alg/test/test_sequence.cpp

   1 #define BOOST_AUTO_TEST_MAIN
   2 #include <boost/test/auto_unit_test.hpp>
   3 #include <boost/filesystem/path.hpp>
   4 #include <boost/filesystem/operations.hpp>
   5 namespace fs=boost::filesystem;
   6
   7 #include <boost/algorithm/string/case_conv.hpp>
   8
   9 #include <list>
  10 #include <iostream>
  11 #include <sstream>
  12
  13 #include <boost/archive/text_oarchive.hpp>
  14 #include <boost/archive/text_iarchive.hpp>
  15 #include <boost/archive/xml_oarchive.hpp>
  16 #include <boost/archive/xml_iarchive.hpp>
  17
  18 #include "alg/sequence.hpp"
  19 #include "mussa_exceptions.hpp"
  20
  21 using namespace std;
  22
  23 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
  24 {
  25         Sequence s;
  26         // make sure that retrieving the sequence doesn't throw an error
  27         BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
  28 }
  29
  30 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
  31 {
  32   std::string str1("AAAAT");
  33   Sequence seq1(str1);
  34   BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
  35
  36   std::string str2("AATTGGCC");
  37   Sequence seq2(str2);
  38   BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
  39 }
  40
  41 //! when we try to load a missing file, do we get an error?
  42 BOOST_AUTO_TEST_CASE( sequence_load_exception )
  43 {
  44   Sequence s;
  45   // there should be errors when we try to load something that doesn't exist
  46   BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
  47   BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
  48 }
  49
  50 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
  51 {
  52   string header(">Header");
  53   string line1("AAAAGGGGCCCCTTTTT");
  54   string line2("AAAAGGGGCCCCTTTTT");
  55   int seq_len = line1.size() + line2.size();
  56
  57   stringstream cr;
  58   cr << header << "\015" << line1 << "\015" << line2 << "\015";
  59   Sequence seq_cr;
  60   seq_cr.load_fasta(cr);
  61
  62   stringstream crlf;
  63   crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
  64   Sequence seq_crlf;
  65   seq_crlf.load_fasta(crlf);
  66
  67   stringstream lf;
  68   lf << header << "\012" << line1 << "\012" << line2 << "\012";
  69   Sequence seq_lf;
  70   seq_lf.load_fasta(lf);
  71
  72   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  73   BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
  74   BOOST_CHECK_EQUAL(seq_cr.size(),   seq_len);
  75 }
  76
  77
  78 //! Do simple operations work correctly?
  79 BOOST_AUTO_TEST_CASE( sequence_filter )
  80 {
  81   const char *core_seq = "AATTGGCC";
  82   Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
  83   BOOST_CHECK_EQUAL(s1, core_seq);
  84
  85   Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
  86   BOOST_CHECK_EQUAL(s2, "AATTGGCC");
  87   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
  88   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
  89   BOOST_CHECK_EQUAL(s2.size(), s2.size());
  90   //We're currently forcing sequences to uppercase
  91   BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
  92
  93   Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
  94   BOOST_CHECK_EQUAL(s3, "ANNNG");
  95   BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
  96
  97   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
  98   BOOST_CHECK_EQUAL(s3, "AA");
  99   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
 100   BOOST_CHECK_EQUAL( s3, "GG");
 101   s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
 102   BOOST_CHECK_EQUAL( s3, "CCTT");
 103
 104   s3 = "AAGGFF";
 105   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 106 }
 107
 108 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
 109 {
 110   std::string agct("AGCT");
 111   Sequence seq(agct, Sequence::nucleic_alphabet);
 112   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 113   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 114
 115   std::string bdv("BDv");
 116   Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
 117   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 118   // forcing sequence to upper case
 119   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
 120                     boost::algorithm::to_upper_copy(bdv));
 121
 122 }
 123
 124 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
 125 {
 126   std::string agct("AGCT");
 127   Sequence seq(agct);
 128   BOOST_CHECK_EQUAL(seq.size(), agct.size());
 129   BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
 130   BOOST_CHECK_EQUAL(seq[0], agct[0]);
 131   BOOST_CHECK_EQUAL(seq[1], agct[1]);
 132   BOOST_CHECK_EQUAL(seq[2], agct[2]);
 133   BOOST_CHECK_EQUAL(seq[3], agct[3]);
 134
 135   std::string bdv("BDv");
 136   Sequence seq_bdv(bdv);
 137   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
 138   // default alphabet only allows AGCTUN
 139   BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
 140 }
 141
 142 BOOST_AUTO_TEST_CASE( subseq_names )
 143 {
 144   Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
 145   s1.set_species("species");
 146   s1.set_fasta_header("a fasta header");
 147   Sequence s2 = s1.subseq(2,2);
 148   BOOST_CHECK_EQUAL(s2, "GG");
 149   BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
 150   BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
 151 }
 152
 153 BOOST_AUTO_TEST_CASE( sequence_start_stop )
 154 {
 155   Sequence s1;
 156   BOOST_CHECK_EQUAL( s1.start(), 0 );
 157   BOOST_CHECK_EQUAL( s1.stop(), 0 );
 158
 159   std::string seq_string("AAGGCCTT");
 160   Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
 161   BOOST_CHECK_EQUAL( s2.start(), 0 );
 162   BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
 163
 164   std::string s3seq_string = seq_string.substr(2,3);
 165   Sequence s3 = s2.subseq(2,3);
 166   BOOST_CHECK_EQUAL( s3.start(), 2);
 167   BOOST_CHECK_EQUAL( s3.stop(), 2+3);
 168   BOOST_CHECK_EQUAL( s3.size(), 3);
 169   BOOST_CHECK_EQUAL( s3, s3seq_string);
 170
 171   std::string s4seq_string = s3seq_string.substr(1,1);
 172   Sequence s4 = s3.subseq(1,1);
 173   BOOST_CHECK_EQUAL( s4.start(), 1 );
 174   BOOST_CHECK_EQUAL( s4.stop(), 1+1);
 175   BOOST_CHECK_EQUAL( s4.size(), 1);
 176   BOOST_CHECK_EQUAL( s4, s4seq_string);
 177 }
 178
 179 //! Can we load data from a file
 180 BOOST_AUTO_TEST_CASE( sequence_load )
 181 {
 182   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
 183   seq_path /=  "human_mck_pro.fa";
 184   Sequence s;
 185   s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
 186   BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
 187   BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
 188   BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
 189                                     "muscle creatine kinase gene (CKMM), "
 190                                     "5' flank");
 191 }
 192
 193 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
 194 {
 195   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 196   seq_path /= "broken.fa";
 197   bool exception_thrown = false;
 198   std::string exception_filename;
 199   Sequence s;
 200   try {
 201     s.load_fasta(seq_path);
 202   } catch(sequence_invalid_load_error e) {
 203     exception_thrown = true;
 204     size_t native_string_size = seq_path.native_file_string().size();
 205     std:string estr(e.what());
 206     BOOST_REQUIRE(estr.size() > native_string_size);
 207     std::copy(estr.begin(), estr.begin()+native_string_size,
 208               std::back_inserter(exception_filename));
 209   }
 210   BOOST_CHECK_EQUAL(exception_thrown, true);
 211   BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
 212 }
 213
 214 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
 215 {
 216   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
 217   seq_path /= "mouse_mck_pro.fa";
 218   fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
 219   annot_path /= "broken.annot";
 220   bool exception_thrown = false;
 221   Sequence s;
 222   s.load_fasta(seq_path);
 223
 224   std::string exception_filename;
 225   try {
 226     s.load_annot(annot_path, 0, 0);
 227   } catch(annotation_load_error e) {
 228     exception_thrown = true;
 229     std:string estr(e.what());
 230     size_t native_string_size = annot_path.native_file_string().size();
 231     BOOST_REQUIRE(estr.size() > native_string_size);
 232     std::copy(estr.begin(), estr.begin()+native_string_size,
 233               std::back_inserter(exception_filename));
 234   }
 235   BOOST_CHECK_EQUAL(exception_thrown, true);
 236   BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
 237 }
 238
 239 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
 240 {
 241   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 242   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 243   std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
 244   std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
 245   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
 246   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 247   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 248   std::stringstream garbage_fasta(garbage_string);
 249
 250   Sequence s;
 251   s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
 252   BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
 253                                  Sequence::reduced_dna_alphabet),
 254                     sequence_invalid_load_error);
 255   BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
 256                                  Sequence::reduced_dna_alphabet),
 257                     sequence_invalid_load_error);
 258   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 259                                  Sequence::reduced_dna_alphabet),
 260                     sequence_invalid_load_error);
 261
 262 }
 263
 264 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
 265 {
 266   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 267   std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
 268   std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
 269   std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
 270   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 271   std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
 272   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 273   std::stringstream garbage_fasta(garbage_string);
 274
 275   Sequence s;
 276   s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
 277   BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
 278                                  Sequence::reduced_rna_alphabet),
 279                     sequence_invalid_load_error);
 280   BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
 281                                  Sequence::reduced_rna_alphabet),
 282                     sequence_invalid_load_error);
 283   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
 284                                  Sequence::reduced_rna_alphabet),
 285                     sequence_invalid_load_error);
 286 }
 287
 288 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
 289 {
 290   std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
 291   std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
 292   std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
 293   std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
 294   std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
 295   std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
 296   std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
 297   std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
 298   std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
 299   std::stringstream garbage_fasta(garbage_string);
 300
 301   Sequence s;
 302   Sequence specific;
 303   // there's two copies of reduced_rna_fasta because i didn't feel like
 304   // figuring out how to properly reset the read pointer in a stringstream
 305   s.load_fasta(reduced_rna_fasta1);
 306   specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
 307   BOOST_CHECK_EQUAL(s, specific);
 308
 309   s.load_fasta(reduced_dna_fasta1);
 310   specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
 311   BOOST_CHECK_EQUAL(s, specific);
 312
 313   BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
 314                     sequence_invalid_load_error);
 315   BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
 316                     sequence_invalid_load_error);
 317 }
 318
 319 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
 320 {
 321   std::string fasta_file(
 322     ">gi|10129974|gb|AF188002.1|AF188002\n"
 323     "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
 324     ">gi|180579|gb|M21487.1|HUMCKMM1\n"
 325     "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
 326     ">gi|1621|emb|X55146.1|OCMCK1\n"
 327     "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
 328   );
 329   istringstream seq1_file(fasta_file);
 330   Sequence seq1;
 331   seq1.load_fasta(seq1_file, 1, 0, 0);
 332   BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
 333
 334   istringstream seq2_file(fasta_file);
 335   Sequence seq2;
 336   seq2.load_fasta(seq2_file, 2, 0, 0);
 337   BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
 338
 339   istringstream seq3_file(fasta_file);
 340   Sequence seq3;
 341   seq3.load_fasta(seq3_file, 3, 0, 0);
 342   BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
 343 }
 344
 345 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
 346 {
 347   std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
 348   Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
 349   Sequence seqr = seq.rev_comp();
 350
 351   BOOST_CHECK( seq != seqr );
 352   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
 353   // forcing sequence to upper case
 354   BOOST_CHECK_EQUAL( seq.get_sequence(),
 355                      boost::algorithm::to_upper_copy(iupac_symbols) );
 356 }
 357
 358 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
 359 {
 360   std::string dna_str("AGCTN");
 361   Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
 362   BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
 363   BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
 364 }
 365
 366 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
 367 {
 368   std::string rna_str("AGCUN");
 369   Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
 370   BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
 371   BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
 372 }
 373
 374 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
 375 {
 376   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 377   Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
 378   Sequence subseq = seq.subseq(8,4);
 379   BOOST_CHECK_EQUAL( subseq, "AAGG");
 380   Sequence rev_subseq = subseq.rev_comp();
 381   BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
 382   BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
 383 }
 384
 385 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
 386 {
 387   std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
 388   std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
 389   Sequence seq(dna_str);
 390   std::string seq_reversed(seq.rbegin(), seq.rend());
 391   BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
 392
 393   std::string substr = dna_str.substr(8,4);
 394   Sequence subseq = seq.subseq(8,4);
 395   BOOST_CHECK_EQUAL(substr, subseq);
 396
 397   std::string substr_reversed(substr.rbegin(), substr.rend());
 398   std::string subseq_reversed(subseq.rbegin(), subseq.rend());
 399   BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
 400 }
 401
 402 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
 403 {
 404   // so what happens with reverse interators when we have no sequence?
 405   Sequence seq1;
 406   Sequence seq2;
 407   Sequence seq3("AGCT");
 408
 409   // all the empty sequences should have equal iterators
 410   BOOST_CHECK(seq1.rbegin() == seq1.rend());
 411   BOOST_CHECK(seq1.rbegin() == seq2.rend());
 412
 413   // none of the seq1 iterators should equal any of the seq3 iterators
 414   BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
 415   BOOST_CHECK(seq1.rbegin() != seq3.rend());
 416   BOOST_CHECK(seq1.rend() != seq3.rbegin());
 417   BOOST_CHECK(seq1.rend() != seq3.rend());
 418
 419   // seq3 iterators should work
 420   BOOST_CHECK(seq3.rbegin() != seq3.rend());
 421
 422 }
 423
 424 BOOST_AUTO_TEST_CASE( annotation_load )
 425 {
 426   string annot_data = "human\n"
 427                       "0 10 name   type\n"
 428                       "10 20 myf7\n"
 429                       "20 30 myod\n"
 430                       "50\t55 anothername\n"
 431                       "60 50 backward\n"
 432                       ">ident3 asdf\n"
 433                       "GCT\n"
 434                       "gCTn\n"
 435                       "75\t90\tname2\ttype2\n"
 436                       "100 120 name-asdf type!@#$%\n"
 437                       ;
 438   string s(100, 'A');
 439   s += "GCTGCTAATT";
 440   Sequence seq(s, Sequence::reduced_dna_alphabet);
 441
 442   //istringstream annot_stream(annot_data);
 443   seq.parse_annot(annot_data, 0, 0);
 444   std::list<annot> annots_list = seq.annotations();
 445   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 446   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 447   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 448   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 449   BOOST_CHECK_EQUAL( annots[0].type, "type");
 450   BOOST_CHECK_EQUAL( annots[0].name, "name");
 451   BOOST_CHECK_EQUAL( annots[1].name, "myf7");
 452   BOOST_CHECK_EQUAL( annots[2].name, "myod");
 453   BOOST_CHECK_EQUAL( annots[3].name, "anothername");
 454   BOOST_CHECK_EQUAL( annots[4].name, "backward");
 455   BOOST_CHECK_EQUAL( annots[5].name, "name2");
 456   BOOST_CHECK_EQUAL( annots[5].end, 90);
 457   BOOST_CHECK_EQUAL( annots[6].begin, 100);
 458   BOOST_CHECK_EQUAL( annots[6].end, 120);
 459   BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
 460   BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
 461   // sequence defined annotations will always be after the
 462   // absolute positions
 463   BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
 464   BOOST_CHECK_EQUAL( annots[7].begin, 100);
 465
 466   //BOOST_CHECK_EQUAL( annots
 467 }
 468
 469 BOOST_AUTO_TEST_CASE( annotation_broken_load )
 470 {
 471   string annot_data = "human\n"
 472                       "0 10 name   type\n"
 473                       "blah60 50 backward\n"
 474                       ">ident3 asdf\n"
 475                       "GCT\n"
 476                       "gCTn\n"
 477                       ;
 478   string s(100, 'A');
 479   s += "GCTGCTAATT";
 480   Sequence seq(s, Sequence::reduced_dna_alphabet);
 481
 482   BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
 483   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 484   }
 485
 486 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
 487 {
 488   // this actually is basically what's returned by UCSC
 489   // (well actually with some of the sequence and copies of fasta blocks
 490   // removed to make the example shorter
 491   string annot_data = "\n"
 492     "<PRE>\n"
 493     ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 494     "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
 495     "&gt;hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
 496     "GGTGGAGACGACCTGGACCCTAACTACGT\n"
 497     "</PRE>\n"
 498     "\n"
 499     "</BODY>\n"
 500     "</HTML>\n"
 501     ;
 502
 503   string s =
 504     "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
 505     "AAAAA"
 506     "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
 507   Sequence seq(s, Sequence::reduced_dna_alphabet);
 508   seq.parse_annot(annot_data);
 509   std::list<annot> annots = seq.annotations();
 510   BOOST_CHECK_EQUAL( annots.size(), 2);
 511 }
 512
 513 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
 514 {
 515   string annot_data = "0 10 name   type\n"
 516                       "10 20 myf7\n"
 517                       "20 30 myod\n"
 518                       "50\t55 anothername\n"
 519                       "60 50 backward\n"
 520                       ">ident3 asdf\n"
 521                       "GCT\n"
 522                       "gCTn\n"
 523                       "75\t90\tname2\ttype2\n"
 524                       "100 120 name-asdf type!@#$%\n"
 525                       ;
 526   string s(100, 'A');
 527   s += "GCTGCTAATT";
 528   Sequence seq(s, Sequence::reduced_dna_alphabet);
 529
 530   //istringstream annot_stream(annot_data);
 531   seq.parse_annot(annot_data, 0, 0);
 532   std::list<annot> annots_list = seq.annotations();
 533   std::vector<annot> annots(annots_list.begin(), annots_list.end());
 534   BOOST_REQUIRE_EQUAL( annots.size(), 8);
 535   BOOST_CHECK_EQUAL( annots[0].begin, 0 );
 536   BOOST_CHECK_EQUAL( annots[0].end, 10 );
 537   BOOST_CHECK_EQUAL( annots[0].type, "type");
 538 }
 539
 540 // ticket:83 when you try to load a sequence from a file that doesn't
 541 // have fasta headers it crashes.
 542 BOOST_AUTO_TEST_CASE( sequence_past_end )
 543 {
 544   fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
 545   seq_path /=  "misformated_seq.fa";
 546   Sequence s;
 547   BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
 548 }
 549
 550 BOOST_AUTO_TEST_CASE ( sequence_empty )
 551 {
 552
 553   Sequence s;
 554   BOOST_CHECK_EQUAL( s.empty(), true );
 555   s = "AAAGGG";
 556   BOOST_CHECK_EQUAL( s.empty(), false );
 557   s.clear();
 558   BOOST_CHECK_EQUAL( s.empty(), true);
 559   s = "";
 560   BOOST_CHECK_EQUAL( s.empty(), true);
 561 }
 562
 563 BOOST_AUTO_TEST_CASE ( sequence_size )
 564 {
 565
 566   Sequence s;
 567   BOOST_CHECK_EQUAL( s.size(), 0);
 568   std::string seq_string("AAAGGG");
 569   s = seq_string;
 570   BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
 571   s.clear();
 572   BOOST_CHECK_EQUAL( s.size(), 0);
 573   s = "";
 574   BOOST_CHECK_EQUAL( s.size(), 0);
 575 }
 576
 577 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
 578 {
 579   Sequence szero("", Sequence::reduced_dna_alphabet);
 580   BOOST_CHECK_EQUAL(szero.empty(), true);
 581   BOOST_CHECK_EQUAL(szero, szero);
 582   BOOST_CHECK_EQUAL(szero, "");
 583
 584   Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
 585   sclear.clear();
 586   BOOST_CHECK_EQUAL(sclear.empty(), true);
 587   BOOST_CHECK_EQUAL(sclear, sclear);
 588   BOOST_CHECK_EQUAL(sclear, szero);
 589   BOOST_CHECK_EQUAL(sclear, "");
 590
 591 }
 592 BOOST_AUTO_TEST_CASE ( sequence_iterators )
 593 {
 594   std::string seq_string = "AAGGCCTTNNTATA";
 595   Sequence s(seq_string, Sequence::reduced_dna_alphabet);
 596   const Sequence cs(s);
 597   std::string::size_type count = 0;
 598
 599   std::string::iterator str_itor;
 600   Sequence::const_iterator s_itor;
 601   Sequence::const_iterator cs_itor;
 602
 603   for( str_itor = seq_string.begin(),
 604        s_itor   = s.begin(),
 605        cs_itor  = cs.begin();
 606        str_itor != seq_string.end() and
 607        s_itor   != s.end() and
 608        cs_itor  != cs.end();
 609        ++str_itor, ++s_itor, ++cs_itor, ++count)
 610   {
 611     BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
 612     BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
 613     BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
 614   }
 615   BOOST_CHECK_EQUAL( seq_string.size(), count );
 616   BOOST_CHECK_EQUAL( s.size(), count );
 617   BOOST_CHECK_EQUAL( cs.size(), count );
 618 }
 619
 620 BOOST_AUTO_TEST_CASE( sequence_motifs )
 621 {
 622   string m("AAAA");
 623   string bogus("AATTGGAA");
 624   Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
 625
 626   list<motif>::const_iterator motif_i = s1.motifs().begin();
 627   list<motif>::const_iterator motif_end = s1.motifs().end();
 628
 629   // do our iterators work?
 630   BOOST_CHECK( motif_i == s1.motifs().begin() );
 631   BOOST_CHECK( motif_end == s1.motifs().end() );
 632   BOOST_CHECK( motif_i == motif_end );
 633
 634   // this shouldn't show up
 635   s1.add_motif(bogus);
 636   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 637   BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
 638
 639   s1.add_motif(m);
 640   BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
 641   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 642
 643   for(motif_i = s1.motifs().begin();
 644       motif_i != s1.motifs().end();
 645       ++motif_i)
 646   {
 647     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 648     BOOST_CHECK_EQUAL( motif_i->name, m);
 649     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 650   }
 651
 652   s1.clear_motifs();
 653   BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
 654
 655   /* FIXME: enable this when i find a way of passing storing the motif name
 656   // does our annotation travel?
 657   Sequence motif_seq(m);
 658   motif_seq.set_fasta_header("hi");
 659   s1.add_motif(motif_seq);
 660
 661   BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
 662   for(motif_i = s1.motifs().begin();
 663       motif_i != s1.motifs().end();
 664       ++motif_i)
 665   {
 666     BOOST_CHECK_EQUAL( motif_i->type, "motif" );
 667     BOOST_CHECK_EQUAL( motif_i->name, "hi");
 668     BOOST_CHECK_EQUAL( motif_i->sequence, m);
 669   }
 670   */
 671 }
 672
 673 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
 674 {
 675   // when searching for a motif on a subsequence we should
 676   // only search the subsequence ticket:199
 677   string aaaa("AAAA");
 678   string cccc("CCCC");
 679   Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
 680
 681   // this shouldn't show up
 682   s1.add_motif(cccc);
 683   BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
 684
 685   s1.add_motif(aaaa);
 686   BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
 687
 688   Sequence subseq1 = s1.subseq(4,5);
 689   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
 690   subseq1.clear_motifs();
 691   BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
 692   // this is outside of our subsequence, and so shouldn't be found
 693   subseq1.add_motif(aaaa);
 694   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
 695
 696   subseq1.add_motif(cccc);
 697   BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
 698   std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
 699   BOOST_REQUIRE(motif_i != subseq1.motifs().end());
 700   BOOST_CHECK_EQUAL(motif_i->begin, 1);
 701   BOOST_CHECK_EQUAL(motif_i->end, 5);
 702 }
 703
 704 BOOST_AUTO_TEST_CASE( annot_test )
 705 {
 706   annot a(0, 10, "test", "thing");
 707
 708   BOOST_CHECK_EQUAL( a.begin, 0 );
 709   BOOST_CHECK_EQUAL( a.end,   10 );
 710   BOOST_CHECK_EQUAL( a.type,  "test" );
 711   BOOST_CHECK_EQUAL( a.name,  "thing" );
 712
 713   motif m(10, "AAGGCC");
 714   BOOST_CHECK_EQUAL( m.begin, 10 );
 715   BOOST_CHECK_EQUAL( m.type, "motif" );
 716   BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
 717   BOOST_CHECK_EQUAL( m.end,  10+6 );
 718 }
 719
 720 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
 721 {
 722   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 723            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 724            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 725            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 726            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 727            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 728            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 729            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 730   string gc("GCCCCC");
 731   string gga("GGACACCTC");
 732   Sequence seq(s, Sequence::reduced_dna_alphabet);
 733
 734   std::list<Sequence> query_list;
 735   std::list<string> string_list;
 736   query_list.push_back(Sequence(gc));
 737   string_list.push_back(gc);
 738   query_list.push_back(Sequence(gga));
 739   string_list.push_back(gga);
 740
 741   BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
 742   seq.find_sequences(query_list.begin(), query_list.end());
 743
 744   int count = 0;
 745   for(list<string>::iterator string_i = string_list.begin();
 746       string_i != string_list.end();
 747       ++string_i)
 748   {
 749     string::size_type pos=0;
 750     while(pos != string::npos) {
 751       pos = s.find(*string_i, pos);
 752       if (pos != string::npos) {
 753         ++count;
 754         ++pos;
 755       }
 756     }
 757   }
 758   BOOST_CHECK_EQUAL(seq.annotations().size(), count);
 759   const std::list<annot> &a = seq.annotations();
 760   for (std::list<annot>::const_iterator annot_i = a.begin();
 761        annot_i != a.end();
 762        ++annot_i)
 763   {
 764     int count = annot_i->end - annot_i->begin ;
 765   }
 766 }
 767
 768 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
 769 {
 770   string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 771            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 772            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 773            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 774            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 775            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 776            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 777            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 778   Sequence seq(s, Sequence::reduced_dna_alphabet);
 779
 780
 781   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 782   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 783   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 784   seq.add_annotation(annot(8, 12, "8-12", "8-12"));
 785   seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
 786
 787   Sequence subseq = seq.subseq(5, 10);
 788   const list<annot> annots = subseq.annotations();
 789   // generate some ground truth
 790   list<annot> correct;
 791   correct.push_back(annot(0, 5, "0-10",  "0-10"));
 792   correct.push_back(annot(5,10, "10-20", "10-20"));
 793   correct.push_back(annot(0,10, "0-20",  "0-20"));
 794   correct.push_back(annot(3, 7, "8-12",  "8-12"));
 795   BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
 796
 797   list<annot>::iterator correct_i = correct.begin();
 798   list<annot>::const_iterator annot_i = annots.begin();
 799   for(; annot_i != annots.end(); ++annot_i, ++correct_i)
 800   {
 801     BOOST_CHECK( *annot_i == *correct_i );
 802   }
 803 }
 804
 805 BOOST_AUTO_TEST_CASE( motif_annotation_update )
 806 {
 807   string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
 808            "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
 809            "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
 810            "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
 811            "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
 812            "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
 813            "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
 814            "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
 815   Sequence seq(s, Sequence::reduced_dna_alphabet);
 816
 817   // starting conditions
 818   BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
 819   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 820   seq.add_annotation(annot(0, 10, "0-10", "0-10"));
 821   seq.add_annotation(annot(10, 20, "10-20", "10-20"));
 822   seq.add_annotation(annot(0, 20, "0-20", "0-20"));
 823   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 824   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 825   seq.add_motif("CCGTCCC");
 826   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 827   BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
 828   seq.clear_motifs();
 829   BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
 830   BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
 831 }
 832
 833 BOOST_AUTO_TEST_CASE( out_operator )
 834 {
 835   string s("AAGGCCTT");
 836   Sequence seq(s, Sequence::reduced_dna_alphabet);
 837
 838   ostringstream buf;
 839   buf << s;
 840   BOOST_CHECK_EQUAL( s, buf.str() );
 841 }
 842
 843 BOOST_AUTO_TEST_CASE( get_name )
 844 {
 845   Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
 846
 847   BOOST_CHECK_EQUAL( seq.get_name(), "" );
 848   seq.set_species("hooman"); // anyone remember tradewars?
 849   BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
 850   seq.set_fasta_header("fasta human");
 851   BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
 852 }
 853
 854 BOOST_AUTO_TEST_CASE( serialize_simple )
 855 {
 856   std::string seq_string = "AAGGCCTT";
 857   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 858   seq.set_species("ribbet");
 859   std::ostringstream oss;
 860   // allocate/deallocate serialization components
 861   {
 862     boost::archive::text_oarchive oarchive(oss);
 863     const Sequence& const_seq(seq);
 864     BOOST_CHECK_EQUAL(seq, const_seq);
 865     oarchive << const_seq;
 866   }
 867   Sequence seq_loaded;
 868   {
 869     std::istringstream iss(oss.str());
 870     boost::archive::text_iarchive iarchive(iss);
 871     iarchive >> seq_loaded;
 872   }
 873   BOOST_CHECK_EQUAL(seq_loaded, seq);
 874   BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
 875 }
 876
 877 BOOST_AUTO_TEST_CASE( serialize_tree )
 878 {
 879   std::string seq_string = "AAGGCCTT";
 880   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 881   seq.set_species("ribbet");
 882   seq.add_motif("AA");
 883   seq.add_motif("GC");
 884   annot a1(6,7,"t","t");
 885   seq.add_annotation(a1);
 886
 887   std::ostringstream oss;
 888   // allocate/deallocate serialization components
 889   {
 890     boost::archive::text_oarchive oarchive(oss);
 891     const Sequence& const_seq(seq);
 892     BOOST_CHECK_EQUAL(seq, const_seq);
 893     oarchive << const_seq;
 894   }
 895
 896   Sequence seq_loaded;
 897   {
 898     std::istringstream iss(oss.str());
 899     boost::archive::text_iarchive iarchive(iss);
 900     iarchive >> seq_loaded;
 901   }
 902   BOOST_CHECK_EQUAL(seq_loaded, seq);
 903 }
 904
 905 // this writes out an "old" style annotated sequence
 906 // with annotations attached as "motifs" and "annots"
 907 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
 908 {
 909   std::string seq_string = "AAGGCCTT";
 910   Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
 911   seq.set_species("ribbet");
 912   seq.add_motif("AA");
 913   seq.add_motif("GC");
 914   annot a1(6,7,"t","t");
 915   seq.add_annotation(a1);
 916
 917   std::ostringstream oss;
 918   // allocate/deallocate serialization components
 919   {
 920     boost::archive::xml_oarchive oarchive(oss);
 921     const Sequence& const_seq(seq);
 922     BOOST_CHECK_EQUAL(seq, const_seq);
 923     oarchive << boost::serialization::make_nvp("root", const_seq);
 924   }
 925   Sequence seq_loaded;
 926   {
 927     std::istringstream iss(oss.str());
 928     boost::archive::xml_iarchive iarchive(iss);
 929     iarchive >> boost::serialization::make_nvp("root", seq_loaded);
 930   }
 931   BOOST_CHECK_EQUAL(seq_loaded, seq);
 932 }
 933
 934 BOOST_AUTO_TEST_CASE( serialize_xml_two )
 935 {
 936   std::string seq_string = "AAGGCCTT";
 937   Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
 938   Sequence seq2(seq1);
 939
 940   std::ostringstream oss;
 941   // allocate/deallocate serialization components
 942   {
 943     boost::archive::xml_oarchive oarchive(oss);
 944     const Sequence& const_seq1(seq1);
 945     const Sequence& const_seq2(seq2);
 946     oarchive << boost::serialization::make_nvp("seq1", const_seq1);
 947     oarchive << boost::serialization::make_nvp("seq2", const_seq2);
 948   }
 949   //std::cout << "xml: " << oss.str() << std::endl;
 950   Sequence seq1_loaded;
 951   Sequence seq2_loaded;
 952   {
 953     std::istringstream iss(oss.str());
 954     boost::archive::xml_iarchive iarchive(iss);
 955     iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
 956     iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
 957   }
 958   BOOST_CHECK_EQUAL(seq1_loaded, seq1);
 959   BOOST_CHECK_EQUAL(seq2_loaded, seq2);
 960   // test if our pointers are the same
 961   BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());
 962 }