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.c_str(), 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, "");
85 BOOST_CHECK_EQUAL(s3, "AAGGNN");
88 BOOST_AUTO_TEST_CASE( subseq_names )
90 Sequence s1("AAGGCCTT");
91 s1.set_species("species");
92 s1.set_fasta_header("a fasta header");
93 Sequence s2 = s1.subseq(2,2);
94 BOOST_CHECK_EQUAL(s2, "GG");
95 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
96 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
99 //! Can we load data from a file
100 BOOST_AUTO_TEST_CASE( sequence_load )
102 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
103 seq_path /= "human_mck_pro.fa";
105 s.load_fasta(seq_path);
106 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
107 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
108 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
109 "muscle creatine kinase gene (CKMM), "
113 BOOST_AUTO_TEST_CASE( annotation_load )
115 string annot_data = "human\n"
119 "50\t55 anothername\n"
124 "75\t90\tname2\ttype2\n"
125 "100 120 name-asdf type!@#$%\n"
131 //istringstream annot_stream(annot_data);
132 seq.parse_annot(annot_data, 0, 0);
133 std::list<annot> annots_list = seq.annotations();
134 std::vector<annot> annots(annots_list.begin(), annots_list.end());
135 BOOST_REQUIRE_EQUAL( annots.size(), 8);
136 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
137 BOOST_CHECK_EQUAL( annots[0].end, 10 );
138 BOOST_CHECK_EQUAL( annots[0].type, "type");
139 BOOST_CHECK_EQUAL( annots[0].name, "name");
140 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
141 BOOST_CHECK_EQUAL( annots[2].name, "myod");
142 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
143 BOOST_CHECK_EQUAL( annots[4].name, "backward");
144 BOOST_CHECK_EQUAL( annots[5].name, "name2");
145 BOOST_CHECK_EQUAL( annots[5].end, 90);
146 BOOST_CHECK_EQUAL( annots[6].begin, 100);
147 BOOST_CHECK_EQUAL( annots[6].end, 120);
148 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
149 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
150 // sequence defined annotations will always be after the
151 // absolute positions
152 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
153 BOOST_CHECK_EQUAL( annots[7].begin, 100);
155 //BOOST_CHECK_EQUAL( annots
159 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
161 // this actually is basically what's returned by UCSC
162 // (well actually with some of the sequence and copies of fasta blocks
163 // removed to make the example shorter
164 string annot_data = "\n"
166 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
167 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
168 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
169 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
177 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
179 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
181 seq.parse_annot(annot_data);
182 std::list<annot> annots = seq.annotations();
183 BOOST_CHECK_EQUAL( annots.size(), 2);
186 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
188 string annot_data = "0 10 name type\n"
191 "50\t55 anothername\n"
196 "75\t90\tname2\ttype2\n"
197 "100 120 name-asdf type!@#$%\n"
203 //istringstream annot_stream(annot_data);
204 seq.parse_annot(annot_data, 0, 0);
205 std::list<annot> annots_list = seq.annotations();
206 std::vector<annot> annots(annots_list.begin(), annots_list.end());
207 BOOST_REQUIRE_EQUAL( annots.size(), 8);
208 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
209 BOOST_CHECK_EQUAL( annots[0].end, 10 );
210 BOOST_CHECK_EQUAL( annots[0].type, "type");
213 // ticket:83 when you try to load a sequence from a file that doesn't
214 // have fasta headers it crashes.
215 BOOST_AUTO_TEST_CASE( sequence_past_end )
217 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
218 seq_path /= "misformated_seq.fa";
220 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
223 BOOST_AUTO_TEST_CASE ( sequence_empty )
226 BOOST_CHECK_EQUAL( s.empty(), true );
228 BOOST_CHECK_EQUAL( s.empty(), false );
231 BOOST_AUTO_TEST_CASE ( sequence_iterators )
233 std::string seq_string = "AAGGCCTTNNTATA";
234 Sequence s(seq_string);
235 const Sequence cs(s);
236 std::string::size_type count = 0;
238 std::string::iterator str_itor;
239 Sequence::iterator s_itor;
240 Sequence::const_iterator cs_itor;
242 for( str_itor = seq_string.begin(),
244 cs_itor = cs.begin();
245 str_itor != seq_string.end() and
246 s_itor != s.end() and
248 ++str_itor, ++s_itor, ++cs_itor, ++count)
250 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
251 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
252 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
254 BOOST_CHECK_EQUAL( seq_string.size(), count );
255 BOOST_CHECK_EQUAL( s.size(), count );
256 BOOST_CHECK_EQUAL( cs.size(), count );
259 BOOST_AUTO_TEST_CASE( sequence_motifs )
262 string bogus("AATTGGAA");
263 Sequence s1("AAAAGGGGCCCCTTTT");
265 list<motif>::const_iterator motif_i = s1.motifs().begin();
266 list<motif>::const_iterator motif_end = s1.motifs().end();
268 // do our iterators work?
269 BOOST_CHECK( motif_i == s1.motifs().begin() );
270 BOOST_CHECK( motif_end == s1.motifs().end() );
271 BOOST_CHECK( motif_i == motif_end );
273 // this shouldn't show up
275 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
276 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
279 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
280 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
282 for(motif_i = s1.motifs().begin();
283 motif_i != s1.motifs().end();
286 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
287 BOOST_CHECK_EQUAL( motif_i->name, m);
288 BOOST_CHECK_EQUAL( motif_i->sequence, m);
292 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
294 /* FIXME: enable this when i find a way of passing storing the motif name
295 // does our annotation travel?
296 Sequence motif_seq(m);
297 motif_seq.set_fasta_header("hi");
298 s1.add_motif(motif_seq);
300 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
301 for(motif_i = s1.motifs().begin();
302 motif_i != s1.motifs().end();
305 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
306 BOOST_CHECK_EQUAL( motif_i->name, "hi");
307 BOOST_CHECK_EQUAL( motif_i->sequence, m);
312 BOOST_AUTO_TEST_CASE( annot_test )
314 annot a(0, 10, "test", "thing");
316 BOOST_CHECK_EQUAL( a.begin, 0 );
317 BOOST_CHECK_EQUAL( a.end, 10 );
318 BOOST_CHECK_EQUAL( a.type, "test" );
319 BOOST_CHECK_EQUAL( a.name, "thing" );
321 motif m(10, "AAGGCC");
322 BOOST_CHECK_EQUAL( m.begin, 10 );
323 BOOST_CHECK_EQUAL( m.type, "motif" );
324 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
325 BOOST_CHECK_EQUAL( m.end, 10+6 );
328 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
330 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
331 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
332 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
333 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
334 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
335 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
336 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
337 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
339 string gga("GGACACCTC");
342 std::list<Sequence> query_list;
343 std::list<string> string_list;
344 query_list.push_back(Sequence(gc));
345 string_list.push_back(gc);
346 query_list.push_back(Sequence(gga));
347 string_list.push_back(gga);
349 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
350 seq.find_sequences(query_list.begin(), query_list.end());
353 for(list<string>::iterator string_i = string_list.begin();
354 string_i != string_list.end();
357 string::size_type pos=0;
358 while(pos != string::npos) {
359 pos = s.find(*string_i, pos);
360 if (pos != string::npos) {
366 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
369 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
371 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
372 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
373 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
374 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
375 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
376 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
377 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
378 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
382 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
383 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
384 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
385 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
386 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
388 Sequence subseq = seq.subseq(5, 10);
389 const list<annot> annots = subseq.annotations();
390 // generate some ground truth
392 correct.push_back(annot(0, 5, "0-10", "0-10"));
393 correct.push_back(annot(5,10, "10-20", "10-20"));
394 correct.push_back(annot(0,10, "0-20", "0-20"));
395 correct.push_back(annot(3, 7, "8-12", "8-12"));
396 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
398 list<annot>::iterator correct_i = correct.begin();
399 list<annot>::const_iterator annot_i = annots.begin();
400 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
402 BOOST_CHECK( *annot_i == *correct_i );
406 BOOST_AUTO_TEST_CASE( motif_annotation_update )
408 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
409 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
410 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
411 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
412 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
413 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
414 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
415 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
418 // starting conditions
419 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
420 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
421 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
422 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
423 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
424 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
425 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
426 seq.add_motif("CCGTCCC");
427 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
428 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
430 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
431 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
434 BOOST_AUTO_TEST_CASE( out_operator )
436 string s("AAGGCCTT");
441 BOOST_CHECK_EQUAL( s, buf.str() );
444 BOOST_AUTO_TEST_CASE( get_name )
446 Sequence seq("AAGGCCTT");
448 BOOST_CHECK_EQUAL( seq.get_name(), "" );
449 seq.set_species("hooman"); // anyone remember tradewars?
450 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
451 seq.set_fasta_header("fasta human");
452 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
455 BOOST_AUTO_TEST_CASE( serialize_simple )
457 std::string seq_string = "AAGGCCTT";
458 Sequence seq(seq_string);
459 seq.set_species("ribbet");
460 std::ostringstream oss;
461 // allocate/deallocate serialization components
463 boost::archive::text_oarchive oarchive(oss);
464 const Sequence& const_seq(seq);
465 BOOST_CHECK_EQUAL(seq, const_seq);
466 oarchive << const_seq;
471 std::istringstream iss(oss.str());
472 boost::archive::text_iarchive iarchive(iss);
473 iarchive >> seq_loaded;
475 BOOST_CHECK_EQUAL(seq_loaded, seq);
476 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
479 BOOST_AUTO_TEST_CASE( serialize_tree )
481 std::string seq_string = "AAGGCCTT";
482 Sequence seq(seq_string);
483 seq.set_species("ribbet");
486 annot a1(6,7,"t","t");
487 seq.add_annotation(a1);
489 std::ostringstream oss;
490 // allocate/deallocate serialization components
492 boost::archive::text_oarchive oarchive(oss);
493 const Sequence& const_seq(seq);
494 BOOST_CHECK_EQUAL(seq, const_seq);
495 oarchive << const_seq;
500 std::istringstream iss(oss.str());
501 boost::archive::text_iarchive iarchive(iss);
502 iarchive >> seq_loaded;
504 BOOST_CHECK_EQUAL(seq_loaded, seq);
507 BOOST_AUTO_TEST_CASE( serialize_xml_tree )
509 std::string seq_string = "AAGGCCTT";
510 Sequence seq(seq_string);
511 seq.set_species("ribbet");
514 annot a1(6,7,"t","t");
515 seq.add_annotation(a1);
517 std::ostringstream oss;
518 // allocate/deallocate serialization components
520 boost::archive::xml_oarchive oarchive(oss);
521 const Sequence& const_seq(seq);
522 BOOST_CHECK_EQUAL(seq, const_seq);
523 oarchive << boost::serialization::make_nvp("seq", const_seq);
528 std::istringstream iss(oss.str());
529 boost::archive::xml_iarchive iarchive(iss);
530 iarchive >> boost::serialization::make_nvp("seq", seq_loaded);
532 BOOST_CHECK_EQUAL(seq_loaded, seq);