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_load_multiple_sequences_one_fasta )
 262 {
 263   std::string fasta_file(
 264     ">gi|10129974|gb|AF188002.1|AF188002\n"
 265     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 266     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 267     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 268     ">gi|1621|emb|X55146.1|OCMCK1\n"
 269     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 270   );
 271   istringstream seq1_file(fasta_file);
 272   Sequence seq1;
 273   seq1.load_fasta(seq1_file, 1, 0, 0);
 274   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 275
 276   istringstream seq2_file(fasta_file);
 277   Sequence seq2;
 278   seq2.load_fasta(seq2_file, 2, 0, 0);
 279   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 280
 281   istringstream seq3_file(fasta_file);
 282   Sequence seq3;
 283   seq3.load_fasta(seq3_file, 3, 0, 0);
 284   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 285 }
 286
 287 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 288 {
 289   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 290   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 291   Sequence seqr = seq.rev_comp();
 292
 293   BOOST_CHECK( seq != seqr );
 294   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 295   // forcing sequence to upper case
 296   BOOST_CHECK_EQUAL( seq.get_sequence(),
 297                      boost::algorithm::to_upper_copy(iupac_symbols) );
 298 }
 299
 300 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 301 {
 302   std::string dna_str("AGCTN");
 303   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 304   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 305   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 306 }
 307
 308 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 309 {
 310   std::string rna_str("AGCUN");
 311   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 312   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 313   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 314 }
 315
 316 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 317 {
 318   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 319   Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
 320   Sequence subseq = seq.subseq(8,4);
 321   BOOST_CHECK_EQUAL( subseq, "AAGG");
 322   Sequence rev_subseq = subseq.rev_comp();
 323   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 324   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 325 }
 326
 327 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 328 {
 329   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 330   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 331   Sequence seq(dna_str);
 332   std::string seq_reversed(seq.rbegin(), seq.rend());
 333   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 334
 335   std::string substr = dna_str.substr(8,4);
 336   Sequence subseq = seq.subseq(8,4);
 337   BOOST_CHECK_EQUAL(substr, subseq);
 338
 339   std::string substr_reversed(substr.rbegin(), substr.rend());
 340   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 341   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 342 }
 343
 344 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 345 {
 346   // so what happens with reverse interators when we have no sequence?
 347   Sequence seq1;
 348   Sequence seq2;
 349   Sequence seq3("AGCT");
 350
 351   // all the empty sequences should have equal iterators
 352   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 353   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 354
 355   // none of the seq1 iterators should equal any of the seq3 iterators
 356   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 357   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 358   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 359   BOOST_CHECK(seq1.rend() != seq3.rend());
 360
 361   // seq3 iterators should work
 362   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 363
 364 }
 365
 366 BOOST_AUTO_TEST_CASE( annotation_load )
 367 {
 368   string annot_data = "human\n"
 369                       "0 10 name   type\n"
 370                       "10 20 myf7\n"
 371                       "20 30 myod\n"
 372                       "50\t55 anothername\n"
 373                       "60 50 backward\n"
 374                       ">ident3 asdf\n"
 375                       "GCT\n"
 376                       "gCTn\n"
 377                       "75\t90\tname2\ttype2\n"
 378                       "100 120 name-asdf type!@#$%\n"
 379                       ;
 380   string s(100, 'A');
 381   s += "GCTGCTAATT";
 382   Sequence seq(s, Sequence::reduced_dna_alphabet);
 383
 384   //istringstream annot_stream(annot_data);
 385   seq.parse_annot(annot_data, 0, 0);
 386   std::list<annot> annots_list = seq.annotations();
 387   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 388   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 389   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 390   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 391   BOOST_CHECK_EQUAL( annots[0].type, "type");
 392   BOOST_CHECK_EQUAL( annots[0].name, "name");
 393   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 394   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 395   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 396   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 397   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 398   BOOST_CHECK_EQUAL( annots[5].end, 90);
 399   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 400   BOOST_CHECK_EQUAL( annots[6].end, 120);
 401   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 402   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 403   // sequence defined annotations will always be after the
 404   // absolute positions
 405   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 406   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 407
 408   //BOOST_CHECK_EQUAL( annots
 409 }
 410
 411 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 412 {
 413   string annot_data = "human\n"
 414                       "0 10 name   type\n"
 415                       "blah60 50 backward\n"
 416                       ">ident3 asdf\n"
 417                       "GCT\n"
 418                       "gCTn\n"
 419                       ;
 420   string s(100, 'A');
 421   s += "GCTGCTAATT";
 422   Sequence seq(s, Sequence::reduced_dna_alphabet);
 423
 424   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 425   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 426   }
 427
 428 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 429 {
 430   // this actually is basically what's returned by UCSC
 431   // (well actually with some of the sequence and copies of fasta blocks
 432   // removed to make the example shorter
 433   string annot_data = "\n"
 434     "<PRE>\n"
 435     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 436     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 437     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 438     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 439     "</PRE>\n"
 440     "\n"
 441     "</BODY>\n"
 442     "</HTML>\n"
 443     ;
 444
 445   string s =
 446     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 447     "AAAAA"
 448     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 449   Sequence seq(s, Sequence::reduced_dna_alphabet);
 450   seq.parse_annot(annot_data);
 451   std::list<annot> annots = seq.annotations();
 452   BOOST_CHECK_EQUAL( annots.size(), 2);
 453 }
 454
 455 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 456 {
 457   string annot_data = "0 10 name   type\n"
 458                       "10 20 myf7\n"
 459                       "20 30 myod\n"
 460                       "50\t55 anothername\n"
 461                       "60 50 backward\n"
 462                       ">ident3 asdf\n"
 463                       "GCT\n"
 464                       "gCTn\n"
 465                       "75\t90\tname2\ttype2\n"
 466                       "100 120 name-asdf type!@#$%\n"
 467                       ;
 468   string s(100, 'A');
 469   s += "GCTGCTAATT";
 470   Sequence seq(s, Sequence::reduced_dna_alphabet);
 471
 472   //istringstream annot_stream(annot_data);
 473   seq.parse_annot(annot_data, 0, 0);
 474   std::list<annot> annots_list = seq.annotations();
 475   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 476   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 477   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 478   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 479   BOOST_CHECK_EQUAL( annots[0].type, "type");
 480 }
 481
 482 // ticket:83 when you try to load a sequence from a file that doesn't
 483 // have fasta headers it crashes.
 484 BOOST_AUTO_TEST_CASE( sequence_past_end )
 485 {
 486   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 487   seq_path /=  "misformated_seq.fa";
 488   Sequence s;
 489   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 490 }
 491
 492 BOOST_AUTO_TEST_CASE ( sequence_empty )
 493 {
 494
 495   Sequence s;
 496   BOOST_CHECK_EQUAL( s.empty(), true );
 497   s = "AAAGGG";
 498   BOOST_CHECK_EQUAL( s.empty(), false );
 499   s.clear();
 500   BOOST_CHECK_EQUAL( s.empty(), true);
 501   s = "";
 502   BOOST_CHECK_EQUAL( s.empty(), true);
 503 }
 504
 505 BOOST_AUTO_TEST_CASE ( sequence_size )
 506 {
 507
 508   Sequence s;
 509   BOOST_CHECK_EQUAL( s.size(), 0);
 510   std::string seq_string("AAAGGG");
 511   s = seq_string;
 512   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 513   s.clear();
 514   BOOST_CHECK_EQUAL( s.size(), 0);
 515   s = "";
 516   BOOST_CHECK_EQUAL( s.size(), 0);
 517 }
 518
 519 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 520 {
 521   Sequence szero("", Sequence::reduced_dna_alphabet);
 522   BOOST_CHECK_EQUAL(szero.empty(), true);
 523   BOOST_CHECK_EQUAL(szero, szero);
 524   BOOST_CHECK_EQUAL(szero, "");
 525
 526   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 527   sclear.clear();
 528   BOOST_CHECK_EQUAL(sclear.empty(), true);
 529   BOOST_CHECK_EQUAL(sclear, sclear);
 530   BOOST_CHECK_EQUAL(sclear, szero);
 531   BOOST_CHECK_EQUAL(sclear, "");
 532
 533 }
 534 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 535 {
 536   std::string seq_string = "AAGGCCTTNNTATA";
 537   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 538   const Sequence cs(s);
 539   std::string::size_type count = 0;
 540
 541   std::string::iterator str_itor;
 542   Sequence::const_iterator s_itor;
 543   Sequence::const_iterator cs_itor;
 544
 545   for( str_itor = seq_string.begin(),
 546        s_itor   = s.begin(),
 547        cs_itor  = cs.begin();
 548        str_itor != seq_string.end() and
 549        s_itor   != s.end() and
 550        cs_itor  != cs.end();
 551        ++str_itor, ++s_itor, ++cs_itor, ++count)
 552   {
 553     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 554     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 555     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 556   }
 557   BOOST_CHECK_EQUAL( seq_string.size(), count );
 558   BOOST_CHECK_EQUAL( s.size(), count );
 559   BOOST_CHECK_EQUAL( cs.size(), count );
 560 }
 561
 562 BOOST_AUTO_TEST_CASE( sequence_motifs )
 563 {
 564   string m("AAAA");
 565   string bogus("AATTGGAA");
 566   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 567
 568   list<motif>::const_iterator motif_i = s1.motifs().begin();
 569   list<motif>::const_iterator motif_end = s1.motifs().end();
 570
 571   // do our iterators work?
 572   BOOST_CHECK( motif_i == s1.motifs().begin() );
 573   BOOST_CHECK( motif_end == s1.motifs().end() );
 574   BOOST_CHECK( motif_i == motif_end );
 575
 576   // this shouldn't show up
 577   s1.add_motif(bogus);
 578   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 579   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 580
 581   s1.add_motif(m);
 582   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 583   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 584
 585   for(motif_i = s1.motifs().begin();
 586       motif_i != s1.motifs().end();
 587       ++motif_i)
 588   {
 589     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 590     BOOST_CHECK_EQUAL( motif_i->name, m);
 591     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 592   }
 593
 594   s1.clear_motifs();
 595   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 596
 597   /* FIXME: enable this when i find a way of passing storing the motif name
 598   // does our annotation travel?
 599   Sequence motif_seq(m);
 600   motif_seq.set_fasta_header("hi");
 601   s1.add_motif(motif_seq);
 602
 603   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 604   for(motif_i = s1.motifs().begin();
 605       motif_i != s1.motifs().end();
 606       ++motif_i)
 607   {
 608     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 609     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 610     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 611   }
 612   */
 613 }
 614
 615 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 616 {
 617   // when searching for a motif on a subsequence we should
 618   // only search the subsequence ticket:199
 619   string aaaa("AAAA");
 620   string cccc("CCCC");
 621   Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
 622
 623   // this shouldn't show up
 624   s1.add_motif(cccc);
 625   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 626
 627   s1.add_motif(aaaa);
 628   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 629
 630   Sequence subseq1 = s1.subseq(4,5);
 631   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 632   subseq1.clear_motifs();
 633   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 634   // this is outside of our subsequence, and so shouldn't be found
 635   subseq1.add_motif(aaaa);
 636   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 637
 638   subseq1.add_motif(cccc);
 639   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 640   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 641   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 642   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 643   BOOST_CHECK_EQUAL(motif_i->end, 5);
 644 }
 645
 646 BOOST_AUTO_TEST_CASE( annot_test )
 647 {
 648   annot a(0, 10, "test", "thing");
 649
 650   BOOST_CHECK_EQUAL( a.begin, 0 );
 651   BOOST_CHECK_EQUAL( a.end,   10 );
 652   BOOST_CHECK_EQUAL( a.type,  "test" );
 653   BOOST_CHECK_EQUAL( a.name,  "thing" );
 654
 655   motif m(10, "AAGGCC");
 656   BOOST_CHECK_EQUAL( m.begin, 10 );
 657   BOOST_CHECK_EQUAL( m.type, "motif" );
 658   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 659   BOOST_CHECK_EQUAL( m.end,  10+6 );
 660 }
 661
 662 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 663 {
 664   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 665            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 666            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 667            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 668            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 669            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 670            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 671            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 672   string gc("GCCCCC");
 673   string gga("GGACACCTC");
 674   Sequence seq(s, Sequence::reduced_dna_alphabet);
 675
 676   std::list<Sequence> query_list;
 677   std::list<string> string_list;
 678   query_list.push_back(Sequence(gc));
 679   string_list.push_back(gc);
 680   query_list.push_back(Sequence(gga));
 681   string_list.push_back(gga);
 682
 683   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 684   seq.find_sequences(query_list.begin(), query_list.end());
 685
 686   int count = 0;
 687   for(list<string>::iterator string_i = string_list.begin();
 688       string_i != string_list.end();
 689       ++string_i)
 690   {
 691     string::size_type pos=0;
 692     while(pos != string::npos) {
 693       pos = s.find(*string_i, pos);
 694       if (pos != string::npos) {
 695         ++count;
 696         ++pos;
 697       }
 698     }
 699   }
 700   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 701   const std::list<annot> &a = seq.annotations();
 702   for (std::list<annot>::const_iterator annot_i = a.begin();
 703        annot_i != a.end();
 704        ++annot_i)
 705   {
 706     int count = annot_i->end - annot_i->begin ;
 707   }
 708 }
 709
 710 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 711 {
 712   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 713            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 714            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 715            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 716            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 717            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 718            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 719            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 720   Sequence seq(s, Sequence::reduced_dna_alphabet);
 721
 722
 723   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 724   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 725   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 726   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 727   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 728
 729   Sequence subseq = seq.subseq(5, 10);
 730   const list<annot> annots = subseq.annotations();
 731   // generate some ground truth
 732   list<annot> correct;
 733   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 734   correct.push_back(annot(5,10, "10-20", "10-20"));
 735   correct.push_back(annot(0,10, "0-20",  "0-20"));
 736   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 737   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 738
 739   list<annot>::iterator correct_i = correct.begin();
 740   list<annot>::const_iterator annot_i = annots.begin();
 741   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 742   {
 743     BOOST_CHECK( *annot_i == *correct_i );
 744   }
 745 }
 746
 747 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 748 {
 749   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 750            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 751            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 752            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 753            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 754            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 755            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 756            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 757   Sequence seq(s, Sequence::reduced_dna_alphabet);
 758
 759   // starting conditions
 760   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 761   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 762   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 763   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 764   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 765   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 766   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 767   seq.add_motif("CCGTCCC");
 768   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 769   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 770   seq.clear_motifs();
 771   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 772   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 773 }
 774
 775 BOOST_AUTO_TEST_CASE( out_operator )
 776 {
 777   string s("AAGGCCTT");
 778   Sequence seq(s, Sequence::reduced_dna_alphabet);
 779
 780   ostringstream buf;
 781   buf << s;
 782   BOOST_CHECK_EQUAL( s, buf.str() );
 783 }
 784
 785 BOOST_AUTO_TEST_CASE( get_name )
 786 {
 787   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 788
 789   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 790   seq.set_species("hooman"); // anyone remember tradewars?
 791   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 792   seq.set_fasta_header("fasta human");
 793   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 794 }
 795
 796 BOOST_AUTO_TEST_CASE( serialize_simple )
 797 {
 798   std::string seq_string = "AAGGCCTT";
 799   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 800   seq.set_species("ribbet");
 801   std::ostringstream oss;
 802   // allocate/deallocate serialization components
 803   {
 804     boost::archive::text_oarchive oarchive(oss);
 805     const Sequence& const_seq(seq);
 806     BOOST_CHECK_EQUAL(seq, const_seq);
 807     oarchive << const_seq;
 808   }
 809   Sequence seq_loaded;
 810   {
 811     std::istringstream iss(oss.str());
 812     boost::archive::text_iarchive iarchive(iss);
 813     iarchive >> seq_loaded;
 814   }
 815   BOOST_CHECK_EQUAL(seq_loaded, seq);
 816   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 817 }
 818
 819 BOOST_AUTO_TEST_CASE( serialize_tree )
 820 {
 821   std::string seq_string = "AAGGCCTT";
 822   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 823   seq.set_species("ribbet");
 824   seq.add_motif("AA");
 825   seq.add_motif("GC");
 826   annot a1(6,7,"t","t");
 827   seq.add_annotation(a1);
 828
 829   std::ostringstream oss;
 830   // allocate/deallocate serialization components
 831   {
 832     boost::archive::text_oarchive oarchive(oss);
 833     const Sequence& const_seq(seq);
 834     BOOST_CHECK_EQUAL(seq, const_seq);
 835     oarchive << const_seq;
 836   }
 837
 838   Sequence seq_loaded;
 839   {
 840     std::istringstream iss(oss.str());
 841     boost::archive::text_iarchive iarchive(iss);
 842     iarchive >> seq_loaded;
 843   }
 844   BOOST_CHECK_EQUAL(seq_loaded, seq);
 845 }
 846
 847 // this writes out an "old" style annotated sequence
 848 // with annotations attached as "motifs" and "annots"
 849 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 850 {
 851   std::string seq_string = "AAGGCCTT";
 852   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 853   seq.set_species("ribbet");
 854   seq.add_motif("AA");
 855   seq.add_motif("GC");
 856   annot a1(6,7,"t","t");
 857   seq.add_annotation(a1);
 858
 859   std::ostringstream oss;
 860   // allocate/deallocate serialization components
 861   {
 862     boost::archive::xml_oarchive oarchive(oss);
 863     const Sequence& const_seq(seq);
 864     BOOST_CHECK_EQUAL(seq, const_seq);
 865     oarchive << boost::serialization::make_nvp("root", const_seq);
 866   }
 867   Sequence seq_loaded;
 868   {
 869     std::istringstream iss(oss.str());
 870     boost::archive::xml_iarchive iarchive(iss);
 871     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 872   }
 873   BOOST_CHECK_EQUAL(seq_loaded, seq);
 874 }
 875
 876 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 877 {
 878   std::string seq_string = "AAGGCCTT";
 879   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 880   Sequence seq2(seq1);
 881
 882   std::ostringstream oss;
 883   // allocate/deallocate serialization components
 884   {
 885     boost::archive::xml_oarchive oarchive(oss);
 886     const Sequence& const_seq1(seq1);
 887     const Sequence& const_seq2(seq2);
 888     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 889     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 890   }
 891   //std::cout << "xml: " << oss.str() << std::endl;
 892   Sequence seq1_loaded;
 893   Sequence seq2_loaded;
 894   {
 895     std::istringstream iss(oss.str());
 896     boost::archive::xml_iarchive iarchive(iss);
 897     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 898     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 899   }
 900   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 901   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 902   // test if our pointers are the same
 903   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 904 }