1 #define BOOST_TEST_DYN_LINK
2 #define BOOST_TEST_MODULE
3 #include <boost/test/unit_test.hpp>
5 #include <boost/filesystem/path.hpp>
6 #include <boost/filesystem/operations.hpp>
7 namespace fs=boost::filesystem;
9 #include <boost/algorithm/string/case_conv.hpp>
15 #include <boost/archive/text_oarchive.hpp>
16 #include <boost/archive/text_iarchive.hpp>
17 #include <boost/archive/xml_oarchive.hpp>
18 #include <boost/archive/xml_iarchive.hpp>
20 #include "alg/sequence.hpp"
21 #include "mussa_exceptions.hpp"
25 BOOST_AUTO_TEST_CASE( sequence_copy_constructor )
27 SequenceRef s(new Sequence("AAAAGGGG"));
28 s->set_species("foo");
29 BOOST_CHECK_EQUAL(s->get_species(), "foo");
31 SequenceRef c(new Sequence(s));
32 BOOST_CHECK_EQUAL(c->get_species(), "foo");
34 c->set_species("bar");
35 BOOST_CHECK_EQUAL(s->get_species(), "foo");
36 BOOST_CHECK_EQUAL(c->get_species(), "bar");
39 BOOST_AUTO_TEST_CASE( sequence_copy_constructor_copy_motifs )
41 SequenceRef s(new Sequence("AAAAGGGGAAAA"));
43 BOOST_CHECK_EQUAL(s->motifs().size(), 1);
45 SequenceRef c(new Sequence(s->subseq()));
46 BOOST_CHECK_EQUAL(c->motifs().size(), 1);
49 BOOST_CHECK_EQUAL(s->motifs().size(), 0);
50 // FIXME: Technically c shouldn't lose its motifs.
51 // FIXME: getting that to work is hard.
52 // BOOST_CHECK_EQUAL(c->motifs().size(), 1);
53 BOOST_CHECK_EQUAL(c->motifs().size(), 0);
56 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
59 // make sure that retrieving the sequence doesn't throw an error
60 BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
63 BOOST_AUTO_TEST_CASE( sequence_from_string )
65 std::string str1("AAAT");
67 BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
70 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
72 std::string str1("AAAAT");
74 BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
76 std::string str2("AATTGGCC");
78 BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
81 //! when we try to load a missing file, do we get an error?
82 BOOST_AUTO_TEST_CASE( sequence_load_exception )
85 // there should be errors when we try to load something that doesn't exist
86 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
87 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
90 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
92 string header(">Header");
93 string line1("AAAAGGGGCCCCTTTTT");
94 string line2("AAAAGGGGCCCCTTTTT");
95 int seq_len = line1.size() + line2.size();
98 cr << header << "\015" << line1 << "\015" << line2 << "\015";
100 seq_cr.load_fasta(cr);
103 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
105 seq_crlf.load_fasta(crlf);
108 lf << header << "\012" << line1 << "\012" << line2 << "\012";
110 seq_lf.load_fasta(lf);
112 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
113 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
114 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
118 //! Do simple operations work correctly?
119 BOOST_AUTO_TEST_CASE( sequence_filter )
121 const char *core_seq = "AATTGGCC";
122 Sequence s1(core_seq, reduced_dna_alphabet);
123 BOOST_CHECK_EQUAL(s1, core_seq);
125 Sequence s2("aattggcc", reduced_dna_alphabet);
126 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
127 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
128 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
129 BOOST_CHECK_EQUAL(s2.size(), s2.size());
130 //We're currently forcing sequences to uppercase
131 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
133 Sequence s3("asdfg", reduced_dna_alphabet);
134 BOOST_CHECK_EQUAL(s3, "ANNNG");
135 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
137 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
138 BOOST_CHECK_EQUAL(s3, "AA");
139 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
140 BOOST_CHECK_EQUAL( s3, "GG");
141 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
142 BOOST_CHECK_EQUAL( s3, "CCTT");
145 BOOST_CHECK_EQUAL(s3, "AAGGNN");
148 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
150 std::string agct("AGCT");
151 Sequence seq(agct, nucleic_alphabet);
152 BOOST_CHECK_EQUAL(seq.size(), agct.size());
153 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
155 std::string bdv("BDv");
156 Sequence seq_bdv(bdv, nucleic_alphabet);
157 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
158 // forcing sequence to upper case
159 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
160 boost::algorithm::to_upper_copy(bdv));
164 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
166 std::string agct("AGCT");
168 BOOST_CHECK_EQUAL(seq.size(), agct.size());
169 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
170 BOOST_CHECK_EQUAL(seq[0], agct[0]);
171 BOOST_CHECK_EQUAL(seq[1], agct[1]);
172 BOOST_CHECK_EQUAL(seq[2], agct[2]);
173 BOOST_CHECK_EQUAL(seq[3], agct[3]);
175 std::string bdv("BDv");
176 Sequence seq_bdv(bdv);
177 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
178 // default alphabet only allows AGCTUN
179 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
182 BOOST_AUTO_TEST_CASE( subseq_names )
184 Sequence s1("AAGGCCTT", reduced_dna_alphabet);
185 s1.set_species("species");
186 s1.set_fasta_header("a fasta header");
187 Sequence s2 = s1.subseq(2,2);
188 BOOST_CHECK_EQUAL(s2, "GG");
189 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
190 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
193 BOOST_AUTO_TEST_CASE( sequence_start_stop )
196 BOOST_CHECK_EQUAL( s1.start(), 0 );
197 BOOST_CHECK_EQUAL( s1.stop(), 0 );
199 std::string seq_string("AAGGCCTT");
200 Sequence s2(seq_string, reduced_dna_alphabet);
201 BOOST_CHECK_EQUAL( s2.start(), 0 );
202 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
204 std::string s3seq_string = seq_string.substr(2,3);
205 Sequence s3 = s2.subseq(2,3);
206 BOOST_CHECK_EQUAL( s3.start(), 2);
207 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
208 BOOST_CHECK_EQUAL( s3.size(), 3);
209 BOOST_CHECK_EQUAL( s3, s3seq_string);
211 std::string s4seq_string = s3seq_string.substr(1,1);
212 Sequence s4 = s3.subseq(1,1);
213 BOOST_CHECK_EQUAL( s4.start(), 1 );
214 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
215 BOOST_CHECK_EQUAL( s4.size(), 1);
216 BOOST_CHECK_EQUAL( s4, s4seq_string);
219 //! Can we load data from a file
220 BOOST_AUTO_TEST_CASE( sequence_load )
222 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
223 seq_path /= "human_mck_pro.fa";
225 s.load_fasta(seq_path, reduced_dna_alphabet);
226 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
227 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
228 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
229 "muscle creatine kinase gene (CKMM), "
233 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
235 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
236 seq_path /= "broken.fa";
237 bool exception_thrown = false;
238 std::string exception_filename;
241 s.load_fasta(seq_path);
242 } catch(sequence_invalid_load_error e) {
243 exception_thrown = true;
244 size_t native_string_size = seq_path.native_file_string().size();
245 std:string estr(e.what());
246 BOOST_REQUIRE(estr.size() > native_string_size);
247 std::copy(estr.begin(), estr.begin()+native_string_size,
248 std::back_inserter(exception_filename));
250 BOOST_CHECK_EQUAL(exception_thrown, true);
251 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
254 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
256 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
257 seq_path /= "mouse_mck_pro.fa";
258 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
259 annot_path /= "broken.annot";
260 bool exception_thrown = false;
262 s.load_fasta(seq_path);
264 std::string exception_filename;
266 s.load_annot(annot_path, 0, 0);
267 } catch(annotation_load_error e) {
268 exception_thrown = true;
269 std:string estr(e.what());
270 size_t native_string_size = annot_path.native_file_string().size();
271 BOOST_REQUIRE(estr.size() > native_string_size);
272 std::copy(estr.begin(), estr.begin()+native_string_size,
273 std::back_inserter(exception_filename));
275 BOOST_CHECK_EQUAL(exception_thrown, true);
276 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
279 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
281 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
282 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
283 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
284 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
285 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
286 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
287 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
288 std::stringstream garbage_fasta(garbage_string);
291 s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
292 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
293 reduced_dna_alphabet),
294 sequence_invalid_load_error);
295 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
296 reduced_dna_alphabet),
297 sequence_invalid_load_error);
298 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
299 reduced_dna_alphabet),
300 sequence_invalid_load_error);
304 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
306 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
307 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
308 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
309 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
310 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
311 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
312 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
313 std::stringstream garbage_fasta(garbage_string);
316 s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
317 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
318 reduced_rna_alphabet),
319 sequence_invalid_load_error);
320 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
321 reduced_rna_alphabet),
322 sequence_invalid_load_error);
323 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
324 reduced_rna_alphabet),
325 sequence_invalid_load_error);
328 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
330 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
331 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
332 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
333 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
334 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
335 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
336 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
337 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
338 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
339 std::stringstream garbage_fasta(garbage_string);
343 // there's two copies of reduced_rna_fasta because i didn't feel like
344 // figuring out how to properly reset the read pointer in a stringstream
345 s.load_fasta(reduced_rna_fasta1);
346 specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
347 BOOST_CHECK_EQUAL(s, specific);
349 s.load_fasta(reduced_dna_fasta1);
350 specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
351 BOOST_CHECK_EQUAL(s, specific);
353 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
354 sequence_invalid_load_error);
355 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
356 sequence_invalid_load_error);
359 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
361 std::string fasta_file(
362 ">gi|10129974|gb|AF188002.1|AF188002\n"
363 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
364 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
365 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
366 ">gi|1621|emb|X55146.1|OCMCK1\n"
367 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
369 istringstream seq1_file(fasta_file);
371 seq1.load_fasta(seq1_file, 1, 0, 0);
372 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
374 istringstream seq2_file(fasta_file);
376 seq2.load_fasta(seq2_file, 2, 0, 0);
377 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
379 istringstream seq3_file(fasta_file);
381 seq3.load_fasta(seq3_file, 3, 0, 0);
382 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
385 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
387 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
388 Sequence seq(iupac_symbols, nucleic_alphabet);
389 Sequence seqr = seq.rev_comp();
391 BOOST_CHECK( seq != seqr );
392 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
393 // forcing sequence to upper case
394 BOOST_CHECK_EQUAL( seq.get_sequence(),
395 boost::algorithm::to_upper_copy(iupac_symbols) );
398 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
400 std::string dna_str("AGCTN");
401 Sequence dna_seq(dna_str, reduced_dna_alphabet);
402 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
403 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
406 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
408 std::string rna_str("AGCUN");
409 Sequence rna_seq(rna_str, reduced_rna_alphabet);
410 BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
411 BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
412 rna_seq.rev_comp().rev_comp().get_sequence());
415 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
417 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
418 Sequence seq(dna_str, reduced_dna_alphabet);
419 Sequence subseq = seq.subseq(8,4);
420 BOOST_CHECK_EQUAL( subseq, "AAGG");
421 Sequence rev_subseq = subseq.rev_comp();
422 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
423 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
426 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
428 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
429 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
430 Sequence seq(dna_str);
431 std::string seq_reversed(seq.rbegin(), seq.rend());
432 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
434 std::string substr = dna_str.substr(8,4);
435 Sequence subseq = seq.subseq(8,4);
436 BOOST_CHECK_EQUAL(substr, subseq);
438 std::string substr_reversed(substr.rbegin(), substr.rend());
439 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
440 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
443 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
445 // so what happens with reverse interators when we have no sequence?
448 Sequence seq3("AGCT");
450 // all the empty sequences should have equal iterators
451 BOOST_CHECK(seq1.rbegin() == seq1.rend());
452 BOOST_CHECK(seq1.rbegin() == seq2.rend());
454 // none of the seq1 iterators should equal any of the seq3 iterators
455 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
456 BOOST_CHECK(seq1.rbegin() != seq3.rend());
457 BOOST_CHECK(seq1.rend() != seq3.rbegin());
458 BOOST_CHECK(seq1.rend() != seq3.rend());
460 // seq3 iterators should work
461 BOOST_CHECK(seq3.rbegin() != seq3.rend());
465 BOOST_AUTO_TEST_CASE( annotation_load )
467 string annot_data = "human\n"
468 "0 10 name type\n" //0
471 "50\t55 anothername\n" //3
472 "60 50 backward\n" //4
473 ">ident3 asdf\n" //7 (as these are added last)
476 "75\t90\tname2\ttype2\n" //5
477 "100 120 name-asdf type!@#$%\n" //6
481 Sequence seq(s, reduced_dna_alphabet);
483 //istringstream annot_stream(annot_data);
484 seq.parse_annot(annot_data, 0, 0);
485 SeqSpanRefList annots_list(seq.annotations());
486 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
487 BOOST_REQUIRE_EQUAL( annots.size(), 8);
488 BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
489 BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
490 BOOST_REQUIRE( annots[0]->annotations() );
491 BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
492 BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
493 BOOST_REQUIRE( annots[1]->annotations() );
494 BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
495 BOOST_REQUIRE( annots[2]->annotations() );
496 BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
497 BOOST_REQUIRE( annots[3]->annotations() );
498 BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
499 BOOST_REQUIRE( annots[4]->annotations() );
500 BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
501 BOOST_REQUIRE( annots[5]->annotations() );
502 BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
503 BOOST_CHECK_EQUAL( annots[5]->start(), 75);
504 BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
505 BOOST_CHECK_EQUAL( annots[6]->start(), 100);
506 BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
507 BOOST_REQUIRE( annots[6]->annotations() );
508 BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
509 BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
510 // sequence defined annotations will always be after the
511 // absolute positions
512 BOOST_REQUIRE( annots[7]->annotations() );
513 BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
514 BOOST_CHECK_EQUAL( annots[7]->start(), 100);
515 BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
517 //BOOST_CHECK_EQUAL( annots
520 BOOST_AUTO_TEST_CASE( annotation_broken_load )
522 string annot_data = "human\n"
524 "blah60 50 backward\n"
531 Sequence seq(s, reduced_dna_alphabet);
533 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
534 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
537 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
539 // this actually is basically what's returned by UCSC
540 // (well actually with some of the sequence and copies of fasta blocks
541 // removed to make the example shorter
542 string annot_data = "\n"
544 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
545 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
546 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
547 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
555 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
557 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
558 Sequence seq(s, reduced_dna_alphabet);
559 seq.parse_annot(annot_data);
560 SeqSpanRefList annots(seq.annotations());
561 BOOST_CHECK_EQUAL( annots.size(), 2);
564 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
566 string annot_data = "0 10 name type\n"
569 "50\t55 anothername\n"
574 "75\t90\tname2\ttype2\n"
575 "100 120 name-asdf type!@#$%\n"
579 Sequence seq(s, reduced_dna_alphabet);
581 //istringstream annot_stream(annot_data);
582 seq.parse_annot(annot_data, 0, 0);
583 SeqSpanRefList annots_list(seq.annotations());
584 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
585 BOOST_REQUIRE_EQUAL( annots.size(), 8);
586 BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
587 BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
588 BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
591 // when we do a subsequence (or something that calls copy_children)
592 // the annotations need to be updated to have the right parent
593 BOOST_AUTO_TEST_CASE( update_annotations_seqref )
595 Sequence s1("AAAAGGGG");
596 s1.add_annotation("A", "A", 0, 4);
597 BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
598 BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
600 Sequence subseq1(s1.subseq(2,4));
601 BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
602 BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
603 BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
604 BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
607 // ticket:83 when you try to load a sequence from a file that doesn't
608 // have fasta headers it crashes.
609 BOOST_AUTO_TEST_CASE( sequence_past_end )
611 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
612 seq_path /= "misformated_seq.fa";
614 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
617 BOOST_AUTO_TEST_CASE ( sequence_empty )
621 BOOST_CHECK_EQUAL( s.empty(), true );
623 BOOST_CHECK_EQUAL( s.empty(), false );
625 BOOST_CHECK_EQUAL( s.empty(), true);
627 BOOST_CHECK_EQUAL( s.empty(), true);
630 BOOST_AUTO_TEST_CASE ( sequence_size )
634 BOOST_CHECK_EQUAL( s.size(), 0);
635 std::string seq_string("AAAGGG");
637 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
639 BOOST_CHECK_EQUAL( s.size(), 0);
641 BOOST_CHECK_EQUAL( s.size(), 0);
644 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
646 Sequence szero("", reduced_dna_alphabet);
647 BOOST_CHECK_EQUAL(szero.empty(), true);
648 BOOST_CHECK_EQUAL(szero, szero);
649 BOOST_CHECK_EQUAL(szero, "");
651 Sequence sclear("AGCT", reduced_dna_alphabet);
653 BOOST_CHECK_EQUAL(sclear.empty(), true);
654 BOOST_CHECK_EQUAL(sclear, sclear);
655 BOOST_CHECK_EQUAL(sclear, szero);
656 BOOST_CHECK_EQUAL(sclear, "");
659 BOOST_AUTO_TEST_CASE ( sequence_iterators )
661 std::string seq_string = "AAGGCCTTNNTATA";
662 Sequence s(seq_string, reduced_dna_alphabet);
663 const Sequence cs(s);
664 std::string::size_type count = 0;
666 std::string::iterator str_itor;
667 Sequence::const_iterator s_itor;
668 Sequence::const_iterator cs_itor;
670 for( str_itor = seq_string.begin(),
672 cs_itor = cs.begin();
673 str_itor != seq_string.end() and
674 s_itor != s.end() and
676 ++str_itor, ++s_itor, ++cs_itor, ++count)
678 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
679 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
680 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
682 BOOST_CHECK_EQUAL( seq_string.size(), count );
683 BOOST_CHECK_EQUAL( s.size(), count );
684 BOOST_CHECK_EQUAL( cs.size(), count );
687 BOOST_AUTO_TEST_CASE( sequence_motifs )
690 string bogus("AATTGGAA");
691 Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
693 list<motif>::const_iterator motif_i = s1.motifs().begin();
694 list<motif>::const_iterator motif_end = s1.motifs().end();
696 // do our iterators work?
697 BOOST_CHECK( motif_i == s1.motifs().begin() );
698 BOOST_CHECK( motif_end == s1.motifs().end() );
699 BOOST_CHECK( motif_i == motif_end );
701 // this shouldn't show up
703 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
704 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
707 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
708 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
710 for(motif_i = s1.motifs().begin();
711 motif_i != s1.motifs().end();
714 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
715 BOOST_CHECK_EQUAL( motif_i->name, m);
716 BOOST_CHECK_EQUAL( motif_i->sequence, m);
720 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
722 /* FIXME: enable this when i find a way of passing storing the motif name
723 // does our annotation travel?
724 Sequence motif_seq(m);
725 motif_seq.set_fasta_header("hi");
726 s1.add_motif(motif_seq);
728 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
729 for(motif_i = s1.motifs().begin();
730 motif_i != s1.motifs().end();
733 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
734 BOOST_CHECK_EQUAL( motif_i->name, "hi");
735 BOOST_CHECK_EQUAL( motif_i->sequence, m);
740 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
742 // when searching for a motif on a subsequence we should
743 // only search the subsequence ticket:199
746 Sequence s1("AAAANCCCC", reduced_dna_alphabet);
748 // this shouldn't show up
750 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
753 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
755 Sequence subseq1 = s1.subseq(4,5);
756 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
757 subseq1.clear_motifs();
758 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
759 // this is outside of our subsequence, and so shouldn't be found
760 subseq1.add_motif(aaaa);
761 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
763 subseq1.add_motif(cccc);
764 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
765 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
766 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
767 BOOST_CHECK_EQUAL(motif_i->begin, 1);
768 BOOST_CHECK_EQUAL(motif_i->end, 5);
771 BOOST_AUTO_TEST_CASE( annot_test )
773 Sequence s("AAAAAAAAAA");
774 s.add_annotation("test", "thing", 0, 10);
775 SeqSpanRef a(s.annotations().front());
777 BOOST_CHECK_EQUAL( a->start(), 0 );
778 BOOST_CHECK_EQUAL( a->stop(), 10 );
779 BOOST_CHECK_EQUAL( a->annotations()->get("name"), "test" );
780 BOOST_CHECK_EQUAL( a->annotations()->get("type"), "thing" );
782 motif m(10, "AAGGCC");
783 BOOST_CHECK_EQUAL( m.begin, 10 );
784 BOOST_CHECK_EQUAL( m.type, "motif" );
785 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
786 BOOST_CHECK_EQUAL( m.end, 10+6 );
789 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
791 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
792 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
793 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
794 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
795 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
796 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
797 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
798 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
800 string gga("GGACACCTC");
801 Sequence seq(s, reduced_dna_alphabet);
803 std::list<Sequence> query_list;
804 std::list<string> string_list;
805 query_list.push_back(Sequence(gc));
806 string_list.push_back(gc);
807 query_list.push_back(Sequence(gga));
808 string_list.push_back(gga);
810 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
811 seq.find_sequences(query_list.begin(), query_list.end());
814 for(list<string>::iterator string_i = string_list.begin();
815 string_i != string_list.end();
818 string::size_type pos=0;
819 while(pos != string::npos) {
820 pos = s.find(*string_i, pos);
821 if (pos != string::npos) {
827 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
828 const SeqSpanRefList& a = seq.annotations();
829 for (SeqSpanRefList::const_iterator annot_i = a.begin();
833 //FIXME: was I doing something here?
834 int count = (*annot_i)->stop() - (*annot_i)->start();
838 BOOST_AUTO_TEST_CASE( sequence_no_trailing_newline )
840 // sorry about the long string...
841 string s = "AATTACACAAGGAATATAGGTAGTTTGAATAAAAATATCTTTAACAGCTTGGAGCTATTGAGACAGGAACACTTCCACGCACATGCACAGTTAAACAACTTGAGTGCAACACACAACATTGGCACTAAACGAGATTGAAGGGGGACTTTTTGTGTGTTTTTTTTTCTCTTTTCTTTTTTTGTTATAGTTACTTCAAGTAACACAGCTTGCTTCATATAAATAAGTTAAAACATCTATTTTTTTTCAAGACAAAGCCATTCAGGACAAAGAGATGAACAGAAAGCAGATCTACTTATACAGGCGCTATAATGGCAATAAACAGGCTCATGATTAAAAGATGAATTAGGGCAACGAGAACAGGGCTTCTTCACAGAAGGAACACAAGGGAGTTTCAGAAAGTCACCTTAGTACTGACACTACGCGGGATCCGCTAATACTGCTCAGTACTTTAAACGCTCAGATACTCAGGGACGGAAGGCCCCTCCTGCCGCGGCCATGCTCATGCTTTTCAGCTTATTATCTTTTTTCCACTTCATTCTCCGGTTTTGGAACCAGATTTTAATTTGTCTCTCGGAGAGGCAAAGAGCATGTGCTATTTCAATCCTCCTTCTGCGGGTCAGGTAACGGTTGAAGTGGAACTCCTTCTCCAGCTCCAGGGTCTGGTAGCGCGTGTAGGCCGTCCGGGCCCTTTTGCCTTCCGGGCCGCCTATGTTGTCTGCAATAGAAAAGTCAGCGGTTTAGCCACCAACTCCTGTCTTCCAAAGTCCGCCAGGGGGACAAGCTTGGGTCATGAGCAGGGAACCCAGGCGAAAAGCTCAACAAGTTCTGCCTACCAGCCCGCACACCCCTCCCGAATTTCCTTCTCTCTTCCTTTCTAGAAAGAAAACAATACGATTTGGACCCTGGGAACAATCTGCCCATCTGAGGCTGGGGCCGTGTCCCGGCGGACTCCGGCTTTCCCTGGCCCCTCTCCTGCCCCCTCCGCCCTGCCCCGGGCGCCCCGATCGGGAGGCACAGCCCTCCCAGGCTGCCCACCGCACAGAAACCCAGGAAGCAAGGCCCTTTCCTGAGCGCCCAAGTGGCCTTCGGGTCACCCTCCCTCAAAGTTCCAGCCCCGAGAGCCGCCTCCCGTTTCCAGCCTGCAGGGTTGGGGAGCCTGTTTTCTTTTTCTTCCCTTTCCTTCTCTCTCCCTCCTGCCCCCAAAATTCAGAATCCTGCAGGCTCTCGCCTCGATTCTTTCCCCCAAGCCCCTTTTCGGGGGCTGTAATTAGTAACGCTGTTTCCCCAGCGTAGCCCTCCTCATAAATTATCCGCCGTGACAAGCCCGATTCACGGCTGCTACAGCCATCCTCTACCTCTCTGCGCCTTGCTCGGCTGGCCTGACCCGGGAGCGCGTCCCAAGGCGTGGGGTTCCAGAGGGGTTTTTTGCTTCCTCCCCCTTCCAACGTCTAAACTGTCCCAGAGAACGCCCATTTCCCCCACTATTTGTGAGCGCAGGGTGCTCGCAAAGAAGAGGAGGAAGGAGGAAGGCAGGGGAGGGAGAACGGCAAGGAGAGCTCCGCAGGGCTGGGAGAAATGAGACCAAGAGAGACTGGGAGAGGGCGGCAGAGAAGAGAGGGGGGACCGAGAGCCGCGTCCCCGCGGTCGCGTGGATTTAGAAAAAGGCTGGCTTTACCATGACTTATGTGCAGCTTGCGCATCCAGGGGTAGATCTGGGGTTGGGCGGGCGGCGCCGGGCTCGGCTCGCTCTGCGCACTCGCCTGCTCGCTGCTGGCAGGGGCGTCCTCCTCGGCTCCGGACGCCGTGCCAACCCCCTCTCTGCTGCTGATGTGGGTGCTGCCGGCGTCGGCCGAGGCGCCGCTGGAGTTGCTTAGGGAGTTTTTCCCGCCGTGGTGGCTGTCGCTGCCGGGCGAGGGGGCCACGGCGGAGCAGGGCAGCGGATCGGGCTGAGGAGAGTGCGTGGACGTGGCCGGCTGGCTGTACCTGGGCTCGGCGGGCGCCGCGCTGGCGCTGGCAGCGTAGCTGCGGGCGCGCTCTCCGGAGCCAAAGTGGCCGGAGCCCGAGCGGCCGACGCTGAGATCCATGCCATTGTAGCCGTAGCCGTACCTGCCGGAGTGCATGCTCGCCGAGTCCCTGAATTGCTCGCTCACGGAACTATGATCTCCATAATTATGCAACTGGTAGTCCGGGCCATTTGGATAGCGACCGCAAAATGAGTTTACAAAATAAGAGCTCATTTGTTTTTTGATATGTGTGCTTGATTTGTGGCTCGCGGTCGTTTGTGCGTCTATAGCACCCTT";
842 std::string species = "HumanHXA5\n";
843 std::string header0 = ">hg18_knownGene_NM_019102_0\n";
844 std::string str0 = "GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG";
845 std::string header1 = ">hg18_knownGene_NM_019102_1\n";
846 std::string str1 = "ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT";
854 // need to convert strings to sequences for reverse complementing
855 Sequence seq0(str0, reduced_dna_alphabet);
856 Sequence seq1(str1, reduced_dna_alphabet);
858 Sequence annotated_seq(s, reduced_dna_alphabet);
859 annotated_seq.load_annot(annot, 0, 0);
861 SeqSpanRefList annots_list = annotated_seq.annotations();
862 // both sequences were found
863 BOOST_REQUIRE_EQUAL( annots_list.size(), 2 );
865 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
866 // are they the same sequence?
867 BOOST_CHECK_EQUAL( annots[0]->size(), seq0.size());
868 BOOST_CHECK_EQUAL( annots[0]->sequence(), seq0.rev_comp() );
869 // this should hopefully catch the case when my hack in
870 // sequence.cpp::push_back_seq::operator() is no longer needed.
871 // spirit (or my grammar was duplicating the last char,
872 // the hack removes the duplicate. but if what ever's causing
873 // the dup gets fixed actual meaningful data will be being removed.
874 // see mussa ticket:265 for more information
875 BOOST_CHECK_EQUAL( annots[1]->size(), seq1.size());
876 BOOST_CHECK_EQUAL( annots[1]->sequence(), seq1.rev_comp() );
880 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
882 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
883 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
884 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
885 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
886 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
887 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
888 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
889 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
890 Sequence seq(s, reduced_dna_alphabet);
892 seq.add_annotation("0-10", "0-10", 0, 10);
893 seq.add_annotation("10-20", "10-20", 10, 20);
894 seq.add_annotation("0-20", "0-20", 0, 20);
895 seq.add_annotation("8-12", "8-12", 8, 12);
896 seq.add_annotation("100-5000", "100-5000", 100, 5000);
898 Sequence subseq = seq.subseq(5, 10);
899 SeqSpanRefList annots_list = subseq.annotations();
900 BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
902 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
903 BOOST_CHECK_EQUAL( annots[0]->parentStart(), 0);
904 BOOST_CHECK_EQUAL( annots[0]->size(), 5);
905 BOOST_REQUIRE( annots[0]->annotations() );
906 BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
908 BOOST_CHECK_EQUAL( annots[1]->parentStart(), 5);
909 BOOST_CHECK_EQUAL( annots[1]->size(), 5);
910 BOOST_REQUIRE( annots[1]->annotations() );
911 BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
913 BOOST_CHECK_EQUAL( annots[2]->parentStart(), 0);
914 BOOST_CHECK_EQUAL( annots[2]->size(), 10);
915 BOOST_REQUIRE( annots[2]->annotations() );
916 BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
918 BOOST_CHECK_EQUAL( annots[3]->parentStart(), 3);
919 BOOST_CHECK_EQUAL( annots[3]->size(), 7);
920 BOOST_REQUIRE( annots[3]->annotations() );
921 BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
924 BOOST_AUTO_TEST_CASE( motif_annotation_update )
926 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
927 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
928 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
929 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
930 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
931 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
932 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
933 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
934 Sequence seq(s, reduced_dna_alphabet);
936 // starting conditions
937 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
938 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
939 seq.add_annotation("0-10", "0-10", 0, 10);
940 seq.add_annotation("10-20", "10-20", 10, 20);
941 seq.add_annotation("0-20", "0-20", 0, 20);
942 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
943 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
944 seq.add_motif("CCGTCCC");
945 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
946 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
948 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
949 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
952 BOOST_AUTO_TEST_CASE( out_operator )
954 string s("AAGGCCTT");
955 Sequence seq(s, reduced_dna_alphabet);
959 BOOST_CHECK_EQUAL( s, buf.str() );
962 BOOST_AUTO_TEST_CASE( get_name )
964 Sequence seq("AAGGCCTT", reduced_dna_alphabet);
966 BOOST_CHECK_EQUAL( seq.get_name(), "" );
967 seq.set_species("hooman"); // anyone remember tradewars?
968 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
969 seq.set_fasta_header("fasta human");
970 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
973 BOOST_AUTO_TEST_CASE( serialize_simple )
975 std::string seq_string = "AAGGCCTT";
976 Sequence seq(seq_string, reduced_dna_alphabet);
977 seq.set_species("ribbet");
978 std::ostringstream oss;
979 // allocate/deallocate serialization components
981 boost::archive::text_oarchive oarchive(oss);
982 const Sequence& const_seq(seq);
983 BOOST_CHECK_EQUAL(seq, const_seq);
984 oarchive << const_seq;
988 std::istringstream iss(oss.str());
989 boost::archive::text_iarchive iarchive(iss);
990 iarchive >> seq_loaded;
992 BOOST_CHECK_EQUAL(seq_loaded, seq);
993 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
996 BOOST_AUTO_TEST_CASE( serialize_tree )
998 std::string seq_string = "AAGGCCTT";
999 Sequence seq(seq_string, reduced_dna_alphabet);
1000 seq.set_species("ribbet");
1001 seq.add_motif("AA");
1002 seq.add_motif("GC");
1003 seq.add_annotation("t", "t", 6, 7);
1005 std::ostringstream oss;
1006 // allocate/deallocate serialization components
1008 boost::archive::text_oarchive oarchive(oss);
1009 const Sequence& const_seq(seq);
1010 BOOST_CHECK_EQUAL(seq, const_seq);
1011 oarchive << const_seq;
1014 Sequence seq_loaded;
1016 std::istringstream iss(oss.str());
1017 boost::archive::text_iarchive iarchive(iss);
1018 iarchive >> seq_loaded;
1020 BOOST_CHECK_EQUAL(seq_loaded, seq);
1023 // this writes out an "old" style annotated sequence
1024 // with annotations attached as "motifs" and "annots"
1025 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
1027 std::string seq_string = "AAGGCCTT";
1028 Sequence seq(seq_string, reduced_dna_alphabet);
1029 seq.set_species("ribbet");
1030 seq.add_motif("AA");
1031 seq.add_motif("GC");
1032 seq.add_annotation("t", "t", 6, 7);
1034 std::ostringstream oss;
1035 // allocate/deallocate serialization components
1037 boost::archive::xml_oarchive oarchive(oss);
1038 const Sequence& const_seq(seq);
1039 BOOST_CHECK_EQUAL(seq, const_seq);
1040 oarchive << boost::serialization::make_nvp("root", const_seq);
1042 Sequence seq_loaded;
1044 std::istringstream iss(oss.str());
1045 boost::archive::xml_iarchive iarchive(iss);
1046 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
1048 BOOST_CHECK_EQUAL(seq_loaded, seq);
1051 BOOST_AUTO_TEST_CASE( serialize_xml_two )
1053 std::string seq_string = "AAGGCCTT";
1054 Sequence seq1(seq_string, reduced_dna_alphabet);
1055 Sequence seq2(seq1);
1057 std::ostringstream oss;
1058 // allocate/deallocate serialization components
1060 boost::archive::xml_oarchive oarchive(oss);
1061 const Sequence& const_seq1(seq1);
1062 const Sequence& const_seq2(seq2);
1063 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
1064 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
1066 //std::cout << "xml: " << oss.str() << std::endl;
1067 Sequence seq1_loaded;
1068 Sequence seq2_loaded;
1070 std::istringstream iss(oss.str());
1071 boost::archive::xml_iarchive iarchive(iss);
1072 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
1073 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
1075 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
1076 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
1077 // test if our pointers are the same
1078 BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());