714   std::string seq_string = "AAGGCCTT";
 715   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 716   seq.set_species("ribbet");
 717   seq.add_motif("AA");
 718   seq.add_motif("GC");
 719   annot a1(6,7,"t","t");
 720   seq.add_annotation(a1);
 721
 722   std::ostringstream oss;
 723   // allocate/deallocate serialization components
 724   {
 725     boost::archive::text_oarchive oarchive(oss);
 726     const Sequence& const_seq(seq);
 727     BOOST_CHECK_EQUAL(seq, const_seq);
 728     oarchive << const_seq;
 729   }
 730
 731   Sequence seq_loaded;
 732   {
 733     std::istringstream iss(oss.str());
 734     boost::archive::text_iarchive iarchive(iss);
 735     iarchive >> seq_loaded;
 736   }
 737   BOOST_CHECK_EQUAL(seq_loaded, seq);
 738 }
 739
 740 // this writes out an "old" style annotated sequence
 741 // with annotations attached as "motifs" and "annots"
 742 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 743 {
 744   std::string seq_string = "AAGGCCTT";
 745   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 746   seq.set_species("ribbet");
 747   seq.add_motif("AA");
 748   seq.add_motif("GC");
 749   annot a1(6,7,"t","t");
 750   seq.add_annotation(a1);
 751
 752   std::ostringstream oss;
 753   // allocate/deallocate serialization components
 754   {
 755     boost::archive::xml_oarchive oarchive(oss);
 756     const Sequence& const_seq(seq);
 757     BOOST_CHECK_EQUAL(seq, const_seq);
 758     oarchive << boost::serialization::make_nvp("root", const_seq);
 759   }
 760   Sequence seq_loaded;
 761   {
 762     std::istringstream iss(oss.str());
 763     boost::archive::xml_iarchive iarchive(iss);
 764     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 765   }
 766   BOOST_CHECK_EQUAL(seq_loaded, seq);
 767 }
 768
 769 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 770 {
 771   std::string seq_string = "AAGGCCTT";
 772   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 773   Sequence seq2(seq1);
 774
 775   std::ostringstream oss;
 776   // allocate/deallocate serialization components
 777   {
 778     boost::archive::xml_oarchive oarchive(oss);
 779     const Sequence& const_seq1(seq1);
 780     const Sequence& const_seq2(seq2);
 781     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 782     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 783   }
 784   //std::cout << "xml: " << oss.str() << std::endl;
 785   Sequence seq1_loaded;
 786   Sequence seq2_loaded;
 787   {
 788     std::istringstream iss(oss.str());
 789     boost::archive::xml_iarchive iarchive(iss);
 790     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 791     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 792   }
 793   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 794   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 795   // test if our pointers are the same
 796   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 797 }