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;
7 #include <boost/algorithm/string/case_conv.hpp>
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>
18 #include "alg/sequence.hpp"
19 #include "mussa_exceptions.hpp"
23 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
26 // make sure that retrieving the sequence doesn't throw an error
27 BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
30 BOOST_AUTO_TEST_CASE( sequence_from_string )
32 std::string str1("AAAT");
34 BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
37 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
39 std::string str1("AAAAT");
41 BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
43 std::string str2("AATTGGCC");
45 BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
48 //! when we try to load a missing file, do we get an error?
49 BOOST_AUTO_TEST_CASE( sequence_load_exception )
52 // there should be errors when we try to load something that doesn't exist
53 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
54 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
57 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
59 string header(">Header");
60 string line1("AAAAGGGGCCCCTTTTT");
61 string line2("AAAAGGGGCCCCTTTTT");
62 int seq_len = line1.size() + line2.size();
65 cr << header << "\015" << line1 << "\015" << line2 << "\015";
67 seq_cr.load_fasta(cr);
70 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
72 seq_crlf.load_fasta(crlf);
75 lf << header << "\012" << line1 << "\012" << line2 << "\012";
77 seq_lf.load_fasta(lf);
79 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
80 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
81 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
85 //! Do simple operations work correctly?
86 BOOST_AUTO_TEST_CASE( sequence_filter )
88 const char *core_seq = "AATTGGCC";
89 Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
90 BOOST_CHECK_EQUAL(s1, core_seq);
92 Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
93 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
94 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
95 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
96 BOOST_CHECK_EQUAL(s2.size(), s2.size());
97 //We're currently forcing sequences to uppercase
98 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
100 Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
101 BOOST_CHECK_EQUAL(s3, "ANNNG");
102 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
104 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
105 BOOST_CHECK_EQUAL(s3, "AA");
106 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
107 BOOST_CHECK_EQUAL( s3, "GG");
108 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
109 BOOST_CHECK_EQUAL( s3, "CCTT");
112 BOOST_CHECK_EQUAL(s3, "AAGGNN");
115 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
117 std::string agct("AGCT");
118 Sequence seq(agct, Sequence::nucleic_alphabet);
119 BOOST_CHECK_EQUAL(seq.size(), agct.size());
120 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
122 std::string bdv("BDv");
123 Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
124 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
125 // forcing sequence to upper case
126 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
127 boost::algorithm::to_upper_copy(bdv));
131 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
133 std::string agct("AGCT");
135 BOOST_CHECK_EQUAL(seq.size(), agct.size());
136 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
137 BOOST_CHECK_EQUAL(seq[0], agct[0]);
138 BOOST_CHECK_EQUAL(seq[1], agct[1]);
139 BOOST_CHECK_EQUAL(seq[2], agct[2]);
140 BOOST_CHECK_EQUAL(seq[3], agct[3]);
142 std::string bdv("BDv");
143 Sequence seq_bdv(bdv);
144 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
145 // default alphabet only allows AGCTUN
146 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
149 BOOST_AUTO_TEST_CASE( subseq_names )
151 Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
152 s1.set_species("species");
153 s1.set_fasta_header("a fasta header");
154 Sequence s2 = s1.subseq(2,2);
155 BOOST_CHECK_EQUAL(s2, "GG");
156 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
157 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
160 BOOST_AUTO_TEST_CASE( sequence_start_stop )
163 BOOST_CHECK_EQUAL( s1.start(), 0 );
164 BOOST_CHECK_EQUAL( s1.stop(), 0 );
166 std::string seq_string("AAGGCCTT");
167 Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
168 BOOST_CHECK_EQUAL( s2.start(), 0 );
169 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
171 std::string s3seq_string = seq_string.substr(2,3);
172 Sequence s3 = s2.subseq(2,3);
173 BOOST_CHECK_EQUAL( s3.start(), 2);
174 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
175 BOOST_CHECK_EQUAL( s3.size(), 3);
176 BOOST_CHECK_EQUAL( s3, s3seq_string);
178 std::string s4seq_string = s3seq_string.substr(1,1);
179 Sequence s4 = s3.subseq(1,1);
180 BOOST_CHECK_EQUAL( s4.start(), 1 );
181 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
182 BOOST_CHECK_EQUAL( s4.size(), 1);
183 BOOST_CHECK_EQUAL( s4, s4seq_string);
186 //! Can we load data from a file
187 BOOST_AUTO_TEST_CASE( sequence_load )
189 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
190 seq_path /= "human_mck_pro.fa";
192 s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
193 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
194 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
195 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
196 "muscle creatine kinase gene (CKMM), "
200 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
202 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
203 seq_path /= "broken.fa";
204 bool exception_thrown = false;
205 std::string exception_filename;
208 s.load_fasta(seq_path);
209 } catch(sequence_invalid_load_error e) {
210 exception_thrown = true;
211 size_t native_string_size = seq_path.native_file_string().size();
212 std:string estr(e.what());
213 BOOST_REQUIRE(estr.size() > native_string_size);
214 std::copy(estr.begin(), estr.begin()+native_string_size,
215 std::back_inserter(exception_filename));
217 BOOST_CHECK_EQUAL(exception_thrown, true);
218 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
221 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
223 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
224 seq_path /= "mouse_mck_pro.fa";
225 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
226 annot_path /= "broken.annot";
227 bool exception_thrown = false;
229 s.load_fasta(seq_path);
231 std::string exception_filename;
233 s.load_annot(annot_path, 0, 0);
234 } catch(annotation_load_error e) {
235 exception_thrown = true;
236 std:string estr(e.what());
237 size_t native_string_size = annot_path.native_file_string().size();
238 BOOST_REQUIRE(estr.size() > native_string_size);
239 std::copy(estr.begin(), estr.begin()+native_string_size,
240 std::back_inserter(exception_filename));
242 BOOST_CHECK_EQUAL(exception_thrown, true);
243 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
246 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
248 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
249 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
250 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
251 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
252 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
253 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
254 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
255 std::stringstream garbage_fasta(garbage_string);
258 s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
259 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
260 Sequence::reduced_dna_alphabet),
261 sequence_invalid_load_error);
262 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
263 Sequence::reduced_dna_alphabet),
264 sequence_invalid_load_error);
265 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
266 Sequence::reduced_dna_alphabet),
267 sequence_invalid_load_error);
271 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
273 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
274 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
275 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
276 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
277 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
278 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
279 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
280 std::stringstream garbage_fasta(garbage_string);
283 s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
284 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
285 Sequence::reduced_rna_alphabet),
286 sequence_invalid_load_error);
287 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
288 Sequence::reduced_rna_alphabet),
289 sequence_invalid_load_error);
290 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
291 Sequence::reduced_rna_alphabet),
292 sequence_invalid_load_error);
295 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
297 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
298 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
299 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
300 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
301 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
302 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
303 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
304 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
305 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
306 std::stringstream garbage_fasta(garbage_string);
310 // there's two copies of reduced_rna_fasta because i didn't feel like
311 // figuring out how to properly reset the read pointer in a stringstream
312 s.load_fasta(reduced_rna_fasta1);
313 specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
314 BOOST_CHECK_EQUAL(s, specific);
316 s.load_fasta(reduced_dna_fasta1);
317 specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
318 BOOST_CHECK_EQUAL(s, specific);
320 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
321 sequence_invalid_load_error);
322 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
323 sequence_invalid_load_error);
326 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
328 std::string fasta_file(
329 ">gi|10129974|gb|AF188002.1|AF188002\n"
330 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
331 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
332 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
333 ">gi|1621|emb|X55146.1|OCMCK1\n"
334 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
336 istringstream seq1_file(fasta_file);
338 seq1.load_fasta(seq1_file, 1, 0, 0);
339 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
341 istringstream seq2_file(fasta_file);
343 seq2.load_fasta(seq2_file, 2, 0, 0);
344 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
346 istringstream seq3_file(fasta_file);
348 seq3.load_fasta(seq3_file, 3, 0, 0);
349 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
352 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
354 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
355 Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
356 Sequence seqr = seq.rev_comp();
358 BOOST_CHECK( seq != seqr );
359 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
360 // forcing sequence to upper case
361 BOOST_CHECK_EQUAL( seq.get_sequence(),
362 boost::algorithm::to_upper_copy(iupac_symbols) );
365 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
367 std::string dna_str("AGCTN");
368 Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
369 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
370 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
373 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
375 std::string rna_str("AGCUN");
376 Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
377 BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
378 BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
381 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
383 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
384 Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
385 Sequence subseq = seq.subseq(8,4);
386 BOOST_CHECK_EQUAL( subseq, "AAGG");
387 Sequence rev_subseq = subseq.rev_comp();
388 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
389 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
392 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
394 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
395 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
396 Sequence seq(dna_str);
397 std::string seq_reversed(seq.rbegin(), seq.rend());
398 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
400 std::string substr = dna_str.substr(8,4);
401 Sequence subseq = seq.subseq(8,4);
402 BOOST_CHECK_EQUAL(substr, subseq);
404 std::string substr_reversed(substr.rbegin(), substr.rend());
405 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
406 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
409 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
411 // so what happens with reverse interators when we have no sequence?
414 Sequence seq3("AGCT");
416 // all the empty sequences should have equal iterators
417 BOOST_CHECK(seq1.rbegin() == seq1.rend());
418 BOOST_CHECK(seq1.rbegin() == seq2.rend());
420 // none of the seq1 iterators should equal any of the seq3 iterators
421 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
422 BOOST_CHECK(seq1.rbegin() != seq3.rend());
423 BOOST_CHECK(seq1.rend() != seq3.rbegin());
424 BOOST_CHECK(seq1.rend() != seq3.rend());
426 // seq3 iterators should work
427 BOOST_CHECK(seq3.rbegin() != seq3.rend());
431 BOOST_AUTO_TEST_CASE( annotation_load )
433 string annot_data = "human\n"
437 "50\t55 anothername\n"
442 "75\t90\tname2\ttype2\n"
443 "100 120 name-asdf type!@#$%\n"
447 Sequence seq(s, Sequence::reduced_dna_alphabet);
449 //istringstream annot_stream(annot_data);
450 seq.parse_annot(annot_data, 0, 0);
451 std::list<annot> annots_list = seq.annotations();
452 std::vector<annot> annots(annots_list.begin(), annots_list.end());
453 BOOST_REQUIRE_EQUAL( annots.size(), 8);
454 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
455 BOOST_CHECK_EQUAL( annots[0].end, 10 );
456 BOOST_CHECK_EQUAL( annots[0].type, "type");
457 BOOST_CHECK_EQUAL( annots[0].name, "name");
458 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
459 BOOST_CHECK_EQUAL( annots[2].name, "myod");
460 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
461 BOOST_CHECK_EQUAL( annots[4].name, "backward");
462 BOOST_CHECK_EQUAL( annots[5].name, "name2");
463 BOOST_CHECK_EQUAL( annots[5].end, 90);
464 BOOST_CHECK_EQUAL( annots[6].begin, 100);
465 BOOST_CHECK_EQUAL( annots[6].end, 120);
466 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
467 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
468 // sequence defined annotations will always be after the
469 // absolute positions
470 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
471 BOOST_CHECK_EQUAL( annots[7].begin, 100);
473 //BOOST_CHECK_EQUAL( annots
476 BOOST_AUTO_TEST_CASE( annotation_broken_load )
478 string annot_data = "human\n"
480 "blah60 50 backward\n"
487 Sequence seq(s, Sequence::reduced_dna_alphabet);
489 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
490 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
493 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
495 // this actually is basically what's returned by UCSC
496 // (well actually with some of the sequence and copies of fasta blocks
497 // removed to make the example shorter
498 string annot_data = "\n"
500 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
501 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
502 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
503 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
511 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
513 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
514 Sequence seq(s, Sequence::reduced_dna_alphabet);
515 seq.parse_annot(annot_data);
516 std::list<annot> annots = seq.annotations();
517 BOOST_CHECK_EQUAL( annots.size(), 2);
520 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
522 string annot_data = "0 10 name type\n"
525 "50\t55 anothername\n"
530 "75\t90\tname2\ttype2\n"
531 "100 120 name-asdf type!@#$%\n"
535 Sequence seq(s, Sequence::reduced_dna_alphabet);
537 //istringstream annot_stream(annot_data);
538 seq.parse_annot(annot_data, 0, 0);
539 std::list<annot> annots_list = seq.annotations();
540 std::vector<annot> annots(annots_list.begin(), annots_list.end());
541 BOOST_REQUIRE_EQUAL( annots.size(), 8);
542 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
543 BOOST_CHECK_EQUAL( annots[0].end, 10 );
544 BOOST_CHECK_EQUAL( annots[0].type, "type");
547 // ticket:83 when you try to load a sequence from a file that doesn't
548 // have fasta headers it crashes.
549 BOOST_AUTO_TEST_CASE( sequence_past_end )
551 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
552 seq_path /= "misformated_seq.fa";
554 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
557 BOOST_AUTO_TEST_CASE ( sequence_empty )
561 BOOST_CHECK_EQUAL( s.empty(), true );
563 BOOST_CHECK_EQUAL( s.empty(), false );
565 BOOST_CHECK_EQUAL( s.empty(), true);
567 BOOST_CHECK_EQUAL( s.empty(), true);
570 BOOST_AUTO_TEST_CASE ( sequence_size )
574 BOOST_CHECK_EQUAL( s.size(), 0);
575 std::string seq_string("AAAGGG");
577 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
579 BOOST_CHECK_EQUAL( s.size(), 0);
581 BOOST_CHECK_EQUAL( s.size(), 0);
584 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
586 Sequence szero("", Sequence::reduced_dna_alphabet);
587 BOOST_CHECK_EQUAL(szero.empty(), true);
588 BOOST_CHECK_EQUAL(szero, szero);
589 BOOST_CHECK_EQUAL(szero, "");
591 Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
593 BOOST_CHECK_EQUAL(sclear.empty(), true);
594 BOOST_CHECK_EQUAL(sclear, sclear);
595 BOOST_CHECK_EQUAL(sclear, szero);
596 BOOST_CHECK_EQUAL(sclear, "");
599 BOOST_AUTO_TEST_CASE ( sequence_iterators )
601 std::string seq_string = "AAGGCCTTNNTATA";
602 Sequence s(seq_string, Sequence::reduced_dna_alphabet);
603 const Sequence cs(s);
604 std::string::size_type count = 0;
606 std::string::iterator str_itor;
607 Sequence::const_iterator s_itor;
608 Sequence::const_iterator cs_itor;
610 for( str_itor = seq_string.begin(),
612 cs_itor = cs.begin();
613 str_itor != seq_string.end() and
614 s_itor != s.end() and
616 ++str_itor, ++s_itor, ++cs_itor, ++count)
618 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
619 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
620 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
622 BOOST_CHECK_EQUAL( seq_string.size(), count );
623 BOOST_CHECK_EQUAL( s.size(), count );
624 BOOST_CHECK_EQUAL( cs.size(), count );
627 BOOST_AUTO_TEST_CASE( sequence_motifs )
630 string bogus("AATTGGAA");
631 Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
633 list<motif>::const_iterator motif_i = s1.motifs().begin();
634 list<motif>::const_iterator motif_end = s1.motifs().end();
636 // do our iterators work?
637 BOOST_CHECK( motif_i == s1.motifs().begin() );
638 BOOST_CHECK( motif_end == s1.motifs().end() );
639 BOOST_CHECK( motif_i == motif_end );
641 // this shouldn't show up
643 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
644 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
647 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
648 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
650 for(motif_i = s1.motifs().begin();
651 motif_i != s1.motifs().end();
654 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
655 BOOST_CHECK_EQUAL( motif_i->name, m);
656 BOOST_CHECK_EQUAL( motif_i->sequence, m);
660 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
662 /* FIXME: enable this when i find a way of passing storing the motif name
663 // does our annotation travel?
664 Sequence motif_seq(m);
665 motif_seq.set_fasta_header("hi");
666 s1.add_motif(motif_seq);
668 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
669 for(motif_i = s1.motifs().begin();
670 motif_i != s1.motifs().end();
673 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
674 BOOST_CHECK_EQUAL( motif_i->name, "hi");
675 BOOST_CHECK_EQUAL( motif_i->sequence, m);
680 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
682 // when searching for a motif on a subsequence we should
683 // only search the subsequence ticket:199
686 Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
688 // this shouldn't show up
690 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
693 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
695 Sequence subseq1 = s1.subseq(4,5);
696 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
697 subseq1.clear_motifs();
698 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
699 // this is outside of our subsequence, and so shouldn't be found
700 subseq1.add_motif(aaaa);
701 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
703 subseq1.add_motif(cccc);
704 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
705 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
706 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
707 BOOST_CHECK_EQUAL(motif_i->begin, 1);
708 BOOST_CHECK_EQUAL(motif_i->end, 5);
711 BOOST_AUTO_TEST_CASE( annot_test )
713 annot a(0, 10, "test", "thing");
715 BOOST_CHECK_EQUAL( a.begin, 0 );
716 BOOST_CHECK_EQUAL( a.end, 10 );
717 BOOST_CHECK_EQUAL( a.type, "test" );
718 BOOST_CHECK_EQUAL( a.name, "thing" );
720 motif m(10, "AAGGCC");
721 BOOST_CHECK_EQUAL( m.begin, 10 );
722 BOOST_CHECK_EQUAL( m.type, "motif" );
723 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
724 BOOST_CHECK_EQUAL( m.end, 10+6 );
727 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
729 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
730 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
731 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
732 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
733 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
734 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
735 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
736 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
738 string gga("GGACACCTC");
739 Sequence seq(s, Sequence::reduced_dna_alphabet);
741 std::list<Sequence> query_list;
742 std::list<string> string_list;
743 query_list.push_back(Sequence(gc));
744 string_list.push_back(gc);
745 query_list.push_back(Sequence(gga));
746 string_list.push_back(gga);
748 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
749 seq.find_sequences(query_list.begin(), query_list.end());
752 for(list<string>::iterator string_i = string_list.begin();
753 string_i != string_list.end();
756 string::size_type pos=0;
757 while(pos != string::npos) {
758 pos = s.find(*string_i, pos);
759 if (pos != string::npos) {
765 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
766 const std::list<annot> &a = seq.annotations();
767 for (std::list<annot>::const_iterator annot_i = a.begin();
771 int count = annot_i->end - annot_i->begin ;
775 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
777 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
778 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
779 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
780 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
781 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
782 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
783 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
784 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
785 Sequence seq(s, Sequence::reduced_dna_alphabet);
788 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
789 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
790 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
791 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
792 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
794 Sequence subseq = seq.subseq(5, 10);
795 const list<annot> annots = subseq.annotations();
796 // generate some ground truth
798 correct.push_back(annot(0, 5, "0-10", "0-10"));
799 correct.push_back(annot(5,10, "10-20", "10-20"));
800 correct.push_back(annot(0,10, "0-20", "0-20"));
801 correct.push_back(annot(3, 7, "8-12", "8-12"));
802 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
804 list<annot>::iterator correct_i = correct.begin();
805 list<annot>::const_iterator annot_i = annots.begin();
806 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
808 BOOST_CHECK( *annot_i == *correct_i );
812 BOOST_AUTO_TEST_CASE( motif_annotation_update )
814 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
815 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
816 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
817 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
818 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
819 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
820 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
821 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
822 Sequence seq(s, Sequence::reduced_dna_alphabet);
824 // starting conditions
825 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
826 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
827 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
828 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
829 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
830 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
831 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
832 seq.add_motif("CCGTCCC");
833 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
834 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
836 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
837 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
840 BOOST_AUTO_TEST_CASE( out_operator )
842 string s("AAGGCCTT");
843 Sequence seq(s, Sequence::reduced_dna_alphabet);
847 BOOST_CHECK_EQUAL( s, buf.str() );
850 BOOST_AUTO_TEST_CASE( get_name )
852 Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
854 BOOST_CHECK_EQUAL( seq.get_name(), "" );
855 seq.set_species("hooman"); // anyone remember tradewars?
856 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
857 seq.set_fasta_header("fasta human");
858 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
861 BOOST_AUTO_TEST_CASE( serialize_simple )
863 std::string seq_string = "AAGGCCTT";
864 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
865 seq.set_species("ribbet");
866 std::ostringstream oss;
867 // allocate/deallocate serialization components
869 boost::archive::text_oarchive oarchive(oss);
870 const Sequence& const_seq(seq);
871 BOOST_CHECK_EQUAL(seq, const_seq);
872 oarchive << const_seq;
876 std::istringstream iss(oss.str());
877 boost::archive::text_iarchive iarchive(iss);
878 iarchive >> seq_loaded;
880 BOOST_CHECK_EQUAL(seq_loaded, seq);
881 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
884 BOOST_AUTO_TEST_CASE( serialize_tree )
886 std::string seq_string = "AAGGCCTT";
887 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
888 seq.set_species("ribbet");
891 annot a1(6,7,"t","t");
892 seq.add_annotation(a1);
894 std::ostringstream oss;
895 // allocate/deallocate serialization components
897 boost::archive::text_oarchive oarchive(oss);
898 const Sequence& const_seq(seq);
899 BOOST_CHECK_EQUAL(seq, const_seq);
900 oarchive << const_seq;
905 std::istringstream iss(oss.str());
906 boost::archive::text_iarchive iarchive(iss);
907 iarchive >> seq_loaded;
909 BOOST_CHECK_EQUAL(seq_loaded, seq);
912 // this writes out an "old" style annotated sequence
913 // with annotations attached as "motifs" and "annots"
914 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
916 std::string seq_string = "AAGGCCTT";
917 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
918 seq.set_species("ribbet");
921 annot a1(6,7,"t","t");
922 seq.add_annotation(a1);
924 std::ostringstream oss;
925 // allocate/deallocate serialization components
927 boost::archive::xml_oarchive oarchive(oss);
928 const Sequence& const_seq(seq);
929 BOOST_CHECK_EQUAL(seq, const_seq);
930 oarchive << boost::serialization::make_nvp("root", const_seq);
934 std::istringstream iss(oss.str());
935 boost::archive::xml_iarchive iarchive(iss);
936 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
938 BOOST_CHECK_EQUAL(seq_loaded, seq);
941 BOOST_AUTO_TEST_CASE( serialize_xml_two )
943 std::string seq_string = "AAGGCCTT";
944 Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
947 std::ostringstream oss;
948 // allocate/deallocate serialization components
950 boost::archive::xml_oarchive oarchive(oss);
951 const Sequence& const_seq1(seq1);
952 const Sequence& const_seq2(seq2);
953 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
954 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
956 //std::cout << "xml: " << oss.str() << std::endl;
957 Sequence seq1_loaded;
958 Sequence seq2_loaded;
960 std::istringstream iss(oss.str());
961 boost::archive::xml_iarchive iarchive(iss);
962 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
963 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
965 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
966 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
967 // test if our pointers are the same
968 BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());