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");
37 BOOST_AUTO_TEST_CASE( sequence_copy_constructor_copy_motifs )
39 SequenceRef s(new Sequence("AAAAGGGGAAAA"));
41 BOOST_CHECK_EQUAL(s->motifs().size(), 1);
43 SequenceRef c(new Sequence(s->subseq()));
44 BOOST_CHECK_EQUAL(c->motifs().size(), 1);
47 BOOST_CHECK_EQUAL(s->motifs().size(), 0);
48 // FIXME: Technically c shouldn't lose its motifs.
49 // FIXME: getting that to work is hard.
50 // BOOST_CHECK_EQUAL(c->motifs().size(), 1);
51 BOOST_CHECK_EQUAL(c->motifs().size(), 0);
54 BOOST_AUTO_TEST_CASE( sequence_get_sequence )
57 // make sure that retrieving the sequence doesn't throw an error
58 BOOST_CHECK_EQUAL(s.get_sequence(), std::string() );
61 BOOST_AUTO_TEST_CASE( sequence_from_string )
63 std::string str1("AAAT");
65 BOOST_CHECK_EQUAL(seq1.get_sequence(), str1);
68 BOOST_AUTO_TEST_CASE( sequence_find_first_not_of )
70 std::string str1("AAAAT");
72 BOOST_CHECK_EQUAL(seq1.find_first_not_of("A"), str1.find_first_not_of("A"));
74 std::string str2("AATTGGCC");
76 BOOST_CHECK_EQUAL(seq2.find_first_not_of("qwer"), str2.find_first_not_of("qwer"));
79 //! when we try to load a missing file, do we get an error?
80 BOOST_AUTO_TEST_CASE( sequence_load_exception )
83 // there should be errors when we try to load something that doesn't exist
84 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
85 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
88 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
90 string header(">Header");
91 string line1("AAAAGGGGCCCCTTTTT");
92 string line2("AAAAGGGGCCCCTTTTT");
93 int seq_len = line1.size() + line2.size();
96 cr << header << "\015" << line1 << "\015" << line2 << "\015";
98 seq_cr.load_fasta(cr);
101 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
103 seq_crlf.load_fasta(crlf);
106 lf << header << "\012" << line1 << "\012" << line2 << "\012";
108 seq_lf.load_fasta(lf);
110 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
111 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
112 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
116 //! Do simple operations work correctly?
117 BOOST_AUTO_TEST_CASE( sequence_filter )
119 const char *core_seq = "AATTGGCC";
120 Sequence s1(core_seq, reduced_dna_alphabet);
121 BOOST_CHECK_EQUAL(s1, core_seq);
123 Sequence s2("aattggcc", reduced_dna_alphabet);
124 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
125 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
126 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
127 BOOST_CHECK_EQUAL(s2.size(), s2.size());
128 //We're currently forcing sequences to uppercase
129 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
131 Sequence s3("asdfg", reduced_dna_alphabet);
132 BOOST_CHECK_EQUAL(s3, "ANNNG");
133 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
135 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 0, 2);
136 BOOST_CHECK_EQUAL(s3, "AA");
137 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 2, 2);
138 BOOST_CHECK_EQUAL( s3, "GG");
139 s3.set_filtered_sequence("AAGGCCTT", reduced_dna_alphabet, 4);
140 BOOST_CHECK_EQUAL( s3, "CCTT");
143 BOOST_CHECK_EQUAL(s3, "AAGGNN");
146 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
148 std::string agct("AGCT");
149 Sequence seq(agct, nucleic_alphabet);
150 BOOST_CHECK_EQUAL(seq.size(), agct.size());
151 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
153 std::string bdv("BDv");
154 Sequence seq_bdv(bdv, nucleic_alphabet);
155 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
156 // forcing sequence to upper case
157 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
158 boost::algorithm::to_upper_copy(bdv));
162 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
164 std::string agct("AGCT");
166 BOOST_CHECK_EQUAL(seq.size(), agct.size());
167 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
168 BOOST_CHECK_EQUAL(seq[0], agct[0]);
169 BOOST_CHECK_EQUAL(seq[1], agct[1]);
170 BOOST_CHECK_EQUAL(seq[2], agct[2]);
171 BOOST_CHECK_EQUAL(seq[3], agct[3]);
173 std::string bdv("BDv");
174 Sequence seq_bdv(bdv);
175 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
176 // default alphabet only allows AGCTUN
177 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
180 BOOST_AUTO_TEST_CASE( subseq_names )
182 Sequence s1("AAGGCCTT", reduced_dna_alphabet);
183 s1.set_species("species");
184 s1.set_fasta_header("a fasta header");
185 Sequence s2 = s1.subseq(2,2);
186 BOOST_CHECK_EQUAL(s2, "GG");
187 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
188 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
191 BOOST_AUTO_TEST_CASE( sequence_start_stop )
194 BOOST_CHECK_EQUAL( s1.start(), 0 );
195 BOOST_CHECK_EQUAL( s1.stop(), 0 );
197 std::string seq_string("AAGGCCTT");
198 Sequence s2(seq_string, reduced_dna_alphabet);
199 BOOST_CHECK_EQUAL( s2.start(), 0 );
200 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
202 std::string s3seq_string = seq_string.substr(2,3);
203 Sequence s3 = s2.subseq(2,3);
204 BOOST_CHECK_EQUAL( s3.start(), 2);
205 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
206 BOOST_CHECK_EQUAL( s3.size(), 3);
207 BOOST_CHECK_EQUAL( s3, s3seq_string);
209 std::string s4seq_string = s3seq_string.substr(1,1);
210 Sequence s4 = s3.subseq(1,1);
211 BOOST_CHECK_EQUAL( s4.start(), 1 );
212 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
213 BOOST_CHECK_EQUAL( s4.size(), 1);
214 BOOST_CHECK_EQUAL( s4, s4seq_string);
217 //! Can we load data from a file
218 BOOST_AUTO_TEST_CASE( sequence_load )
220 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
221 seq_path /= "human_mck_pro.fa";
223 s.load_fasta(seq_path, reduced_dna_alphabet);
224 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
225 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
226 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
227 "muscle creatine kinase gene (CKMM), "
231 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
233 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
234 seq_path /= "broken.fa";
235 bool exception_thrown = false;
236 std::string exception_filename;
239 s.load_fasta(seq_path);
240 } catch(sequence_invalid_load_error e) {
241 exception_thrown = true;
242 size_t native_string_size = seq_path.native_file_string().size();
243 std:string estr(e.what());
244 BOOST_REQUIRE(estr.size() > native_string_size);
245 std::copy(estr.begin(), estr.begin()+native_string_size,
246 std::back_inserter(exception_filename));
248 BOOST_CHECK_EQUAL(exception_thrown, true);
249 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
252 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
254 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
255 seq_path /= "mouse_mck_pro.fa";
256 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
257 annot_path /= "broken.annot";
258 bool exception_thrown = false;
260 s.load_fasta(seq_path);
262 std::string exception_filename;
264 s.load_annot(annot_path, 0, 0);
265 } catch(annotation_load_error e) {
266 exception_thrown = true;
267 std:string estr(e.what());
268 size_t native_string_size = annot_path.native_file_string().size();
269 BOOST_REQUIRE(estr.size() > native_string_size);
270 std::copy(estr.begin(), estr.begin()+native_string_size,
271 std::back_inserter(exception_filename));
273 BOOST_CHECK_EQUAL(exception_thrown, true);
274 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
277 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
279 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
280 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
281 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
282 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
283 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
284 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
285 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
286 std::stringstream garbage_fasta(garbage_string);
289 s.load_fasta(reduced_dna_fasta, reduced_dna_alphabet);
290 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
291 reduced_dna_alphabet),
292 sequence_invalid_load_error);
293 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
294 reduced_dna_alphabet),
295 sequence_invalid_load_error);
296 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
297 reduced_dna_alphabet),
298 sequence_invalid_load_error);
302 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
304 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
305 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
306 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
307 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
308 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
309 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
310 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
311 std::stringstream garbage_fasta(garbage_string);
314 s.load_fasta(reduced_rna_fasta, reduced_rna_alphabet);
315 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
316 reduced_rna_alphabet),
317 sequence_invalid_load_error);
318 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
319 reduced_rna_alphabet),
320 sequence_invalid_load_error);
321 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
322 reduced_rna_alphabet),
323 sequence_invalid_load_error);
326 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
328 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
329 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
330 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
331 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
332 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
333 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
334 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
335 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
336 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
337 std::stringstream garbage_fasta(garbage_string);
341 // there's two copies of reduced_rna_fasta because i didn't feel like
342 // figuring out how to properly reset the read pointer in a stringstream
343 s.load_fasta(reduced_rna_fasta1);
344 specific.load_fasta(reduced_rna_fasta2, reduced_nucleic_alphabet);
345 BOOST_CHECK_EQUAL(s, specific);
347 s.load_fasta(reduced_dna_fasta1);
348 specific.load_fasta(reduced_dna_fasta2, reduced_nucleic_alphabet);
349 BOOST_CHECK_EQUAL(s, specific);
351 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
352 sequence_invalid_load_error);
353 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
354 sequence_invalid_load_error);
357 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
359 std::string fasta_file(
360 ">gi|10129974|gb|AF188002.1|AF188002\n"
361 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
362 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
363 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
364 ">gi|1621|emb|X55146.1|OCMCK1\n"
365 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
367 istringstream seq1_file(fasta_file);
369 seq1.load_fasta(seq1_file, 1, 0, 0);
370 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
372 istringstream seq2_file(fasta_file);
374 seq2.load_fasta(seq2_file, 2, 0, 0);
375 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
377 istringstream seq3_file(fasta_file);
379 seq3.load_fasta(seq3_file, 3, 0, 0);
380 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
383 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
385 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
386 Sequence seq(iupac_symbols, nucleic_alphabet);
387 Sequence seqr = seq.rev_comp();
389 BOOST_CHECK( seq != seqr );
390 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
391 // forcing sequence to upper case
392 BOOST_CHECK_EQUAL( seq.get_sequence(),
393 boost::algorithm::to_upper_copy(iupac_symbols) );
396 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
398 std::string dna_str("AGCTN");
399 Sequence dna_seq(dna_str, reduced_dna_alphabet);
400 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
401 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
404 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
406 std::string rna_str("AGCUN");
407 Sequence rna_seq(rna_str, reduced_rna_alphabet);
408 BOOST_CHECK_EQUAL(rna_seq.rev_comp().get_sequence(), "NAGCU");
409 BOOST_CHECK_EQUAL(rna_seq.get_sequence(),
410 rna_seq.rev_comp().rev_comp().get_sequence());
413 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
415 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
416 Sequence seq(dna_str, reduced_dna_alphabet);
417 Sequence subseq = seq.subseq(8,4);
418 BOOST_CHECK_EQUAL( subseq, "AAGG");
419 Sequence rev_subseq = subseq.rev_comp();
420 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
421 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
424 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
426 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
427 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
428 Sequence seq(dna_str);
429 std::string seq_reversed(seq.rbegin(), seq.rend());
430 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
432 std::string substr = dna_str.substr(8,4);
433 Sequence subseq = seq.subseq(8,4);
434 BOOST_CHECK_EQUAL(substr, subseq);
436 std::string substr_reversed(substr.rbegin(), substr.rend());
437 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
438 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
441 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
443 // so what happens with reverse interators when we have no sequence?
446 Sequence seq3("AGCT");
448 // all the empty sequences should have equal iterators
449 BOOST_CHECK(seq1.rbegin() == seq1.rend());
450 BOOST_CHECK(seq1.rbegin() == seq2.rend());
452 // none of the seq1 iterators should equal any of the seq3 iterators
453 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
454 BOOST_CHECK(seq1.rbegin() != seq3.rend());
455 BOOST_CHECK(seq1.rend() != seq3.rbegin());
456 BOOST_CHECK(seq1.rend() != seq3.rend());
458 // seq3 iterators should work
459 BOOST_CHECK(seq3.rbegin() != seq3.rend());
463 BOOST_AUTO_TEST_CASE( annotation_load )
465 string annot_data = "human\n"
466 "0 10 name type\n" //0
469 "50\t55 anothername\n" //3
470 "60 50 backward\n" //4
471 ">ident3 asdf\n" //7 (as these are added last)
474 "75\t90\tname2\ttype2\n" //5
475 "100 120 name-asdf type!@#$%\n" //6
479 Sequence seq(s, reduced_dna_alphabet);
481 //istringstream annot_stream(annot_data);
482 seq.parse_annot(annot_data, 0, 0);
483 SeqSpanRefList annots_list(seq.annotations());
484 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
485 BOOST_REQUIRE_EQUAL( annots.size(), 8);
486 BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
487 BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
488 BOOST_REQUIRE( annots[0]->annotations() );
489 BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
490 BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "name");
491 BOOST_REQUIRE( annots[1]->annotations() );
492 BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "myf7");
493 BOOST_REQUIRE( annots[2]->annotations() );
494 BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "myod");
495 BOOST_REQUIRE( annots[3]->annotations() );
496 BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "anothername");
497 BOOST_REQUIRE( annots[4]->annotations() );
498 BOOST_CHECK_EQUAL( annots[4]->annotations()->name(), "backward");
499 BOOST_REQUIRE( annots[5]->annotations() );
500 BOOST_CHECK_EQUAL( annots[5]->annotations()->name(), "name2");
501 BOOST_CHECK_EQUAL( annots[5]->start(), 75);
502 BOOST_CHECK_EQUAL( annots[5]->stop(), 90);
503 BOOST_CHECK_EQUAL( annots[6]->start(), 100);
504 BOOST_CHECK_EQUAL( annots[6]->stop(), 110);
505 BOOST_REQUIRE( annots[6]->annotations() );
506 BOOST_CHECK_EQUAL( annots[6]->annotations()->name(), "name-asdf");
507 BOOST_CHECK_EQUAL( annots[6]->annotations()->get("type"), "type!@#$%");
508 // sequence defined annotations will always be after the
509 // absolute positions
510 BOOST_REQUIRE( annots[7]->annotations() );
511 BOOST_CHECK_EQUAL( annots[7]->annotations()->name(), "ident3 asdf");
512 BOOST_CHECK_EQUAL( annots[7]->start(), 100);
513 BOOST_CHECK_EQUAL( annots[7]->stop(), 107);
515 //BOOST_CHECK_EQUAL( annots
518 BOOST_AUTO_TEST_CASE( annotation_broken_load )
520 string annot_data = "human\n"
522 "blah60 50 backward\n"
529 Sequence seq(s, reduced_dna_alphabet);
531 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
532 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
535 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
537 // this actually is basically what's returned by UCSC
538 // (well actually with some of the sequence and copies of fasta blocks
539 // removed to make the example shorter
540 string annot_data = "\n"
542 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
543 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
544 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
545 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
553 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
555 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
556 Sequence seq(s, reduced_dna_alphabet);
557 seq.parse_annot(annot_data);
558 SeqSpanRefList annots(seq.annotations());
559 BOOST_CHECK_EQUAL( annots.size(), 2);
562 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
564 string annot_data = "0 10 name type\n"
567 "50\t55 anothername\n"
572 "75\t90\tname2\ttype2\n"
573 "100 120 name-asdf type!@#$%\n"
577 Sequence seq(s, reduced_dna_alphabet);
579 //istringstream annot_stream(annot_data);
580 seq.parse_annot(annot_data, 0, 0);
581 SeqSpanRefList annots_list(seq.annotations());
582 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
583 BOOST_REQUIRE_EQUAL( annots.size(), 8);
584 BOOST_CHECK_EQUAL( annots[0]->start(), 0 );
585 BOOST_CHECK_EQUAL( annots[0]->stop(), 10 );
586 BOOST_CHECK_EQUAL( annots[0]->annotations()->get("type"), "type");
589 // when we do a subsequence (or something that calls copy_children)
590 // the annotations need to be updated to have the right parent
591 BOOST_AUTO_TEST_CASE( update_annotations_seqref )
593 Sequence s1("AAAAGGGG");
594 s1.add_annotation("A", "A", 0, 4);
595 BOOST_CHECK_EQUAL(s1.annotations().size(), 1);
596 BOOST_CHECK_EQUAL(s1.seqspan(), s1.annotations().front()->parent() );
598 Sequence subseq1(s1.subseq(2,4));
599 BOOST_CHECK_EQUAL(subseq1.annotations().size(), 1);
600 BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStart(), 0 );
601 BOOST_CHECK_EQUAL(subseq1.annotations().front()->parentStop(), 2 );
602 BOOST_CHECK_EQUAL(subseq1.seqspan(), subseq1.annotations().front()->parent() );
605 // ticket:83 when you try to load a sequence from a file that doesn't
606 // have fasta headers it crashes.
607 BOOST_AUTO_TEST_CASE( sequence_past_end )
609 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
610 seq_path /= "misformated_seq.fa";
612 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
615 BOOST_AUTO_TEST_CASE ( sequence_empty )
619 BOOST_CHECK_EQUAL( s.empty(), true );
621 BOOST_CHECK_EQUAL( s.empty(), false );
623 BOOST_CHECK_EQUAL( s.empty(), true);
625 BOOST_CHECK_EQUAL( s.empty(), true);
628 BOOST_AUTO_TEST_CASE ( sequence_size )
632 BOOST_CHECK_EQUAL( s.size(), 0);
633 std::string seq_string("AAAGGG");
635 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
637 BOOST_CHECK_EQUAL( s.size(), 0);
639 BOOST_CHECK_EQUAL( s.size(), 0);
642 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
644 Sequence szero("", reduced_dna_alphabet);
645 BOOST_CHECK_EQUAL(szero.empty(), true);
646 BOOST_CHECK_EQUAL(szero, szero);
647 BOOST_CHECK_EQUAL(szero, "");
649 Sequence sclear("AGCT", reduced_dna_alphabet);
651 BOOST_CHECK_EQUAL(sclear.empty(), true);
652 BOOST_CHECK_EQUAL(sclear, sclear);
653 BOOST_CHECK_EQUAL(sclear, szero);
654 BOOST_CHECK_EQUAL(sclear, "");
657 BOOST_AUTO_TEST_CASE ( sequence_iterators )
659 std::string seq_string = "AAGGCCTTNNTATA";
660 Sequence s(seq_string, reduced_dna_alphabet);
661 const Sequence cs(s);
662 std::string::size_type count = 0;
664 std::string::iterator str_itor;
665 Sequence::const_iterator s_itor;
666 Sequence::const_iterator cs_itor;
668 for( str_itor = seq_string.begin(),
670 cs_itor = cs.begin();
671 str_itor != seq_string.end() and
672 s_itor != s.end() and
674 ++str_itor, ++s_itor, ++cs_itor, ++count)
676 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
677 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
678 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
680 BOOST_CHECK_EQUAL( seq_string.size(), count );
681 BOOST_CHECK_EQUAL( s.size(), count );
682 BOOST_CHECK_EQUAL( cs.size(), count );
685 BOOST_AUTO_TEST_CASE( sequence_motifs )
688 string bogus("AATTGGAA");
689 Sequence s1("AAAAGGGGCCCCTTTT", reduced_dna_alphabet);
691 list<motif>::const_iterator motif_i = s1.motifs().begin();
692 list<motif>::const_iterator motif_end = s1.motifs().end();
694 // do our iterators work?
695 BOOST_CHECK( motif_i == s1.motifs().begin() );
696 BOOST_CHECK( motif_end == s1.motifs().end() );
697 BOOST_CHECK( motif_i == motif_end );
699 // this shouldn't show up
701 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
702 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
705 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
706 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
708 for(motif_i = s1.motifs().begin();
709 motif_i != s1.motifs().end();
712 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
713 BOOST_CHECK_EQUAL( motif_i->name, m);
714 BOOST_CHECK_EQUAL( motif_i->sequence, m);
718 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
720 /* FIXME: enable this when i find a way of passing storing the motif name
721 // does our annotation travel?
722 Sequence motif_seq(m);
723 motif_seq.set_fasta_header("hi");
724 s1.add_motif(motif_seq);
726 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
727 for(motif_i = s1.motifs().begin();
728 motif_i != s1.motifs().end();
731 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
732 BOOST_CHECK_EQUAL( motif_i->name, "hi");
733 BOOST_CHECK_EQUAL( motif_i->sequence, m);
738 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
740 // when searching for a motif on a subsequence we should
741 // only search the subsequence ticket:199
744 Sequence s1("AAAANCCCC", reduced_dna_alphabet);
746 // this shouldn't show up
748 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
751 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
753 Sequence subseq1 = s1.subseq(4,5);
754 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
755 subseq1.clear_motifs();
756 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
757 // this is outside of our subsequence, and so shouldn't be found
758 subseq1.add_motif(aaaa);
759 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
761 subseq1.add_motif(cccc);
762 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
763 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
764 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
765 BOOST_CHECK_EQUAL(motif_i->begin, 1);
766 BOOST_CHECK_EQUAL(motif_i->end, 5);
769 BOOST_AUTO_TEST_CASE( annot_test )
771 Sequence s("AAAAAAAAAA");
772 s.add_annotation("test", "thing", 0, 10);
773 SeqSpanRef a(s.annotations().front());
775 BOOST_CHECK_EQUAL( a->start(), 0 );
776 BOOST_CHECK_EQUAL( a->stop(), 10 );
777 BOOST_CHECK_EQUAL( a->annotations()->get("name"), "test" );
778 BOOST_CHECK_EQUAL( a->annotations()->get("type"), "thing" );
780 motif m(10, "AAGGCC");
781 BOOST_CHECK_EQUAL( m.begin, 10 );
782 BOOST_CHECK_EQUAL( m.type, "motif" );
783 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
784 BOOST_CHECK_EQUAL( m.end, 10+6 );
787 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
789 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
790 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
791 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
792 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
793 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
794 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
795 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
796 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
798 string gga("GGACACCTC");
799 Sequence seq(s, reduced_dna_alphabet);
801 std::list<Sequence> query_list;
802 std::list<string> string_list;
803 query_list.push_back(Sequence(gc));
804 string_list.push_back(gc);
805 query_list.push_back(Sequence(gga));
806 string_list.push_back(gga);
808 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
809 seq.find_sequences(query_list.begin(), query_list.end());
812 for(list<string>::iterator string_i = string_list.begin();
813 string_i != string_list.end();
816 string::size_type pos=0;
817 while(pos != string::npos) {
818 pos = s.find(*string_i, pos);
819 if (pos != string::npos) {
825 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
826 const SeqSpanRefList& a = seq.annotations();
827 for (SeqSpanRefList::const_iterator annot_i = a.begin();
831 //FIXME: was I doing something here?
832 int count = (*annot_i)->stop() - (*annot_i)->start();
836 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
838 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
839 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
840 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
841 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
842 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
843 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
844 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
845 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
846 Sequence seq(s, reduced_dna_alphabet);
848 seq.add_annotation("0-10", "0-10", 0, 10);
849 seq.add_annotation("10-20", "10-20", 10, 20);
850 seq.add_annotation("0-20", "0-20", 0, 20);
851 seq.add_annotation("8-12", "8-12", 8, 12);
852 seq.add_annotation("100-5000", "100-5000", 100, 5000);
854 Sequence subseq = seq.subseq(5, 10);
855 SeqSpanRefList annots_list = subseq.annotations();
856 BOOST_REQUIRE_EQUAL( annots_list.size(), 4 );
858 std::vector<SeqSpanRef> annots(annots_list.begin(), annots_list.end());
859 BOOST_CHECK_EQUAL( annots[0]->parentStart(), 0);
860 BOOST_CHECK_EQUAL( annots[0]->size(), 5);
861 BOOST_REQUIRE( annots[0]->annotations() );
862 BOOST_CHECK_EQUAL( annots[0]->annotations()->name(), "0-10");
864 BOOST_CHECK_EQUAL( annots[1]->parentStart(), 5);
865 BOOST_CHECK_EQUAL( annots[1]->size(), 5);
866 BOOST_REQUIRE( annots[1]->annotations() );
867 BOOST_CHECK_EQUAL( annots[1]->annotations()->name(), "10-20");
869 BOOST_CHECK_EQUAL( annots[2]->parentStart(), 0);
870 BOOST_CHECK_EQUAL( annots[2]->size(), 10);
871 BOOST_REQUIRE( annots[2]->annotations() );
872 BOOST_CHECK_EQUAL( annots[2]->annotations()->name(), "0-20");
874 BOOST_CHECK_EQUAL( annots[3]->parentStart(), 3);
875 BOOST_CHECK_EQUAL( annots[3]->size(), 7);
876 BOOST_REQUIRE( annots[3]->annotations() );
877 BOOST_CHECK_EQUAL( annots[3]->annotations()->name(), "8-12");
880 BOOST_AUTO_TEST_CASE( motif_annotation_update )
882 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
883 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
884 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
885 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
886 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
887 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
888 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
889 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
890 Sequence seq(s, reduced_dna_alphabet);
892 // starting conditions
893 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
894 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
895 seq.add_annotation("0-10", "0-10", 0, 10);
896 seq.add_annotation("10-20", "10-20", 10, 20);
897 seq.add_annotation("0-20", "0-20", 0, 20);
898 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
899 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
900 seq.add_motif("CCGTCCC");
901 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
902 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
904 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
905 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
908 BOOST_AUTO_TEST_CASE( out_operator )
910 string s("AAGGCCTT");
911 Sequence seq(s, reduced_dna_alphabet);
915 BOOST_CHECK_EQUAL( s, buf.str() );
918 BOOST_AUTO_TEST_CASE( get_name )
920 Sequence seq("AAGGCCTT", reduced_dna_alphabet);
922 BOOST_CHECK_EQUAL( seq.get_name(), "" );
923 seq.set_species("hooman"); // anyone remember tradewars?
924 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
925 seq.set_fasta_header("fasta human");
926 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
929 BOOST_AUTO_TEST_CASE( serialize_simple )
931 std::string seq_string = "AAGGCCTT";
932 Sequence seq(seq_string, reduced_dna_alphabet);
933 seq.set_species("ribbet");
934 std::ostringstream oss;
935 // allocate/deallocate serialization components
937 boost::archive::text_oarchive oarchive(oss);
938 const Sequence& const_seq(seq);
939 BOOST_CHECK_EQUAL(seq, const_seq);
940 oarchive << const_seq;
944 std::istringstream iss(oss.str());
945 boost::archive::text_iarchive iarchive(iss);
946 iarchive >> seq_loaded;
948 BOOST_CHECK_EQUAL(seq_loaded, seq);
949 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
952 BOOST_AUTO_TEST_CASE( serialize_tree )
954 std::string seq_string = "AAGGCCTT";
955 Sequence seq(seq_string, reduced_dna_alphabet);
956 seq.set_species("ribbet");
959 seq.add_annotation("t", "t", 6, 7);
961 std::ostringstream oss;
962 // allocate/deallocate serialization components
964 boost::archive::text_oarchive oarchive(oss);
965 const Sequence& const_seq(seq);
966 BOOST_CHECK_EQUAL(seq, const_seq);
967 oarchive << const_seq;
972 std::istringstream iss(oss.str());
973 boost::archive::text_iarchive iarchive(iss);
974 iarchive >> seq_loaded;
976 BOOST_CHECK_EQUAL(seq_loaded, seq);
979 // this writes out an "old" style annotated sequence
980 // with annotations attached as "motifs" and "annots"
981 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
983 std::string seq_string = "AAGGCCTT";
984 Sequence seq(seq_string, reduced_dna_alphabet);
985 seq.set_species("ribbet");
988 seq.add_annotation("t", "t", 6, 7);
990 std::ostringstream oss;
991 // allocate/deallocate serialization components
993 boost::archive::xml_oarchive oarchive(oss);
994 const Sequence& const_seq(seq);
995 BOOST_CHECK_EQUAL(seq, const_seq);
996 oarchive << boost::serialization::make_nvp("root", const_seq);
1000 std::istringstream iss(oss.str());
1001 boost::archive::xml_iarchive iarchive(iss);
1002 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
1004 BOOST_CHECK_EQUAL(seq_loaded, seq);
1007 BOOST_AUTO_TEST_CASE( serialize_xml_two )
1009 std::string seq_string = "AAGGCCTT";
1010 Sequence seq1(seq_string, reduced_dna_alphabet);
1011 Sequence seq2(seq1);
1013 std::ostringstream oss;
1014 // allocate/deallocate serialization components
1016 boost::archive::xml_oarchive oarchive(oss);
1017 const Sequence& const_seq1(seq1);
1018 const Sequence& const_seq2(seq2);
1019 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
1020 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
1022 //std::cout << "xml: " << oss.str() << std::endl;
1023 Sequence seq1_loaded;
1024 Sequence seq2_loaded;
1026 std::istringstream iss(oss.str());
1027 boost::archive::xml_iarchive iarchive(iss);
1028 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
1029 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
1031 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
1032 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
1033 // test if our pointers are the same
1034 BOOST_CHECK_EQUAL(seq1_loaded.data(), seq2_loaded.data());