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 //! when we try to load a missing file, do we get an error?
31 BOOST_AUTO_TEST_CASE( sequence_load_exception )
34 // there should be errors when we try to load something that doesn't exist
35 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
36 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
39 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
41 string header(">Header");
42 string line1("AAAAGGGGCCCCTTTTT");
43 string line2("AAAAGGGGCCCCTTTTT");
44 int seq_len = line1.size() + line2.size();
47 cr << header << "\015" << line1 << "\015" << line2 << "\015";
49 seq_cr.load_fasta(cr);
52 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
54 seq_crlf.load_fasta(crlf);
57 lf << header << "\012" << line1 << "\012" << line2 << "\012";
59 seq_lf.load_fasta(lf);
61 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
62 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
63 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
67 //! Do simple operations work correctly?
68 BOOST_AUTO_TEST_CASE( sequence_filter )
70 const char *core_seq = "AATTGGCC";
71 Sequence s1(core_seq, Sequence::reduced_dna_alphabet);
72 BOOST_CHECK_EQUAL(s1, core_seq);
74 Sequence s2("aattggcc", Sequence::reduced_dna_alphabet);
75 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
76 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
77 BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
78 BOOST_CHECK_EQUAL(s2.size(), s2.size());
79 //We're currently forcing sequences to uppercase
80 BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC");
82 Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
83 BOOST_CHECK_EQUAL(s3, "ANNNG");
84 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
86 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 0, 2);
87 BOOST_CHECK_EQUAL(s3, "AA");
88 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 2, 2);
89 BOOST_CHECK_EQUAL( s3, "GG");
90 s3.set_filtered_sequence("AAGGCCTT", Sequence::reduced_dna_alphabet, 4);
91 BOOST_CHECK_EQUAL( s3, "CCTT");
94 BOOST_CHECK_EQUAL(s3, "AAGGNN");
97 BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
99 std::string agct("AGCT");
100 Sequence seq(agct, Sequence::nucleic_alphabet);
101 BOOST_CHECK_EQUAL(seq.size(), agct.size());
102 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
104 std::string bdv("BDv");
105 Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
106 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
107 // forcing sequence to upper case
108 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(),
109 boost::algorithm::to_upper_copy(bdv));
113 BOOST_AUTO_TEST_CASE( sequence_default_alphabet )
115 std::string agct("AGCT");
117 BOOST_CHECK_EQUAL(seq.size(), agct.size());
118 BOOST_CHECK_EQUAL(seq.get_sequence(), agct);
119 BOOST_CHECK_EQUAL(seq[0], agct[0]);
120 BOOST_CHECK_EQUAL(seq[1], agct[1]);
121 BOOST_CHECK_EQUAL(seq[2], agct[2]);
122 BOOST_CHECK_EQUAL(seq[3], agct[3]);
124 std::string bdv("BDv");
125 Sequence seq_bdv(bdv);
126 BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
127 // default alphabet only allows AGCTUN
128 BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), "NNN");
131 BOOST_AUTO_TEST_CASE( subseq_names )
133 Sequence s1("AAGGCCTT", Sequence::reduced_dna_alphabet);
134 s1.set_species("species");
135 s1.set_fasta_header("a fasta header");
136 Sequence s2 = s1.subseq(2,2);
137 BOOST_CHECK_EQUAL(s2, "GG");
138 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
139 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
142 BOOST_AUTO_TEST_CASE( sequence_start_stop )
145 BOOST_CHECK_EQUAL( s1.start(), 0 );
146 BOOST_CHECK_EQUAL( s1.stop(), 0 );
148 std::string seq_string("AAGGCCTT");
149 Sequence s2(seq_string, Sequence::reduced_dna_alphabet);
150 BOOST_CHECK_EQUAL( s2.start(), 0 );
151 BOOST_CHECK_EQUAL( s2.stop(), seq_string.size() );
153 std::string s3seq_string = seq_string.substr(2,3);
154 Sequence s3 = s2.subseq(2,3);
155 BOOST_CHECK_EQUAL( s3.start(), 2);
156 BOOST_CHECK_EQUAL( s3.stop(), 2+3);
157 BOOST_CHECK_EQUAL( s3.size(), 3);
158 BOOST_CHECK_EQUAL( s3, s3seq_string);
160 std::string s4seq_string = s3seq_string.substr(1,1);
161 Sequence s4 = s3.subseq(1,1);
162 BOOST_CHECK_EQUAL( s4.start(), 1 );
163 BOOST_CHECK_EQUAL( s4.stop(), 1+1);
164 BOOST_CHECK_EQUAL( s4.size(), 1);
165 BOOST_CHECK_EQUAL( s4, s4seq_string);
168 //! Can we load data from a file
169 BOOST_AUTO_TEST_CASE( sequence_load )
171 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq");
172 seq_path /= "human_mck_pro.fa";
174 s.load_fasta(seq_path, Sequence::reduced_dna_alphabet);
175 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
176 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
177 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
178 "muscle creatine kinase gene (CKMM), "
182 BOOST_AUTO_TEST_CASE( sequence_load_fasta_error )
184 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
185 seq_path /= "broken.fa";
186 bool exception_thrown = false;
187 std::string exception_filename;
190 s.load_fasta(seq_path);
191 } catch(sequence_invalid_load_error e) {
192 exception_thrown = true;
193 size_t native_string_size = seq_path.native_file_string().size();
194 std:string estr(e.what());
195 BOOST_REQUIRE(estr.size() > native_string_size);
196 std::copy(estr.begin(), estr.begin()+native_string_size,
197 std::back_inserter(exception_filename));
199 BOOST_CHECK_EQUAL(exception_thrown, true);
200 BOOST_CHECK_EQUAL(seq_path.native_file_string(), exception_filename);
203 BOOST_AUTO_TEST_CASE( sequence_load_annot_error )
205 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/"seq");
206 seq_path /= "mouse_mck_pro.fa";
207 fs::path annot_path(fs::path(EXAMPLE_DIR, fs::native));
208 annot_path /= "broken.annot";
209 bool exception_thrown = false;
211 s.load_fasta(seq_path);
213 std::string exception_filename;
215 s.load_annot(annot_path, 0, 0);
216 } catch(annotation_load_error e) {
217 exception_thrown = true;
218 std:string estr(e.what());
219 size_t native_string_size = annot_path.native_file_string().size();
220 BOOST_REQUIRE(estr.size() > native_string_size);
221 std::copy(estr.begin(), estr.begin()+native_string_size,
222 std::back_inserter(exception_filename));
224 BOOST_CHECK_EQUAL(exception_thrown, true);
225 BOOST_CHECK_EQUAL(annot_path.native_file_string(), exception_filename);
228 BOOST_AUTO_TEST_CASE( sequence_load_dna_reduced )
230 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
231 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
232 std::string invalid_dna_fasta_string(">wrong\nAUSSI\n");
233 std::stringstream invalid_dna_fasta(invalid_dna_fasta_string);
234 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN-\n");
235 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
236 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
237 std::stringstream garbage_fasta(garbage_string);
240 s.load_fasta(reduced_dna_fasta, Sequence::reduced_dna_alphabet);
241 BOOST_CHECK_THROW(s.load_fasta(invalid_dna_fasta,
242 Sequence::reduced_dna_alphabet),
243 sequence_invalid_load_error);
244 BOOST_CHECK_THROW(s.load_fasta(reduced_rna_fasta,
245 Sequence::reduced_dna_alphabet),
246 sequence_invalid_load_error);
247 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
248 Sequence::reduced_dna_alphabet),
249 sequence_invalid_load_error);
253 BOOST_AUTO_TEST_CASE( sequence_load_rna_reduced )
255 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
256 std::stringstream reduced_rna_fasta(reduced_rna_fasta_string);
257 std::string invalid_rna_fasta_string(">wrong\nATSSI\n");
258 std::stringstream invalid_rna_fasta(invalid_rna_fasta_string);
259 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
260 std::stringstream reduced_dna_fasta(reduced_dna_fasta_string);
261 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
262 std::stringstream garbage_fasta(garbage_string);
265 s.load_fasta(reduced_rna_fasta, Sequence::reduced_rna_alphabet);
266 BOOST_CHECK_THROW(s.load_fasta(invalid_rna_fasta,
267 Sequence::reduced_rna_alphabet),
268 sequence_invalid_load_error);
269 BOOST_CHECK_THROW(s.load_fasta(reduced_dna_fasta,
270 Sequence::reduced_rna_alphabet),
271 sequence_invalid_load_error);
272 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta,
273 Sequence::reduced_rna_alphabet),
274 sequence_invalid_load_error);
277 BOOST_AUTO_TEST_CASE( sequence_load_fasta_default )
279 std::string reduced_rna_fasta_string(">foo\nAAGGCCUUNN\n");
280 std::stringstream reduced_rna_fasta1(reduced_rna_fasta_string);
281 std::stringstream reduced_rna_fasta2(reduced_rna_fasta_string);
282 std::string invalid_nucleotide_fasta_string(">wrong\nATSSI\n");
283 std::stringstream invalid_nucleotide_fasta(invalid_nucleotide_fasta_string);
284 std::string reduced_dna_fasta_string(">foo\nAAGGCCTTNN\n");
285 std::stringstream reduced_dna_fasta1(reduced_dna_fasta_string);
286 std::stringstream reduced_dna_fasta2(reduced_dna_fasta_string);
287 std::string garbage_string(">foo\na34ralk3547oilk,jual;(*&^#%-\n");
288 std::stringstream garbage_fasta(garbage_string);
292 // there's two copies of reduced_rna_fasta because i didn't feel like
293 // figuring out how to properly reset the read pointer in a stringstream
294 s.load_fasta(reduced_rna_fasta1);
295 specific.load_fasta(reduced_rna_fasta2, Sequence::reduced_nucleic_alphabet);
296 BOOST_CHECK_EQUAL(s, specific);
298 s.load_fasta(reduced_dna_fasta1);
299 specific.load_fasta(reduced_dna_fasta2, Sequence::reduced_nucleic_alphabet);
300 BOOST_CHECK_EQUAL(s, specific);
302 BOOST_CHECK_THROW(s.load_fasta(invalid_nucleotide_fasta),
303 sequence_invalid_load_error);
304 BOOST_CHECK_THROW(s.load_fasta(garbage_fasta),
305 sequence_invalid_load_error);
308 BOOST_AUTO_TEST_CASE( sequence_load_multiple_sequences_one_fasta )
310 std::string fasta_file(
311 ">gi|10129974|gb|AF188002.1|AF188002\n"
312 "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC\n"
313 ">gi|180579|gb|M21487.1|HUMCKMM1\n"
314 "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC\n"
315 ">gi|1621|emb|X55146.1|OCMCK1\n"
316 "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC\n"
318 istringstream seq1_file(fasta_file);
320 seq1.load_fasta(seq1_file, 1, 0, 0);
321 BOOST_CHECK_EQUAL(seq1.get_sequence(), "AAAAGGCTCCTGTCATATTGTGTCCTGCTCTGGTCTGC");
323 istringstream seq2_file(fasta_file);
325 seq2.load_fasta(seq2_file, 2, 0, 0);
326 BOOST_CHECK_EQUAL(seq2.get_sequence(), "CGCCGAGAGCGCTTGCTCTGCCCAGATCTCGGCGAGTC");
328 istringstream seq3_file(fasta_file);
330 seq3.load_fasta(seq3_file, 3, 0, 0);
331 BOOST_CHECK_EQUAL(seq3.get_sequence(), "CTCCCTGAGGGGAGTGCCCCGCTTAGCCC");
334 BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
336 std::string iupac_symbols("AaCcGgTtRrYySsWwKkMmBbDdHhVvNn-~.?");
337 Sequence seq(iupac_symbols, Sequence::nucleic_alphabet);
338 Sequence seqr = seq.rev_comp();
340 BOOST_CHECK( seq != seqr );
341 BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
342 // forcing sequence to upper case
343 BOOST_CHECK_EQUAL( seq.get_sequence(),
344 boost::algorithm::to_upper_copy(iupac_symbols) );
347 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )
349 std::string dna_str("AGCTN");
350 Sequence dna_seq(dna_str, Sequence::reduced_dna_alphabet);
351 BOOST_CHECK_EQUAL(dna_seq.rev_comp(), "NAGCT");
352 BOOST_CHECK_EQUAL(dna_seq, dna_seq.rev_comp().rev_comp());
355 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_rna )
357 std::string rna_str("AGCUN");
358 Sequence rna_seq(rna_str, Sequence::reduced_rna_alphabet);
359 BOOST_CHECK_EQUAL(rna_seq.rev_comp(), "NAGCU");
360 BOOST_CHECK_EQUAL(rna_seq, rna_seq.rev_comp().rev_comp());
363 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_subseq )
365 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
366 Sequence seq(dna_str, Sequence::reduced_dna_alphabet);
367 Sequence subseq = seq.subseq(8,4);
368 BOOST_CHECK_EQUAL( subseq, "AAGG");
369 Sequence rev_subseq = subseq.rev_comp();
370 BOOST_CHECK_EQUAL( rev_subseq.size(), subseq.size() );
371 BOOST_CHECK_EQUAL( rev_subseq.get_sequence(), "CCTT");
374 BOOST_AUTO_TEST_CASE( sequence_reverse_iterator )
376 std::string dna_str("AAAAAAAAAAGGGGGGGGGGG");
377 std::string dna_str_reversed(dna_str.rbegin(), dna_str.rend());
378 Sequence seq(dna_str);
379 std::string seq_reversed(seq.rbegin(), seq.rend());
380 BOOST_CHECK_EQUAL(seq_reversed, dna_str_reversed);
382 std::string substr = dna_str.substr(8,4);
383 Sequence subseq = seq.subseq(8,4);
384 BOOST_CHECK_EQUAL(substr, subseq);
386 std::string substr_reversed(substr.rbegin(), substr.rend());
387 std::string subseq_reversed(subseq.rbegin(), subseq.rend());
388 BOOST_CHECK_EQUAL(substr_reversed, subseq_reversed);
391 BOOST_AUTO_TEST_CASE( sequence_empty_reverse_iterator)
393 // so what happens with reverse interators when we have no sequence?
396 Sequence seq3("AGCT");
398 // all the empty sequences should have equal iterators
399 BOOST_CHECK(seq1.rbegin() == seq1.rend());
400 BOOST_CHECK(seq1.rbegin() == seq2.rend());
402 // none of the seq1 iterators should equal any of the seq3 iterators
403 BOOST_CHECK(seq1.rbegin() != seq3.rbegin());
404 BOOST_CHECK(seq1.rbegin() != seq3.rend());
405 BOOST_CHECK(seq1.rend() != seq3.rbegin());
406 BOOST_CHECK(seq1.rend() != seq3.rend());
408 // seq3 iterators should work
409 BOOST_CHECK(seq3.rbegin() != seq3.rend());
413 BOOST_AUTO_TEST_CASE( annotation_load )
415 string annot_data = "human\n"
419 "50\t55 anothername\n"
424 "75\t90\tname2\ttype2\n"
425 "100 120 name-asdf type!@#$%\n"
429 Sequence seq(s, Sequence::reduced_dna_alphabet);
431 //istringstream annot_stream(annot_data);
432 seq.parse_annot(annot_data, 0, 0);
433 std::list<annot> annots_list = seq.annotations();
434 std::vector<annot> annots(annots_list.begin(), annots_list.end());
435 BOOST_REQUIRE_EQUAL( annots.size(), 8);
436 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
437 BOOST_CHECK_EQUAL( annots[0].end, 10 );
438 BOOST_CHECK_EQUAL( annots[0].type, "type");
439 BOOST_CHECK_EQUAL( annots[0].name, "name");
440 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
441 BOOST_CHECK_EQUAL( annots[2].name, "myod");
442 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
443 BOOST_CHECK_EQUAL( annots[4].name, "backward");
444 BOOST_CHECK_EQUAL( annots[5].name, "name2");
445 BOOST_CHECK_EQUAL( annots[5].end, 90);
446 BOOST_CHECK_EQUAL( annots[6].begin, 100);
447 BOOST_CHECK_EQUAL( annots[6].end, 120);
448 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
449 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
450 // sequence defined annotations will always be after the
451 // absolute positions
452 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
453 BOOST_CHECK_EQUAL( annots[7].begin, 100);
455 //BOOST_CHECK_EQUAL( annots
458 BOOST_AUTO_TEST_CASE( annotation_broken_load )
460 string annot_data = "human\n"
462 "blah60 50 backward\n"
469 Sequence seq(s, Sequence::reduced_dna_alphabet);
471 BOOST_CHECK_THROW(seq.parse_annot(annot_data, 0, 0), annotation_load_error);
472 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
475 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
477 // this actually is basically what's returned by UCSC
478 // (well actually with some of the sequence and copies of fasta blocks
479 // removed to make the example shorter
480 string annot_data = "\n"
482 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
483 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
484 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
485 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
493 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
495 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
496 Sequence seq(s, Sequence::reduced_dna_alphabet);
497 seq.parse_annot(annot_data);
498 std::list<annot> annots = seq.annotations();
499 BOOST_CHECK_EQUAL( annots.size(), 2);
502 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
504 string annot_data = "0 10 name type\n"
507 "50\t55 anothername\n"
512 "75\t90\tname2\ttype2\n"
513 "100 120 name-asdf type!@#$%\n"
517 Sequence seq(s, Sequence::reduced_dna_alphabet);
519 //istringstream annot_stream(annot_data);
520 seq.parse_annot(annot_data, 0, 0);
521 std::list<annot> annots_list = seq.annotations();
522 std::vector<annot> annots(annots_list.begin(), annots_list.end());
523 BOOST_REQUIRE_EQUAL( annots.size(), 8);
524 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
525 BOOST_CHECK_EQUAL( annots[0].end, 10 );
526 BOOST_CHECK_EQUAL( annots[0].type, "type");
529 // ticket:83 when you try to load a sequence from a file that doesn't
530 // have fasta headers it crashes.
531 BOOST_AUTO_TEST_CASE( sequence_past_end )
533 fs::path seq_path(fs::path(EXAMPLE_DIR, fs::native)/ "seq" );
534 seq_path /= "misformated_seq.fa";
536 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
539 BOOST_AUTO_TEST_CASE ( sequence_empty )
543 BOOST_CHECK_EQUAL( s.empty(), true );
545 BOOST_CHECK_EQUAL( s.empty(), false );
547 BOOST_CHECK_EQUAL( s.empty(), true);
549 BOOST_CHECK_EQUAL( s.empty(), true);
552 BOOST_AUTO_TEST_CASE ( sequence_size )
556 BOOST_CHECK_EQUAL( s.size(), 0);
557 std::string seq_string("AAAGGG");
559 BOOST_CHECK_EQUAL( s.size(), seq_string.size() );
561 BOOST_CHECK_EQUAL( s.size(), 0);
563 BOOST_CHECK_EQUAL( s.size(), 0);
566 BOOST_AUTO_TEST_CASE( sequence_empty_equality )
568 Sequence szero("", Sequence::reduced_dna_alphabet);
569 BOOST_CHECK_EQUAL(szero.empty(), true);
570 BOOST_CHECK_EQUAL(szero, szero);
571 BOOST_CHECK_EQUAL(szero, "");
573 Sequence sclear("AGCT", Sequence::reduced_dna_alphabet);
575 BOOST_CHECK_EQUAL(sclear.empty(), true);
576 BOOST_CHECK_EQUAL(sclear, sclear);
577 BOOST_CHECK_EQUAL(sclear, szero);
578 BOOST_CHECK_EQUAL(sclear, "");
581 BOOST_AUTO_TEST_CASE ( sequence_iterators )
583 std::string seq_string = "AAGGCCTTNNTATA";
584 Sequence s(seq_string, Sequence::reduced_dna_alphabet);
585 const Sequence cs(s);
586 std::string::size_type count = 0;
588 std::string::iterator str_itor;
589 Sequence::const_iterator s_itor;
590 Sequence::const_iterator cs_itor;
592 for( str_itor = seq_string.begin(),
594 cs_itor = cs.begin();
595 str_itor != seq_string.end() and
596 s_itor != s.end() and
598 ++str_itor, ++s_itor, ++cs_itor, ++count)
600 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
601 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
602 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
604 BOOST_CHECK_EQUAL( seq_string.size(), count );
605 BOOST_CHECK_EQUAL( s.size(), count );
606 BOOST_CHECK_EQUAL( cs.size(), count );
609 BOOST_AUTO_TEST_CASE( sequence_motifs )
612 string bogus("AATTGGAA");
613 Sequence s1("AAAAGGGGCCCCTTTT", Sequence::reduced_dna_alphabet);
615 list<motif>::const_iterator motif_i = s1.motifs().begin();
616 list<motif>::const_iterator motif_end = s1.motifs().end();
618 // do our iterators work?
619 BOOST_CHECK( motif_i == s1.motifs().begin() );
620 BOOST_CHECK( motif_end == s1.motifs().end() );
621 BOOST_CHECK( motif_i == motif_end );
623 // this shouldn't show up
625 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
626 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
629 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
630 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
632 for(motif_i = s1.motifs().begin();
633 motif_i != s1.motifs().end();
636 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
637 BOOST_CHECK_EQUAL( motif_i->name, m);
638 BOOST_CHECK_EQUAL( motif_i->sequence, m);
642 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
644 /* FIXME: enable this when i find a way of passing storing the motif name
645 // does our annotation travel?
646 Sequence motif_seq(m);
647 motif_seq.set_fasta_header("hi");
648 s1.add_motif(motif_seq);
650 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
651 for(motif_i = s1.motifs().begin();
652 motif_i != s1.motifs().end();
655 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
656 BOOST_CHECK_EQUAL( motif_i->name, "hi");
657 BOOST_CHECK_EQUAL( motif_i->sequence, m);
662 BOOST_AUTO_TEST_CASE( sequence_motif_subseq)
664 // when searching for a motif on a subsequence we should
665 // only search the subsequence ticket:199
668 Sequence s1("AAAANCCCC", Sequence::reduced_dna_alphabet);
670 // this shouldn't show up
672 BOOST_CHECK_EQUAL( s1.motifs().size(), 1 );
675 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
677 Sequence subseq1 = s1.subseq(4,5);
678 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 2);
679 subseq1.clear_motifs();
680 BOOST_CHECK_EQUAL(subseq1.motifs().size(), 0);
681 // this is outside of our subsequence, and so shouldn't be found
682 subseq1.add_motif(aaaa);
683 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 0 );
685 subseq1.add_motif(cccc);
686 BOOST_CHECK_EQUAL( subseq1.motifs().size(), 1);
687 std::list<motif>::const_iterator motif_i = subseq1.motifs().begin();
688 BOOST_REQUIRE(motif_i != subseq1.motifs().end());
689 BOOST_CHECK_EQUAL(motif_i->begin, 1);
690 BOOST_CHECK_EQUAL(motif_i->end, 5);
693 BOOST_AUTO_TEST_CASE( annot_test )
695 annot a(0, 10, "test", "thing");
697 BOOST_CHECK_EQUAL( a.begin, 0 );
698 BOOST_CHECK_EQUAL( a.end, 10 );
699 BOOST_CHECK_EQUAL( a.type, "test" );
700 BOOST_CHECK_EQUAL( a.name, "thing" );
702 motif m(10, "AAGGCC");
703 BOOST_CHECK_EQUAL( m.begin, 10 );
704 BOOST_CHECK_EQUAL( m.type, "motif" );
705 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
706 BOOST_CHECK_EQUAL( m.end, 10+6 );
709 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
711 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
712 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
713 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
714 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
715 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
716 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
717 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
718 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
720 string gga("GGACACCTC");
721 Sequence seq(s, Sequence::reduced_dna_alphabet);
723 std::list<Sequence> query_list;
724 std::list<string> string_list;
725 query_list.push_back(Sequence(gc));
726 string_list.push_back(gc);
727 query_list.push_back(Sequence(gga));
728 string_list.push_back(gga);
730 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
731 seq.find_sequences(query_list.begin(), query_list.end());
734 for(list<string>::iterator string_i = string_list.begin();
735 string_i != string_list.end();
738 string::size_type pos=0;
739 while(pos != string::npos) {
740 pos = s.find(*string_i, pos);
741 if (pos != string::npos) {
747 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
748 const std::list<annot> &a = seq.annotations();
749 for (std::list<annot>::const_iterator annot_i = a.begin();
753 int count = annot_i->end - annot_i->begin ;
757 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
759 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
760 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
761 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
762 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
763 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
764 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
765 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
766 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
767 Sequence seq(s, Sequence::reduced_dna_alphabet);
770 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
771 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
772 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
773 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
774 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
776 Sequence subseq = seq.subseq(5, 10);
777 const list<annot> annots = subseq.annotations();
778 // generate some ground truth
780 correct.push_back(annot(0, 5, "0-10", "0-10"));
781 correct.push_back(annot(5,10, "10-20", "10-20"));
782 correct.push_back(annot(0,10, "0-20", "0-20"));
783 correct.push_back(annot(3, 7, "8-12", "8-12"));
784 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
786 list<annot>::iterator correct_i = correct.begin();
787 list<annot>::const_iterator annot_i = annots.begin();
788 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
790 BOOST_CHECK( *annot_i == *correct_i );
794 BOOST_AUTO_TEST_CASE( motif_annotation_update )
796 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
797 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
798 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
799 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
800 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
801 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
802 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
803 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
804 Sequence seq(s, Sequence::reduced_dna_alphabet);
806 // starting conditions
807 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
808 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
809 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
810 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
811 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
812 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
813 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
814 seq.add_motif("CCGTCCC");
815 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
816 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
818 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
819 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
822 BOOST_AUTO_TEST_CASE( out_operator )
824 string s("AAGGCCTT");
825 Sequence seq(s, Sequence::reduced_dna_alphabet);
829 BOOST_CHECK_EQUAL( s, buf.str() );
832 BOOST_AUTO_TEST_CASE( get_name )
834 Sequence seq("AAGGCCTT", Sequence::reduced_dna_alphabet);
836 BOOST_CHECK_EQUAL( seq.get_name(), "" );
837 seq.set_species("hooman"); // anyone remember tradewars?
838 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
839 seq.set_fasta_header("fasta human");
840 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
843 BOOST_AUTO_TEST_CASE( serialize_simple )
845 std::string seq_string = "AAGGCCTT";
846 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
847 seq.set_species("ribbet");
848 std::ostringstream oss;
849 // allocate/deallocate serialization components
851 boost::archive::text_oarchive oarchive(oss);
852 const Sequence& const_seq(seq);
853 BOOST_CHECK_EQUAL(seq, const_seq);
854 oarchive << const_seq;
858 std::istringstream iss(oss.str());
859 boost::archive::text_iarchive iarchive(iss);
860 iarchive >> seq_loaded;
862 BOOST_CHECK_EQUAL(seq_loaded, seq);
863 BOOST_CHECK_EQUAL(seq.get_species(), "ribbet");
866 BOOST_AUTO_TEST_CASE( serialize_tree )
868 std::string seq_string = "AAGGCCTT";
869 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
870 seq.set_species("ribbet");
873 annot a1(6,7,"t","t");
874 seq.add_annotation(a1);
876 std::ostringstream oss;
877 // allocate/deallocate serialization components
879 boost::archive::text_oarchive oarchive(oss);
880 const Sequence& const_seq(seq);
881 BOOST_CHECK_EQUAL(seq, const_seq);
882 oarchive << const_seq;
887 std::istringstream iss(oss.str());
888 boost::archive::text_iarchive iarchive(iss);
889 iarchive >> seq_loaded;
891 BOOST_CHECK_EQUAL(seq_loaded, seq);
894 // this writes out an "old" style annotated sequence
895 // with annotations attached as "motifs" and "annots"
896 BOOST_AUTO_TEST_CASE( serialize_xml_sequence )
898 std::string seq_string = "AAGGCCTT";
899 Sequence seq(seq_string, Sequence::reduced_dna_alphabet);
900 seq.set_species("ribbet");
903 annot a1(6,7,"t","t");
904 seq.add_annotation(a1);
906 std::ostringstream oss;
907 // allocate/deallocate serialization components
909 boost::archive::xml_oarchive oarchive(oss);
910 const Sequence& const_seq(seq);
911 BOOST_CHECK_EQUAL(seq, const_seq);
912 oarchive << boost::serialization::make_nvp("root", const_seq);
916 std::istringstream iss(oss.str());
917 boost::archive::xml_iarchive iarchive(iss);
918 iarchive >> boost::serialization::make_nvp("root", seq_loaded);
920 BOOST_CHECK_EQUAL(seq_loaded, seq);
923 BOOST_AUTO_TEST_CASE( serialize_xml_two )
925 std::string seq_string = "AAGGCCTT";
926 Sequence seq1(seq_string, Sequence::reduced_dna_alphabet);
929 std::ostringstream oss;
930 // allocate/deallocate serialization components
932 boost::archive::xml_oarchive oarchive(oss);
933 const Sequence& const_seq1(seq1);
934 const Sequence& const_seq2(seq2);
935 oarchive << boost::serialization::make_nvp("seq1", const_seq1);
936 oarchive << boost::serialization::make_nvp("seq2", const_seq2);
938 //std::cout << "xml: " << oss.str() << std::endl;
939 Sequence seq1_loaded;
940 Sequence seq2_loaded;
942 std::istringstream iss(oss.str());
943 boost::archive::xml_iarchive iarchive(iss);
944 iarchive >> boost::serialization::make_nvp("seq1", seq1_loaded);
945 iarchive >> boost::serialization::make_nvp("seq2", seq2_loaded);
947 BOOST_CHECK_EQUAL(seq1_loaded, seq1);
948 BOOST_CHECK_EQUAL(seq2_loaded, seq2);
949 // test if our pointers are the same
950 BOOST_CHECK_EQUAL(seq1_loaded.c_str(), seq2_loaded.c_str());