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;
10 #include <boost/archive/text_oarchive.hpp>
11 #include <boost/archive/text_iarchive.hpp>
12 #include <boost/archive/xml_oarchive.hpp>
13 #include <boost/archive/xml_iarchive.hpp>
15 #include "alg/sequence.hpp"
16 #include "mussa_exceptions.hpp"
20 //! when we try to load a missing file, do we get an error?
21 BOOST_AUTO_TEST_CASE( sequence_load_exception )
24 // there should be errors when we try to load something that doesn't exist
25 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
26 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
29 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
31 string header(">Header");
32 string line1("AAAAGGGGCCCCTTTTT");
33 string line2("AAAAGGGGCCCCTTTTT");
34 int seq_len = line1.size() + line2.size();
37 cr << header << "\015" << line1 << "\015" << line2 << "\015";
39 seq_cr.load_fasta(cr);
42 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
44 seq_crlf.load_fasta(crlf);
47 lf << header << "\012" << line1 << "\012" << line2 << "\012";
49 seq_lf.load_fasta(lf);
51 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
52 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
53 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
57 //! Do simple operations work correctly?
58 BOOST_AUTO_TEST_CASE( sequence_filter )
60 const char *core_seq = "AATTGGCC";
61 Sequence s1(core_seq);
62 BOOST_CHECK_EQUAL(s1, core_seq);
64 Sequence s2("aattggcc");
65 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
66 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
67 BOOST_CHECK_EQUAL(s2.size(), s2.size());
68 BOOST_CHECK_EQUAL(s2.get_sequence(), core_seq);
71 BOOST_CHECK_EQUAL(s3, "ANNNG");
72 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
74 s3.set_filtered_sequence("AAGGCCTT", 0, 2);
75 BOOST_CHECK_EQUAL(s3, "AA");
76 s3.set_filtered_sequence("AAGGCCTT", 2, 2);
77 BOOST_CHECK_EQUAL( s3, "GG");
78 s3.set_filtered_sequence("AAGGCCTT", 4);
79 BOOST_CHECK_EQUAL( s3, "CCTT");
82 BOOST_CHECK_EQUAL(s3, "AAGGNN");
85 BOOST_AUTO_TEST_CASE( subseq_names )
87 Sequence s1("AAGGCCTT");
88 s1.set_species("species");
89 s1.set_fasta_header("a fasta header");
90 Sequence s2 = s1.subseq(2,2);
91 BOOST_CHECK_EQUAL(s2, "GG");
92 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
93 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
96 //! Can we load data from a file
97 BOOST_AUTO_TEST_CASE( sequence_load )
99 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
100 seq_path /= "human_mck_pro.fa";
102 s.load_fasta(seq_path);
103 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
104 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
105 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
106 "muscle creatine kinase gene (CKMM), "
110 BOOST_AUTO_TEST_CASE( annotation_load )
112 string annot_data = "human\n"
116 "50\t55 anothername\n"
121 "75\t90\tname2\ttype2\n"
122 "100 120 name-asdf type!@#$%\n"
128 //istringstream annot_stream(annot_data);
129 seq.parse_annot(annot_data, 0, 0);
130 std::list<annot> annots_list = seq.annotations();
131 std::vector<annot> annots(annots_list.begin(), annots_list.end());
132 BOOST_REQUIRE_EQUAL( annots.size(), 8);
133 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
134 BOOST_CHECK_EQUAL( annots[0].end, 10 );
135 BOOST_CHECK_EQUAL( annots[0].type, "type");
136 BOOST_CHECK_EQUAL( annots[0].name, "name");
137 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
138 BOOST_CHECK_EQUAL( annots[2].name, "myod");
139 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
140 BOOST_CHECK_EQUAL( annots[4].name, "backward");
141 BOOST_CHECK_EQUAL( annots[5].name, "name2");
142 BOOST_CHECK_EQUAL( annots[5].end, 90);
143 BOOST_CHECK_EQUAL( annots[6].begin, 100);
144 BOOST_CHECK_EQUAL( annots[6].end, 120);
145 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
146 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
147 // sequence defined annotations will always be after the
148 // absolute positions
149 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
150 BOOST_CHECK_EQUAL( annots[7].begin, 100);
152 //BOOST_CHECK_EQUAL( annots
156 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
158 // this actually is basically what's returned by UCSC
159 // (well actually with some of the sequence and copies of fasta blocks
160 // removed to make the example shorter
161 string annot_data = "\n"
163 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
164 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
165 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
166 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
174 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
176 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
178 seq.parse_annot(annot_data);
179 std::list<annot> annots = seq.annotations();
180 BOOST_CHECK_EQUAL( annots.size(), 2);
183 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
185 string annot_data = "0 10 name type\n"
188 "50\t55 anothername\n"
193 "75\t90\tname2\ttype2\n"
194 "100 120 name-asdf type!@#$%\n"
200 //istringstream annot_stream(annot_data);
201 seq.parse_annot(annot_data, 0, 0);
202 std::list<annot> annots_list = seq.annotations();
203 std::vector<annot> annots(annots_list.begin(), annots_list.end());
204 BOOST_REQUIRE_EQUAL( annots.size(), 8);
205 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
206 BOOST_CHECK_EQUAL( annots[0].end, 10 );
207 BOOST_CHECK_EQUAL( annots[0].type, "type");
210 // ticket:83 when you try to load a sequence from a file that doesn't
211 // have fasta headers it crashes.
212 BOOST_AUTO_TEST_CASE( sequence_past_end )
214 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
215 seq_path /= "misformated_seq.fa";
217 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
220 BOOST_AUTO_TEST_CASE ( sequence_empty )
224 BOOST_CHECK_EQUAL( s.empty(), true );
226 BOOST_CHECK_EQUAL( s.empty(), false );
228 BOOST_CHECK_EQUAL( s.empty(), true);
230 BOOST_CHECK_EQUAL( s.empty(), true);
233 BOOST_AUTO_TEST_CASE ( sequence_size )
237 BOOST_CHECK_EQUAL( s.size(), 0);
238 std::string seq_string("AAAGGG");
240 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
242 BOOST_CHECK_EQUAL( s.size(), 0);
244 BOOST_CHECK_EQUAL( s.size(), 0);
247 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
250 BOOST_CHECK_EQUAL(szero.empty(), true);
251 BOOST_CHECK_EQUAL(szero, szero);
252 BOOST_CHECK_EQUAL(szero, "");
254 Sequence sclear("AGCT");
256 BOOST_CHECK_EQUAL(sclear.empty(), true);
257 BOOST_CHECK_EQUAL(sclear, sclear);
258 BOOST_CHECK_EQUAL(sclear, szero);
259 BOOST_CHECK_EQUAL(sclear, "");
262 BOOST_AUTO_TEST_CASE ( sequence_iterators )
264 std::string seq_string = "AAGGCCTTNNTATA";
265 Sequence s(seq_string);
266 const Sequence cs(s);
267 std::string::size_type count = 0;
269 std::string::iterator str_itor;
270 Sequence::const_iterator s_itor;
271 Sequence::const_iterator cs_itor;
273 for( str_itor = seq_string.begin(),
275 cs_itor = cs.begin();
276 str_itor != seq_string.end() and
277 s_itor != s.end() and
279 ++str_itor, ++s_itor, ++cs_itor, ++count)
281 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
282 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
283 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
285 BOOST_CHECK_EQUAL( seq_string.size(), count );
286 BOOST_CHECK_EQUAL( s.size(), count );
287 BOOST_CHECK_EQUAL( cs.size(), count );
290 BOOST_AUTO_TEST_CASE( sequence_motifs )
293 string bogus("AATTGGAA");
294 Sequence s1("AAAAGGGGCCCCTTTT");
296 list<motif>::const_iterator motif_i = s1.motifs().begin();
297 list<motif>::const_iterator motif_end = s1.motifs().end();
299 // do our iterators work?
300 BOOST_CHECK( motif_i == s1.motifs().begin() );
301 BOOST_CHECK( motif_end == s1.motifs().end() );
302 BOOST_CHECK( motif_i == motif_end );
304 // this shouldn't show up
306 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
307 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
310 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
311 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
313 for(motif_i = s1.motifs().begin();
314 motif_i != s1.motifs().end();
317 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
318 BOOST_CHECK_EQUAL( motif_i->name, m);
319 BOOST_CHECK_EQUAL( motif_i->sequence, m);
323 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
325 /* FIXME: enable this when i find a way of passing storing the motif name
326 // does our annotation travel?
327 Sequence motif_seq(m);
328 motif_seq.set_fasta_header("hi");
329 s1.add_motif(motif_seq);
331 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
332 for(motif_i = s1.motifs().begin();
333 motif_i != s1.motifs().end();
336 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
337 BOOST_CHECK_EQUAL( motif_i->name, "hi");
338 BOOST_CHECK_EQUAL( motif_i->sequence, m);
343 BOOST_AUTO_TEST_CASE( annot_test )
345 annot a(0, 10, "test", "thing");
347 BOOST_CHECK_EQUAL( a.begin, 0 );
348 BOOST_CHECK_EQUAL( a.end, 10 );
349 BOOST_CHECK_EQUAL( a.type, "test" );
350 BOOST_CHECK_EQUAL( a.name, "thing" );
352 motif m(10, "AAGGCC");
353 BOOST_CHECK_EQUAL( m.begin, 10 );
354 BOOST_CHECK_EQUAL( m.type, "motif" );
355 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
356 BOOST_CHECK_EQUAL( m.end, 10+6 );
359 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
361 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
362 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
363 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
364 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
365 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
366 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
367 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
368 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
370 string gga("GGACACCTC");
373 std::list<Sequence> query_list;
374 std::list<string> string_list;
375 query_list.push_back(Sequence(gc));
376 string_list.push_back(gc);
377 query_list.push_back(Sequence(gga));
378 string_list.push_back(gga);
380 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
381 seq.find_sequences(query_list.begin(), query_list.end());
384 for(list<string>::iterator string_i = string_list.begin();
385 string_i != string_list.end();
388 string::size_type pos=0;
389 while(pos != string::npos) {
390 pos = s.find(*string_i, pos);
391 if (pos != string::npos) {
397 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
400 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
402 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
403 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
404 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
405 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
406 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
407 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
408 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
409 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
413 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
414 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
415 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
416 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
417 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
419 Sequence subseq = seq.subseq(5, 10);
420 const list<annot> annots = subseq.annotations();
421 // generate some ground truth
423 correct.push_back(annot(0, 5, "0-10", "0-10"));
424 correct.push_back(annot(5,10, "10-20", "10-20"));
425 correct.push_back(annot(0,10, "0-20", "0-20"));
426 correct.push_back(annot(3, 7, "8-12", "8-12"));
427 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
429 list<annot>::iterator correct_i = correct.begin();
430 list<annot>::const_iterator annot_i = annots.begin();
431 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
433 BOOST_CHECK( *annot_i == *correct_i );
437 BOOST_AUTO_TEST_CASE( motif_annotation_update )
439 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
440 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
441 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
442 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
443 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
444 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
445 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
446 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
449 // starting conditions
450 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
451 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
452 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
453 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
454 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
455 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
456 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
457 seq.add_motif("CCGTCCC");
458 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
459 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
461 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
462 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
465 BOOST_AUTO_TEST_CASE( out_operator )
467 string s("AAGGCCTT");
472 BOOST_CHECK_EQUAL( s, buf.str() );
475 BOOST_AUTO_TEST_CASE( get_name )
477 Sequence seq("AAGGCCTT");
479 BOOST_CHECK_EQUAL( seq.get_name(), "" );
480 seq.set_species("hooman"); // anyone remember tradewars?
481 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
482 seq.set_fasta_header("fasta human");
483 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
486 BOOST_AUTO_TEST_CASE( serialize_simple )
488 std::string seq_string = "AAGGCCTT";
489 Sequence seq(seq_string);
490 seq.set_species("ribbet");
491 std::ostringstream oss;
492 // allocate/deallocate serialization components
494 boost::archive::text_oarchive oarchive(oss);
495 const Sequence& const_seq(seq);
496 BOOST_CHECK_EQUAL(seq, const_seq);
497 oarchive << const_seq;
501 std::istringstream iss(oss.str());
502 boost::archive::text_iarchive iarchive(iss);
503 iarchive >> seq_loaded;
505 BOOST_CHECK_EQUAL(seq_loaded, seq);
506 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
509 BOOST_AUTO_TEST_CASE( serialize_tree )
511 std::string seq_string = "AAGGCCTT";
512 Sequence seq(seq_string);
513 seq.set_species("ribbet");
516 annot a1(6,7,"t","t");
517 seq.add_annotation(a1);
519 std::ostringstream oss;
520 // allocate/deallocate serialization components
522 boost::archive::text_oarchive oarchive(oss);
523 const Sequence& const_seq(seq);
524 BOOST_CHECK_EQUAL(seq, const_seq);
525 oarchive << const_seq;
530 std::istringstream iss(oss.str());
531 boost::archive::text_iarchive iarchive(iss);
532 iarchive >> seq_loaded;
534 BOOST_CHECK_EQUAL(seq_loaded, seq);
537 // this writes out an "old" style annotated sequence
538 // with annotations attached as "motifs" and "annots"
539 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
541 std::string seq_string = "AAGGCCTT";
542 Sequence seq(seq_string);
543 seq.set_species("ribbet");
546 annot a1(6,7,"t","t");
547 seq.add_annotation(a1);
549 std::ostringstream oss;
550 // allocate/deallocate serialization components
552 boost::archive::xml_oarchive oarchive(oss);
553 const Sequence& const_seq(seq);
554 BOOST_CHECK_EQUAL(seq, const_seq);
555 oarchive << boost::serialization::make_nvp("root", const_seq);
559 std::istringstream iss(oss.str());
560 boost::archive::xml_iarchive iarchive(iss);
561 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
563 BOOST_CHECK_EQUAL(seq_loaded, seq);
566 BOOST_AUTO_TEST_CASE( serialize_xml_two )
568 std::string seq_string = "AAGGCCTT";
569 Sequence seq1(seq_string);
572 std::ostringstream oss;
573 // allocate/deallocate serialization components
575 boost::archive::xml_oarchive oarchive(oss);
576 const Sequence& const_seq1(seq1);
577 const Sequence& const_seq2(seq2);
578 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
579 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
581 //std::cout << "xml: " << oss.str() << std::endl;
582 Sequence seq1_loaded;
583 Sequence seq2_loaded;
585 std::istringstream iss(oss.str());
586 boost::archive::xml_iarchive iarchive(iss);
587 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
588 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
590 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
591 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
592 // test if our pointers are the same
593 BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());