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_copy_constructor )
25 SequenceRef s(new Sequence("AAAAGGGG"));
26 s->set_species("foo");
27 BOOST_CHECK_EQUAL(s->get_species(), "foo");
29 SequenceRef c(new Sequence(s));
30 BOOST_CHECK_EQUAL(c->get_species(), "foo");
32 c->set_species("bar");
33 BOOST_CHECK_EQUAL(s->get_species(), "foo");
34 BOOST_CHECK_EQUAL(c->get_species(), "bar");
36 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
39 // make sure that retrieving the sequence doesn't throw an error
40 BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
43 BOOST_AUTO_TEST_CASE( sequence_from_string )
45 std::string str1("AAAT");
47 BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
50 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
52 std::string str1("AAAAT");
54 BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
56 std::string str2("AATTGGCC");
58 BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
61 //! when we try to load a missing file, do we get an error?
62 BOOST_AUTO_TEST_CASE( sequence_load_exception )
65 // there should be errors when we try to load something that doesn't exist
66 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
67 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
70 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
72 string header(">Header");
73 string line1("AAAAGGGGCCCCTTTTT");
74 string line2("AAAAGGGGCCCCTTTTT");
75 int seq_len = line1.size() + line2.size();
78 cr << header << "\015" << line1 << "\015" << line2 << "\015";
80 seq_cr.load_fasta(cr);
83 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
85 seq_crlf.load_fasta(crlf);
88 lf << header << "\012" << line1 << "\012" << line2 << "\012";
90 seq_lf.load_fasta(lf);
92 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
93 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
94 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
98 //! Do simple operations work correctly?
99 BOOST_AUTO_TEST_CASE( sequence_filter )
101 const char *core_seq = "AATTGGCC";
102 Sequence s1(core_seq, reduced_dna_alphabet);
103 BOOST_CHECK_EQUAL(s1, core_seq);
105 Sequence s2("aattggcc", reduced_dna_alphabet);
106 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
107 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
108 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
109 BOOST_CHECK_EQUAL(s2.size(), s2.size());
110 //We're currently forcing sequences to uppercase
111 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
113 Sequence s3("asdfg", reduced_dna_alphabet);
114 BOOST_CHECK_EQUAL(s3, "ANNNG");
115 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
117 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
118 BOOST_CHECK_EQUAL(s3, "AA");
119 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
120 BOOST_CHECK_EQUAL( s3, "GG");
121 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
122 BOOST_CHECK_EQUAL( s3, "CCTT");
125 BOOST_CHECK_EQUAL(s3, "AAGGNN");
128 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
130 std::string agct("AGCT");
131 Sequence seq(agct, nucleic_alphabet);
132 BOOST_CHECK_EQUAL(seq.size(), agct.size());
133 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
135 std::string bdv("BDv");
136 Sequence seq_bdv(bdv, nucleic_alphabet);
137 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
138 // forcing sequence to upper case
139 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
140 boost::algorithm::to_upper_copy(bdv));
144 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
146 std::string agct("AGCT");
148 BOOST_CHECK_EQUAL(seq.size(), agct.size());
149 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
150 BOOST_CHECK_EQUAL(seq[0], agct[0]);
151 BOOST_CHECK_EQUAL(seq[1], agct[1]);
152 BOOST_CHECK_EQUAL(seq[2], agct[2]);
153 BOOST_CHECK_EQUAL(seq[3], agct[3]);
155 std::string bdv("BDv");
156 Sequence seq_bdv(bdv);
157 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
158 // default alphabet only allows AGCTUN
159 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
162 BOOST_AUTO_TEST_CASE( subseq_names )
164 Sequence s1("AAGGCCTT", reduced_dna_alphabet);
165 s1.set_species("species");
166 s1.set_fasta_header("a fasta header");
167 Sequence s2 = s1.subseq(2,2);
168 BOOST_CHECK_EQUAL(s2, "GG");
169 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
170 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
173 BOOST_AUTO_TEST_CASE( sequence_start_stop )
176 BOOST_CHECK_EQUAL( s1.start(), 0 );
177 BOOST_CHECK_EQUAL( s1.stop(), 0 );
179 std::string seq_string("AAGGCCTT");
180 Sequence s2(seq_string, reduced_dna_alphabet);
181 BOOST_CHECK_EQUAL( s2.start(), 0 );
182 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
184 std::string s3seq_string = seq_string.substr(2,3);
185 Sequence s3 = s2.subseq(2,3);
186 BOOST_CHECK_EQUAL( s3.start(), 2);
187 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
188 BOOST_CHECK_EQUAL( s3.size(), 3);
189 BOOST_CHECK_EQUAL( s3, s3seq_string);
191 std::string s4seq_string = s3seq_string.substr(1,1);
192 Sequence s4 = s3.subseq(1,1);
193 BOOST_CHECK_EQUAL( s4.start(), 1 );
194 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
195 BOOST_CHECK_EQUAL( s4.size(), 1);
196 BOOST_CHECK_EQUAL( s4, s4seq_string);
199 //! Can we load data from a file
200 BOOST_AUTO_TEST_CASE( sequence_load )
202 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
203 seq_path /= "human_mck_pro.fa";
205 s.load_fasta(seq_path, reduced_dna_alphabet);
206 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
207 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
208 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
209 "muscle creatine kinase gene (CKMM), "
213 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
215 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
216 seq_path /= "broken.fa";
217 bool exception_thrown = false;
218 std::string exception_filename;
221 s.load_fasta(seq_path);
222 } catch(sequence_invalid_load_error e) {
223 exception_thrown = true;
224 size_t native_string_size = seq_path.native_file_string().size();
225 std:string estr(e.what());
226 BOOST_REQUIRE(estr.size() > native_string_size);
227 std::copy(estr.begin(), estr.begin()+native_string_size,
228 std::back_inserter(exception_filename));
230 BOOST_CHECK_EQUAL(exception_thrown, true);
231 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
234 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
236 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
237 seq_path /= "mouse_mck_pro.fa";
238 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
239 annot_path /= "broken.annot";
240 bool exception_thrown = false;
242 s.load_fasta(seq_path);
244 std::string exception_filename;
246 s.load_annot(annot_path, 0, 0);
247 } catch(annotation_load_error e) {
248 exception_thrown = true;
249 std:string estr(e.what());
250 size_t native_string_size = annot_path.native_file_string().size();
251 BOOST_REQUIRE(estr.size() > native_string_size);
252 std::copy(estr.begin(), estr.begin()+native_string_size,
253 std::back_inserter(exception_filename));
255 BOOST_CHECK_EQUAL(exception_thrown, true);
256 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
259 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
261 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
262 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
263 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
264 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
265 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
266 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
267 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
268 std::stringstream garbage_fasta(garbage_string);
271 s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
272 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
273 reduced_dna_alphabet),
274 sequence_invalid_load_error);
275 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
276 reduced_dna_alphabet),
277 sequence_invalid_load_error);
278 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
279 reduced_dna_alphabet),
280 sequence_invalid_load_error);
284 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
286 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
287 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
288 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
289 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
290 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
291 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
292 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
293 std::stringstream garbage_fasta(garbage_string);
296 s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
297 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
298 reduced_rna_alphabet),
299 sequence_invalid_load_error);
300 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
301 reduced_rna_alphabet),
302 sequence_invalid_load_error);
303 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
304 reduced_rna_alphabet),
305 sequence_invalid_load_error);
308 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
310 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
311 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
312 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
313 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
314 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
315 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
316 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
317 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
318 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
319 std::stringstream garbage_fasta(garbage_string);
323 // there's two copies of reduced_rna_fasta because i didn't feel like
324 // figuring out how to properly reset the read pointer in a stringstream
325 s.load_fasta(reduced_rna_fasta1);
326 specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
327 BOOST_CHECK_EQUAL(s, specific);
329 s.load_fasta(reduced_dna_fasta1);
330 specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
331 BOOST_CHECK_EQUAL(s, specific);
333 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
334 sequence_invalid_load_error);
335 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
336 sequence_invalid_load_error);
339 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
341 std::string fasta_file(
342 ">gi|10129974|gb|AF188002.1|AF188002\n"
343 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
344 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
345 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
346 ">gi|1621|emb|X55146.1|OCMCK1\n"
347 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
349 istringstream seq1_file(fasta_file);
351 seq1.load_fasta(seq1_file, 1, 0, 0);
352 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
354 istringstream seq2_file(fasta_file);
356 seq2.load_fasta(seq2_file, 2, 0, 0);
357 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
359 istringstream seq3_file(fasta_file);
361 seq3.load_fasta(seq3_file, 3, 0, 0);
362 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
365 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
367 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
368 Sequence seq(iupac_symbols, nucleic_alphabet);
369 Sequence seqr = seq.rev_comp();
371 BOOST_CHECK( seq != seqr );
372 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
373 // forcing sequence to upper case
374 BOOST_CHECK_EQUAL( seq.get_sequence(),
375 boost::algorithm::to_upper_copy(iupac_symbols) );
378 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
380 std::string dna_str("AGCTN");
381 Sequence dna_seq(dna_str, reduced_dna_alphabet);
382 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
383 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
386 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
388 std::string rna_str("AGCUN");
389 Sequence rna_seq(rna_str, reduced_rna_alphabet);
390 BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
391 BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
392 rna_seq.rev_comp().rev_comp().get_sequence());
395 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
397 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
398 Sequence seq(dna_str, reduced_dna_alphabet);
399 Sequence subseq = seq.subseq(8,4);
400 BOOST_CHECK_EQUAL( subseq, "AAGG");
401 Sequence rev_subseq = subseq.rev_comp();
402 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
403 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
406 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
408 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
409 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
410 Sequence seq(dna_str);
411 std::string seq_reversed(seq.rbegin(), seq.rend());
412 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
414 std::string substr = dna_str.substr(8,4);
415 Sequence subseq = seq.subseq(8,4);
416 BOOST_CHECK_EQUAL(substr, subseq);
418 std::string substr_reversed(substr.rbegin(), substr.rend());
419 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
420 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
423 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
425 // so what happens with reverse interators when we have no sequence?
428 Sequence seq3("AGCT");
430 // all the empty sequences should have equal iterators
431 BOOST_CHECK(seq1.rbegin() == seq1.rend());
432 BOOST_CHECK(seq1.rbegin() == seq2.rend());
434 // none of the seq1 iterators should equal any of the seq3 iterators
435 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
436 BOOST_CHECK(seq1.rbegin() != seq3.rend());
437 BOOST_CHECK(seq1.rend() != seq3.rbegin());
438 BOOST_CHECK(seq1.rend() != seq3.rend());
440 // seq3 iterators should work
441 BOOST_CHECK(seq3.rbegin() != seq3.rend());
445 BOOST_AUTO_TEST_CASE( annotation_load )
447 string annot_data = "human\n"
451 "50\t55 anothername\n"
456 "75\t90\tname2\ttype2\n"
457 "100 120 name-asdf type!@#$%\n"
461 Sequence seq(s, reduced_dna_alphabet);
463 //istringstream annot_stream(annot_data);
464 seq.parse_annot(annot_data, 0, 0);
465 std::list<annot> annots_list = seq.annotations();
466 std::vector<annot> annots(annots_list.begin(), annots_list.end());
467 BOOST_REQUIRE_EQUAL( annots.size(), 8);
468 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
469 BOOST_CHECK_EQUAL( annots[0].end, 10 );
470 BOOST_CHECK_EQUAL( annots[0].type, "type");
471 BOOST_CHECK_EQUAL( annots[0].name, "name");
472 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
473 BOOST_CHECK_EQUAL( annots[2].name, "myod");
474 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
475 BOOST_CHECK_EQUAL( annots[4].name, "backward");
476 BOOST_CHECK_EQUAL( annots[5].name, "name2");
477 BOOST_CHECK_EQUAL( annots[5].end, 90);
478 BOOST_CHECK_EQUAL( annots[6].begin, 100);
479 BOOST_CHECK_EQUAL( annots[6].end, 120);
480 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
481 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
482 // sequence defined annotations will always be after the
483 // absolute positions
484 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
485 BOOST_CHECK_EQUAL( annots[7].begin, 100);
487 //BOOST_CHECK_EQUAL( annots
490 BOOST_AUTO_TEST_CASE( annotation_broken_load )
492 string annot_data = "human\n"
494 "blah60 50 backward\n"
501 Sequence seq(s, reduced_dna_alphabet);
503 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
504 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
507 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
509 // this actually is basically what's returned by UCSC
510 // (well actually with some of the sequence and copies of fasta blocks
511 // removed to make the example shorter
512 string annot_data = "\n"
514 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
515 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
516 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
517 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
525 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
527 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
528 Sequence seq(s, reduced_dna_alphabet);
529 seq.parse_annot(annot_data);
530 std::list<annot> annots = seq.annotations();
531 BOOST_CHECK_EQUAL( annots.size(), 2);
534 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
536 string annot_data = "0 10 name type\n"
539 "50\t55 anothername\n"
544 "75\t90\tname2\ttype2\n"
545 "100 120 name-asdf type!@#$%\n"
549 Sequence seq(s, reduced_dna_alphabet);
551 //istringstream annot_stream(annot_data);
552 seq.parse_annot(annot_data, 0, 0);
553 std::list<annot> annots_list = seq.annotations();
554 std::vector<annot> annots(annots_list.begin(), annots_list.end());
555 BOOST_REQUIRE_EQUAL( annots.size(), 8);
556 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
557 BOOST_CHECK_EQUAL( annots[0].end, 10 );
558 BOOST_CHECK_EQUAL( annots[0].type, "type");
561 // ticket:83 when you try to load a sequence from a file that doesn't
562 // have fasta headers it crashes.
563 BOOST_AUTO_TEST_CASE( sequence_past_end )
565 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
566 seq_path /= "misformated_seq.fa";
568 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
571 BOOST_AUTO_TEST_CASE ( sequence_empty )
575 BOOST_CHECK_EQUAL( s.empty(), true );
577 BOOST_CHECK_EQUAL( s.empty(), false );
579 BOOST_CHECK_EQUAL( s.empty(), true);
581 BOOST_CHECK_EQUAL( s.empty(), true);
584 BOOST_AUTO_TEST_CASE ( sequence_size )
588 BOOST_CHECK_EQUAL( s.size(), 0);
589 std::string seq_string("AAAGGG");
591 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
593 BOOST_CHECK_EQUAL( s.size(), 0);
595 BOOST_CHECK_EQUAL( s.size(), 0);
598 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
600 Sequence szero("", reduced_dna_alphabet);
601 BOOST_CHECK_EQUAL(szero.empty(), true);
602 BOOST_CHECK_EQUAL(szero, szero);
603 BOOST_CHECK_EQUAL(szero, "");
605 Sequence sclear("AGCT", reduced_dna_alphabet);
607 BOOST_CHECK_EQUAL(sclear.empty(), true);
608 BOOST_CHECK_EQUAL(sclear, sclear);
609 BOOST_CHECK_EQUAL(sclear, szero);
610 BOOST_CHECK_EQUAL(sclear, "");
613 BOOST_AUTO_TEST_CASE ( sequence_iterators )
615 std::string seq_string = "AAGGCCTTNNTATA";
616 Sequence s(seq_string, reduced_dna_alphabet);
617 const Sequence cs(s);
618 std::string::size_type count = 0;
620 std::string::iterator str_itor;
621 Sequence::const_iterator s_itor;
622 Sequence::const_iterator cs_itor;
624 for( str_itor = seq_string.begin(),
626 cs_itor = cs.begin();
627 str_itor != seq_string.end() and
628 s_itor != s.end() and
630 ++str_itor, ++s_itor, ++cs_itor, ++count)
632 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
633 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
634 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
636 BOOST_CHECK_EQUAL( seq_string.size(), count );
637 BOOST_CHECK_EQUAL( s.size(), count );
638 BOOST_CHECK_EQUAL( cs.size(), count );
641 BOOST_AUTO_TEST_CASE( sequence_motifs )
644 string bogus("AATTGGAA");
645 Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
647 list<motif>::const_iterator motif_i = s1.motifs().begin();
648 list<motif>::const_iterator motif_end = s1.motifs().end();
650 // do our iterators work?
651 BOOST_CHECK( motif_i == s1.motifs().begin() );
652 BOOST_CHECK( motif_end == s1.motifs().end() );
653 BOOST_CHECK( motif_i == motif_end );
655 // this shouldn't show up
657 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
658 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
661 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
662 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
664 for(motif_i = s1.motifs().begin();
665 motif_i != s1.motifs().end();
668 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
669 BOOST_CHECK_EQUAL( motif_i->name, m);
670 BOOST_CHECK_EQUAL( motif_i->sequence, m);
674 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
676 /* FIXME: enable this when i find a way of passing storing the motif name
677 // does our annotation travel?
678 Sequence motif_seq(m);
679 motif_seq.set_fasta_header("hi");
680 s1.add_motif(motif_seq);
682 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
683 for(motif_i = s1.motifs().begin();
684 motif_i != s1.motifs().end();
687 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
688 BOOST_CHECK_EQUAL( motif_i->name, "hi");
689 BOOST_CHECK_EQUAL( motif_i->sequence, m);
694 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
696 // when searching for a motif on a subsequence we should
697 // only search the subsequence ticket:199
700 Sequence s1("AAAANCCCC", reduced_dna_alphabet);
702 // this shouldn't show up
704 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
707 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
709 Sequence subseq1 = s1.subseq(4,5);
710 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
711 subseq1.clear_motifs();
712 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
713 // this is outside of our subsequence, and so shouldn't be found
714 subseq1.add_motif(aaaa);
715 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
717 subseq1.add_motif(cccc);
718 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
719 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
720 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
721 BOOST_CHECK_EQUAL(motif_i->begin, 1);
722 BOOST_CHECK_EQUAL(motif_i->end, 5);
725 BOOST_AUTO_TEST_CASE( annot_test )
727 annot a(0, 10, "test", "thing");
729 BOOST_CHECK_EQUAL( a.begin, 0 );
730 BOOST_CHECK_EQUAL( a.end, 10 );
731 BOOST_CHECK_EQUAL( a.type, "test" );
732 BOOST_CHECK_EQUAL( a.name, "thing" );
734 motif m(10, "AAGGCC");
735 BOOST_CHECK_EQUAL( m.begin, 10 );
736 BOOST_CHECK_EQUAL( m.type, "motif" );
737 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
738 BOOST_CHECK_EQUAL( m.end, 10+6 );
741 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
743 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
744 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
745 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
746 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
747 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
748 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
749 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
750 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
752 string gga("GGACACCTC");
753 Sequence seq(s, reduced_dna_alphabet);
755 std::list<Sequence> query_list;
756 std::list<string> string_list;
757 query_list.push_back(Sequence(gc));
758 string_list.push_back(gc);
759 query_list.push_back(Sequence(gga));
760 string_list.push_back(gga);
762 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
763 seq.find_sequences(query_list.begin(), query_list.end());
766 for(list<string>::iterator string_i = string_list.begin();
767 string_i != string_list.end();
770 string::size_type pos=0;
771 while(pos != string::npos) {
772 pos = s.find(*string_i, pos);
773 if (pos != string::npos) {
779 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
780 const std::list<annot> &a = seq.annotations();
781 for (std::list<annot>::const_iterator annot_i = a.begin();
785 int count = annot_i->end - annot_i->begin ;
789 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
791 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
792 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
793 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
794 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
795 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
796 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
797 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
798 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
799 Sequence seq(s, reduced_dna_alphabet);
802 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
803 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
804 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
805 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
806 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
808 Sequence subseq = seq.subseq(5, 10);
809 const list<annot> annots = subseq.annotations();
810 // generate some ground truth
812 correct.push_back(annot(0, 5, "0-10", "0-10"));
813 correct.push_back(annot(5,10, "10-20", "10-20"));
814 correct.push_back(annot(0,10, "0-20", "0-20"));
815 correct.push_back(annot(3, 7, "8-12", "8-12"));
816 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
818 list<annot>::iterator correct_i = correct.begin();
819 list<annot>::const_iterator annot_i = annots.begin();
820 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
822 BOOST_CHECK( *annot_i == *correct_i );
826 BOOST_AUTO_TEST_CASE( motif_annotation_update )
828 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
829 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
830 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
831 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
832 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
833 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
834 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
835 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
836 Sequence seq(s, reduced_dna_alphabet);
838 // starting conditions
839 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
840 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
841 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
842 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
843 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
844 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
845 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
846 seq.add_motif("CCGTCCC");
847 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
848 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
850 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
851 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
854 BOOST_AUTO_TEST_CASE( out_operator )
856 string s("AAGGCCTT");
857 Sequence seq(s, reduced_dna_alphabet);
861 BOOST_CHECK_EQUAL( s, buf.str() );
864 BOOST_AUTO_TEST_CASE( get_name )
866 Sequence seq("AAGGCCTT", reduced_dna_alphabet);
868 BOOST_CHECK_EQUAL( seq.get_name(), "" );
869 seq.set_species("hooman"); // anyone remember tradewars?
870 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
871 seq.set_fasta_header("fasta human");
872 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
875 BOOST_AUTO_TEST_CASE( serialize_simple )
877 std::string seq_string = "AAGGCCTT";
878 Sequence seq(seq_string, reduced_dna_alphabet);
879 seq.set_species("ribbet");
880 std::ostringstream oss;
881 // allocate/deallocate serialization components
883 boost::archive::text_oarchive oarchive(oss);
884 const Sequence& const_seq(seq);
885 BOOST_CHECK_EQUAL(seq, const_seq);
886 oarchive << const_seq;
890 std::istringstream iss(oss.str());
891 boost::archive::text_iarchive iarchive(iss);
892 iarchive >> seq_loaded;
894 BOOST_CHECK_EQUAL(seq_loaded, seq);
895 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
898 BOOST_AUTO_TEST_CASE( serialize_tree )
900 std::string seq_string = "AAGGCCTT";
901 Sequence seq(seq_string, reduced_dna_alphabet);
902 seq.set_species("ribbet");
905 annot a1(6,7,"t","t");
906 seq.add_annotation(a1);
908 std::ostringstream oss;
909 // allocate/deallocate serialization components
911 boost::archive::text_oarchive oarchive(oss);
912 const Sequence& const_seq(seq);
913 BOOST_CHECK_EQUAL(seq, const_seq);
914 oarchive << const_seq;
919 std::istringstream iss(oss.str());
920 boost::archive::text_iarchive iarchive(iss);
921 iarchive >> seq_loaded;
923 BOOST_CHECK_EQUAL(seq_loaded, seq);
926 // this writes out an "old" style annotated sequence
927 // with annotations attached as "motifs" and "annots"
928 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
930 std::string seq_string = "AAGGCCTT";
931 Sequence seq(seq_string, reduced_dna_alphabet);
932 seq.set_species("ribbet");
935 annot a1(6,7,"t","t");
936 seq.add_annotation(a1);
938 std::ostringstream oss;
939 // allocate/deallocate serialization components
941 boost::archive::xml_oarchive oarchive(oss);
942 const Sequence& const_seq(seq);
943 BOOST_CHECK_EQUAL(seq, const_seq);
944 oarchive << boost::serialization::make_nvp("root", const_seq);
948 std::istringstream iss(oss.str());
949 boost::archive::xml_iarchive iarchive(iss);
950 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
952 BOOST_CHECK_EQUAL(seq_loaded, seq);
955 BOOST_AUTO_TEST_CASE( serialize_xml_two )
957 std::string seq_string = "AAGGCCTT";
958 Sequence seq1(seq_string, reduced_dna_alphabet);
961 std::ostringstream oss;
962 // allocate/deallocate serialization components
964 boost::archive::xml_oarchive oarchive(oss);
965 const Sequence& const_seq1(seq1);
966 const Sequence& const_seq2(seq2);
967 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
968 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
970 //std::cout << "xml: " << oss.str() << std::endl;
971 Sequence seq1_loaded;
972 Sequence seq2_loaded;
974 std::istringstream iss(oss.str());
975 boost::archive::xml_iarchive iarchive(iss);
976 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
977 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
979 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
980 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
981 // test if our pointers are the same
982 BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());