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;
6 #include <boost/algorithm/string/case_conv.hpp>
12 #include <boost/archive/text_oarchive.hpp>
13 #include <boost/archive/text_iarchive.hpp>
14 #include <boost/archive/xml_oarchive.hpp>
15 #include <boost/archive/xml_iarchive.hpp>
17 #include "alg/sequence.hpp"
18 #include "mussa_exceptions.hpp"
22 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
25 // make sure that retrieving the sequence doesn't throw an error
26 BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
29 //! when we try to load a missing file, do we get an error?
30 BOOST_AUTO_TEST_CASE( sequence_load_exception )
33 // there should be errors when we try to load something that doesn't exist
34 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
35 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
38 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
40 string header(">Header");
41 string line1("AAAAGGGGCCCCTTTTT");
42 string line2("AAAAGGGGCCCCTTTTT");
43 int seq_len = line1.size() + line2.size();
46 cr << header << "\015" << line1 << "\015" << line2 << "\015";
48 seq_cr.load_fasta(cr);
51 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
53 seq_crlf.load_fasta(crlf);
56 lf << header << "\012" << line1 << "\012" << line2 << "\012";
58 seq_lf.load_fasta(lf);
60 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
61 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
62 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
66 //! Do simple operations work correctly?
67 BOOST_AUTO_TEST_CASE( sequence_filter )
69 const char *core_seq = "AATTGGCC";
70 Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
71 BOOST_CHECK_EQUAL(s1, core_seq);
73 Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
74 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
75 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
76 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
77 BOOST_CHECK_EQUAL(s2.size(), s2.size());
78 //We're currently forcing sequences to uppercase
79 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
81 Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
82 BOOST_CHECK_EQUAL(s3, "ANNNG");
83 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
85 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
86 BOOST_CHECK_EQUAL(s3, "AA");
87 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
88 BOOST_CHECK_EQUAL( s3, "GG");
89 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
90 BOOST_CHECK_EQUAL( s3, "CCTT");
93 BOOST_CHECK_EQUAL(s3, "AAGGNN");
96 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
98 std::string agct("AGCT");
99 Sequence seq(agct, Sequence::nucleic_alphabet);
100 BOOST_CHECK_EQUAL(seq.size(), agct.size());
101 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
103 std::string bdv("BDv");
104 Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
105 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
106 // forcing sequence to upper case
107 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
108 boost::algorithm::to_upper_copy(bdv));
112 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
114 std::string agct("AGCT");
116 BOOST_CHECK_EQUAL(seq.size(), agct.size());
117 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
118 BOOST_CHECK_EQUAL(seq[0], agct[0]);
119 BOOST_CHECK_EQUAL(seq[1], agct[1]);
120 BOOST_CHECK_EQUAL(seq[2], agct[2]);
121 BOOST_CHECK_EQUAL(seq[3], agct[3]);
123 std::string bdv("BDv");
124 Sequence seq_bdv(bdv);
125 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
126 // default alphabet only allows AGCTUN
127 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
130 BOOST_AUTO_TEST_CASE( subseq_names )
132 Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
133 s1.set_species("species");
134 s1.set_fasta_header("a fasta header");
135 Sequence s2 = s1.subseq(2,2);
136 BOOST_CHECK_EQUAL(s2, "GG");
137 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
138 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
141 BOOST_AUTO_TEST_CASE( sequence_start_stop )
144 BOOST_CHECK_EQUAL( s1.start(), 0 );
145 BOOST_CHECK_EQUAL( s1.stop(), 0 );
147 std::string seq_string("AAGGCCTT");
148 Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
149 BOOST_CHECK_EQUAL( s2.start(), 0 );
150 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
152 std::string s3seq_string = seq_string.substr(2,3);
153 Sequence s3 = s2.subseq(2,3);
154 BOOST_CHECK_EQUAL( s3.start(), 2);
155 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
156 BOOST_CHECK_EQUAL( s3.size(), 3);
157 BOOST_CHECK_EQUAL( s3, s3seq_string);
159 std::string s4seq_string = s3seq_string.substr(1,1);
160 Sequence s4 = s3.subseq(1,1);
161 BOOST_CHECK_EQUAL( s4.start(), 1 );
162 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
163 BOOST_CHECK_EQUAL( s4.size(), 1);
164 BOOST_CHECK_EQUAL( s4, s4seq_string);
167 //! Can we load data from a file
168 BOOST_AUTO_TEST_CASE( sequence_load )
170 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
171 seq_path /= "human_mck_pro.fa";
173 s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
174 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
175 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
176 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
177 "muscle creatine kinase gene (CKMM), "
181 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
183 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
184 seq_path /= "broken.fa";
185 bool exception_thrown = false;
186 std::string exception_filename;
189 s.load_fasta(seq_path);
190 } catch(sequence_invalid_load_error e) {
191 exception_thrown = true;
192 size_t native_string_size = seq_path.native_file_string().size();
193 std:string estr(e.what());
194 BOOST_REQUIRE(estr.size() > native_string_size);
195 std::copy(estr.begin(), estr.begin()+native_string_size,
196 std::back_inserter(exception_filename));
198 BOOST_CHECK_EQUAL(exception_thrown, true);
199 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
202 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
204 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
205 seq_path /= "mouse_mck_pro.fa";
206 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
207 annot_path /= "broken.annot";
208 bool exception_thrown = false;
210 s.load_fasta(seq_path);
212 std::string exception_filename;
214 s.load_annot(annot_path, 0, 0);
215 } catch(annotation_load_error e) {
216 exception_thrown = true;
217 std:string estr(e.what());
218 size_t native_string_size = annot_path.native_file_string().size();
219 BOOST_REQUIRE(estr.size() > native_string_size);
220 std::copy(estr.begin(), estr.begin()+native_string_size,
221 std::back_inserter(exception_filename));
223 BOOST_CHECK_EQUAL(exception_thrown, true);
224 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
227 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
229 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
230 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
231 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
232 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
233 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
234 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
235 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
236 std::stringstream garbage_fasta(garbage_string);
239 s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
240 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
241 Sequence::reduced_dna_alphabet),
242 sequence_invalid_load_error);
243 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
244 Sequence::reduced_dna_alphabet),
245 sequence_invalid_load_error);
246 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
247 Sequence::reduced_dna_alphabet),
248 sequence_invalid_load_error);
252 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
254 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
255 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
256 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
257 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
258 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
259 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
260 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
261 std::stringstream garbage_fasta(garbage_string);
264 s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
265 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
266 Sequence::reduced_rna_alphabet),
267 sequence_invalid_load_error);
268 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
269 Sequence::reduced_rna_alphabet),
270 sequence_invalid_load_error);
271 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
272 Sequence::reduced_rna_alphabet),
273 sequence_invalid_load_error);
276 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
278 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
279 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
280 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
281 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
282 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
283 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
284 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
285 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
286 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
287 std::stringstream garbage_fasta(garbage_string);
291 // there's two copies of reduced_rna_fasta because i didn't feel like
292 // figuring out how to properly reset the read pointer in a stringstream
293 s.load_fasta(reduced_rna_fasta1);
294 specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
295 BOOST_CHECK_EQUAL(s, specific);
297 s.load_fasta(reduced_dna_fasta1);
298 specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
299 BOOST_CHECK_EQUAL(s, specific);
301 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
302 sequence_invalid_load_error);
303 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
304 sequence_invalid_load_error);
307 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
309 std::string fasta_file(
310 ">gi|10129974|gb|AF188002.1|AF188002\n"
311 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
312 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
313 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
314 ">gi|1621|emb|X55146.1|OCMCK1\n"
315 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
317 istringstream seq1_file(fasta_file);
319 seq1.load_fasta(seq1_file, 1, 0, 0);
320 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
322 istringstream seq2_file(fasta_file);
324 seq2.load_fasta(seq2_file, 2, 0, 0);
325 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
327 istringstream seq3_file(fasta_file);
329 seq3.load_fasta(seq3_file, 3, 0, 0);
330 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
333 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
335 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
336 Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
337 Sequence seqr = seq.rev_comp();
339 BOOST_CHECK( seq != seqr );
340 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
341 // forcing sequence to upper case
342 BOOST_CHECK_EQUAL( seq.get_sequence(),
343 boost::algorithm::to_upper_copy(iupac_symbols) );
346 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
348 std::string dna_str("AGCTN");
349 Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
350 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
351 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
354 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
356 std::string rna_str("AGCUN");
357 Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
358 BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
359 BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
362 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
364 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
365 Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
366 Sequence subseq = seq.subseq(8,4);
367 BOOST_CHECK_EQUAL( subseq, "AAGG");
368 Sequence rev_subseq = subseq.rev_comp();
369 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
370 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
373 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
375 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
376 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
377 Sequence seq(dna_str);
378 std::string seq_reversed(seq.rbegin(), seq.rend());
379 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
381 std::string substr = dna_str.substr(8,4);
382 Sequence subseq = seq.subseq(8,4);
383 BOOST_CHECK_EQUAL(substr, subseq);
385 std::string substr_reversed(substr.rbegin(), substr.rend());
386 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
387 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
390 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
392 // so what happens with reverse interators when we have no sequence?
395 Sequence seq3("AGCT");
397 // all the empty sequences should have equal iterators
398 BOOST_CHECK(seq1.rbegin() == seq1.rend());
399 BOOST_CHECK(seq1.rbegin() == seq2.rend());
401 // none of the seq1 iterators should equal any of the seq3 iterators
402 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
403 BOOST_CHECK(seq1.rbegin() != seq3.rend());
404 BOOST_CHECK(seq1.rend() != seq3.rbegin());
405 BOOST_CHECK(seq1.rend() != seq3.rend());
407 // seq3 iterators should work
408 BOOST_CHECK(seq3.rbegin() != seq3.rend());
412 BOOST_AUTO_TEST_CASE( annotation_load )
414 string annot_data = "human\n"
418 "50\t55 anothername\n"
423 "75\t90\tname2\ttype2\n"
424 "100 120 name-asdf type!@#$%\n"
428 Sequence seq(s, Sequence::reduced_dna_alphabet);
430 //istringstream annot_stream(annot_data);
431 seq.parse_annot(annot_data, 0, 0);
432 std::list<annot> annots_list = seq.annotations();
433 std::vector<annot> annots(annots_list.begin(), annots_list.end());
434 BOOST_REQUIRE_EQUAL( annots.size(), 8);
435 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
436 BOOST_CHECK_EQUAL( annots[0].end, 10 );
437 BOOST_CHECK_EQUAL( annots[0].type, "type");
438 BOOST_CHECK_EQUAL( annots[0].name, "name");
439 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
440 BOOST_CHECK_EQUAL( annots[2].name, "myod");
441 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
442 BOOST_CHECK_EQUAL( annots[4].name, "backward");
443 BOOST_CHECK_EQUAL( annots[5].name, "name2");
444 BOOST_CHECK_EQUAL( annots[5].end, 90);
445 BOOST_CHECK_EQUAL( annots[6].begin, 100);
446 BOOST_CHECK_EQUAL( annots[6].end, 120);
447 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
448 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
449 // sequence defined annotations will always be after the
450 // absolute positions
451 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
452 BOOST_CHECK_EQUAL( annots[7].begin, 100);
454 //BOOST_CHECK_EQUAL( annots
457 BOOST_AUTO_TEST_CASE( annotation_broken_load )
459 string annot_data = "human\n"
461 "blah60 50 backward\n"
468 Sequence seq(s, Sequence::reduced_dna_alphabet);
470 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
471 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
474 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
476 // this actually is basically what's returned by UCSC
477 // (well actually with some of the sequence and copies of fasta blocks
478 // removed to make the example shorter
479 string annot_data = "\n"
481 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
482 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
483 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
484 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
492 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
494 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
495 Sequence seq(s, Sequence::reduced_dna_alphabet);
496 seq.parse_annot(annot_data);
497 std::list<annot> annots = seq.annotations();
498 BOOST_CHECK_EQUAL( annots.size(), 2);
501 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
503 string annot_data = "0 10 name type\n"
506 "50\t55 anothername\n"
511 "75\t90\tname2\ttype2\n"
512 "100 120 name-asdf type!@#$%\n"
516 Sequence seq(s, Sequence::reduced_dna_alphabet);
518 //istringstream annot_stream(annot_data);
519 seq.parse_annot(annot_data, 0, 0);
520 std::list<annot> annots_list = seq.annotations();
521 std::vector<annot> annots(annots_list.begin(), annots_list.end());
522 BOOST_REQUIRE_EQUAL( annots.size(), 8);
523 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
524 BOOST_CHECK_EQUAL( annots[0].end, 10 );
525 BOOST_CHECK_EQUAL( annots[0].type, "type");
528 // ticket:83 when you try to load a sequence from a file that doesn't
529 // have fasta headers it crashes.
530 BOOST_AUTO_TEST_CASE( sequence_past_end )
532 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
533 seq_path /= "misformated_seq.fa";
535 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
538 BOOST_AUTO_TEST_CASE ( sequence_empty )
542 BOOST_CHECK_EQUAL( s.empty(), true );
544 BOOST_CHECK_EQUAL( s.empty(), false );
546 BOOST_CHECK_EQUAL( s.empty(), true);
548 BOOST_CHECK_EQUAL( s.empty(), true);
551 BOOST_AUTO_TEST_CASE ( sequence_size )
555 BOOST_CHECK_EQUAL( s.size(), 0);
556 std::string seq_string("AAAGGG");
558 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
560 BOOST_CHECK_EQUAL( s.size(), 0);
562 BOOST_CHECK_EQUAL( s.size(), 0);
565 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
567 Sequence szero("", Sequence::reduced_dna_alphabet);
568 BOOST_CHECK_EQUAL(szero.empty(), true);
569 BOOST_CHECK_EQUAL(szero, szero);
570 BOOST_CHECK_EQUAL(szero, "");
572 Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
574 BOOST_CHECK_EQUAL(sclear.empty(), true);
575 BOOST_CHECK_EQUAL(sclear, sclear);
576 BOOST_CHECK_EQUAL(sclear, szero);
577 BOOST_CHECK_EQUAL(sclear, "");
580 BOOST_AUTO_TEST_CASE ( sequence_iterators )
582 std::string seq_string = "AAGGCCTTNNTATA";
583 Sequence s(seq_string, Sequence::reduced_dna_alphabet);
584 const Sequence cs(s);
585 std::string::size_type count = 0;
587 std::string::iterator str_itor;
588 Sequence::const_iterator s_itor;
589 Sequence::const_iterator cs_itor;
591 for( str_itor = seq_string.begin(),
593 cs_itor = cs.begin();
594 str_itor != seq_string.end() and
595 s_itor != s.end() and
597 ++str_itor, ++s_itor, ++cs_itor, ++count)
599 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
600 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
601 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
603 BOOST_CHECK_EQUAL( seq_string.size(), count );
604 BOOST_CHECK_EQUAL( s.size(), count );
605 BOOST_CHECK_EQUAL( cs.size(), count );
608 BOOST_AUTO_TEST_CASE( sequence_motifs )
611 string bogus("AATTGGAA");
612 Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
614 list<motif>::const_iterator motif_i = s1.motifs().begin();
615 list<motif>::const_iterator motif_end = s1.motifs().end();
617 // do our iterators work?
618 BOOST_CHECK( motif_i == s1.motifs().begin() );
619 BOOST_CHECK( motif_end == s1.motifs().end() );
620 BOOST_CHECK( motif_i == motif_end );
622 // this shouldn't show up
624 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
625 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
628 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
629 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
631 for(motif_i = s1.motifs().begin();
632 motif_i != s1.motifs().end();
635 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
636 BOOST_CHECK_EQUAL( motif_i->name, m);
637 BOOST_CHECK_EQUAL( motif_i->sequence, m);
641 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
643 /* FIXME: enable this when i find a way of passing storing the motif name
644 // does our annotation travel?
645 Sequence motif_seq(m);
646 motif_seq.set_fasta_header("hi");
647 s1.add_motif(motif_seq);
649 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, "hi");
656 BOOST_CHECK_EQUAL( motif_i->sequence, m);
661 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
663 // when searching for a motif on a subsequence we should
664 // only search the subsequence ticket:199
667 Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
669 // this shouldn't show up
671 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
674 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
676 Sequence subseq1 = s1.subseq(4,5);
677 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
678 subseq1.clear_motifs();
679 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
680 // this is outside of our subsequence, and so shouldn't be found
681 subseq1.add_motif(aaaa);
682 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
684 subseq1.add_motif(cccc);
685 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
686 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
687 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
688 BOOST_CHECK_EQUAL(motif_i->begin, 1);
689 BOOST_CHECK_EQUAL(motif_i->end, 5);
692 BOOST_AUTO_TEST_CASE( annot_test )
694 annot a(0, 10, "test", "thing");
696 BOOST_CHECK_EQUAL( a.begin, 0 );
697 BOOST_CHECK_EQUAL( a.end, 10 );
698 BOOST_CHECK_EQUAL( a.type, "test" );
699 BOOST_CHECK_EQUAL( a.name, "thing" );
701 motif m(10, "AAGGCC");
702 BOOST_CHECK_EQUAL( m.begin, 10 );
703 BOOST_CHECK_EQUAL( m.type, "motif" );
704 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
705 BOOST_CHECK_EQUAL( m.end, 10+6 );
708 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
710 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
711 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
712 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
713 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
714 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
715 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
716 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
717 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
719 string gga("GGACACCTC");
720 Sequence seq(s, Sequence::reduced_dna_alphabet);
722 std::list<Sequence> query_list;
723 std::list<string> string_list;
724 query_list.push_back(Sequence(gc));
725 string_list.push_back(gc);
726 query_list.push_back(Sequence(gga));
727 string_list.push_back(gga);
729 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
730 seq.find_sequences(query_list.begin(), query_list.end());
733 for(list<string>::iterator string_i = string_list.begin();
734 string_i != string_list.end();
737 string::size_type pos=0;
738 while(pos != string::npos) {
739 pos = s.find(*string_i, pos);
740 if (pos != string::npos) {
746 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
747 const std::list<annot> &a = seq.annotations();
748 for (std::list<annot>::const_iterator annot_i = a.begin();
752 int count = annot_i->end - annot_i->begin ;
756 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
758 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
759 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
760 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
761 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
762 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
763 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
764 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
765 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
766 Sequence seq(s, Sequence::reduced_dna_alphabet);
769 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
770 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
771 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
772 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
773 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
775 Sequence subseq = seq.subseq(5, 10);
776 const list<annot> annots = subseq.annotations();
777 // generate some ground truth
779 correct.push_back(annot(0, 5, "0-10", "0-10"));
780 correct.push_back(annot(5,10, "10-20", "10-20"));
781 correct.push_back(annot(0,10, "0-20", "0-20"));
782 correct.push_back(annot(3, 7, "8-12", "8-12"));
783 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
785 list<annot>::iterator correct_i = correct.begin();
786 list<annot>::const_iterator annot_i = annots.begin();
787 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
789 BOOST_CHECK( *annot_i == *correct_i );
793 BOOST_AUTO_TEST_CASE( motif_annotation_update )
795 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
796 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
797 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
798 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
799 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
800 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
801 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
802 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
803 Sequence seq(s, Sequence::reduced_dna_alphabet);
805 // starting conditions
806 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
807 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
808 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
809 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
810 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
811 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
812 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
813 seq.add_motif("CCGTCCC");
814 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
815 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
817 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
818 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
821 BOOST_AUTO_TEST_CASE( out_operator )
823 string s("AAGGCCTT");
824 Sequence seq(s, Sequence::reduced_dna_alphabet);
828 BOOST_CHECK_EQUAL( s, buf.str() );
831 BOOST_AUTO_TEST_CASE( get_name )
833 Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
835 BOOST_CHECK_EQUAL( seq.get_name(), "" );
836 seq.set_species("hooman"); // anyone remember tradewars?
837 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
838 seq.set_fasta_header("fasta human");
839 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
842 BOOST_AUTO_TEST_CASE( serialize_simple )
844 std::string seq_string = "AAGGCCTT";
845 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
846 seq.set_species("ribbet");
847 std::ostringstream oss;
848 // allocate/deallocate serialization components
850 boost::archive::text_oarchive oarchive(oss);
851 const Sequence& const_seq(seq);
852 BOOST_CHECK_EQUAL(seq, const_seq);
853 oarchive << const_seq;
857 std::istringstream iss(oss.str());
858 boost::archive::text_iarchive iarchive(iss);
859 iarchive >> seq_loaded;
861 BOOST_CHECK_EQUAL(seq_loaded, seq);
862 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
865 BOOST_AUTO_TEST_CASE( serialize_tree )
867 std::string seq_string = "AAGGCCTT";
868 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
869 seq.set_species("ribbet");
872 annot a1(6,7,"t","t");
873 seq.add_annotation(a1);
875 std::ostringstream oss;
876 // allocate/deallocate serialization components
878 boost::archive::text_oarchive oarchive(oss);
879 const Sequence& const_seq(seq);
880 BOOST_CHECK_EQUAL(seq, const_seq);
881 oarchive << const_seq;
886 std::istringstream iss(oss.str());
887 boost::archive::text_iarchive iarchive(iss);
888 iarchive >> seq_loaded;
890 BOOST_CHECK_EQUAL(seq_loaded, seq);
893 // this writes out an "old" style annotated sequence
894 // with annotations attached as "motifs" and "annots"
895 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
897 std::string seq_string = "AAGGCCTT";
898 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
899 seq.set_species("ribbet");
902 annot a1(6,7,"t","t");
903 seq.add_annotation(a1);
905 std::ostringstream oss;
906 // allocate/deallocate serialization components
908 boost::archive::xml_oarchive oarchive(oss);
909 const Sequence& const_seq(seq);
910 BOOST_CHECK_EQUAL(seq, const_seq);
911 oarchive << boost::serialization::make_nvp("root", const_seq);
915 std::istringstream iss(oss.str());
916 boost::archive::xml_iarchive iarchive(iss);
917 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
919 BOOST_CHECK_EQUAL(seq_loaded, seq);
922 BOOST_AUTO_TEST_CASE( serialize_xml_two )
924 std::string seq_string = "AAGGCCTT";
925 Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
928 std::ostringstream oss;
929 // allocate/deallocate serialization components
931 boost::archive::xml_oarchive oarchive(oss);
932 const Sequence& const_seq1(seq1);
933 const Sequence& const_seq2(seq2);
934 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
935 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
937 //std::cout << "xml: " << oss.str() << std::endl;
938 Sequence seq1_loaded;
939 Sequence seq2_loaded;
941 std::istringstream iss(oss.str());
942 boost::archive::xml_iarchive iarchive(iss);
943 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
944 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
946 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
947 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
948 // test if our pointers are the same
949 BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());