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;
10 #include <boost/archive/text_oarchive.hpp>
11 #include <boost/archive/text_iarchive.hpp>
13 #include "alg/sequence.hpp"
14 #include "mussa_exceptions.hpp"
18 //! when we try to load a missing file, do we get an error?
19 BOOST_AUTO_TEST_CASE( sequence_load_exception )
22 // there should be errors when we try to load something that doesn't exist
23 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
24 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
27 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
29 string header(">Header");
30 string line1("AAAAGGGGCCCCTTTTT");
31 string line2("AAAAGGGGCCCCTTTTT");
32 int seq_len = line1.size() + line2.size();
35 cr << header << "\015" << line1 << "\015" << line2 << "\015";
37 seq_cr.load_fasta(cr);
40 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
42 seq_crlf.load_fasta(crlf);
45 lf << header << "\012" << line1 << "\012" << line2 << "\012";
47 seq_lf.load_fasta(lf);
49 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
50 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
51 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
55 //! Do simple operations work correctly?
56 BOOST_AUTO_TEST_CASE( sequence_filter )
58 const char *core_seq = "AATTGGCC";
59 Sequence s1(core_seq);
60 BOOST_CHECK_EQUAL(s1, core_seq);
62 Sequence s2("aattggcc");
63 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
64 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
65 BOOST_CHECK_EQUAL(s2.size(), s2.size());
66 BOOST_CHECK_EQUAL(s2.c_str(), core_seq);
69 BOOST_CHECK_EQUAL(s3, "ANNNG");
70 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
72 s3.set_filtered_sequence("AAGGCCTT", 0, 2);
73 BOOST_CHECK_EQUAL(s3, "AA");
74 s3.set_filtered_sequence("AAGGCCTT", 2, 2);
75 BOOST_CHECK_EQUAL( s3, "GG");
76 s3.set_filtered_sequence("AAGGCCTT", 4);
77 BOOST_CHECK_EQUAL( s3, "CCTT");
80 BOOST_CHECK_EQUAL(s3, "");
83 BOOST_CHECK_EQUAL(s3, "AAGGNN");
86 BOOST_AUTO_TEST_CASE( subseq_names )
88 Sequence s1("AAGGCCTT");
89 s1.set_species("species");
90 s1.set_fasta_header("a fasta header");
91 Sequence s2 = s1.subseq(2,2);
92 BOOST_CHECK_EQUAL(s2, "GG");
93 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
94 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
97 //! Can we load data from a file
98 BOOST_AUTO_TEST_CASE( sequence_load )
100 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
101 seq_path /= "human_mck_pro.fa";
103 s.load_fasta(seq_path);
104 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
105 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
106 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
107 "muscle creatine kinase gene (CKMM), "
111 BOOST_AUTO_TEST_CASE( annotation_load )
113 string annot_data = "human\n"
117 "50\t55 anothername\n"
122 "75\t90\tname2\ttype2\n"
123 "100 120 name-asdf type!@#$%\n"
129 //istringstream annot_stream(annot_data);
130 seq.parse_annot(annot_data, 0, 0);
131 std::list<annot> annots_list = seq.annotations();
132 std::vector<annot> annots(annots_list.begin(), annots_list.end());
133 BOOST_REQUIRE_EQUAL( annots.size(), 8);
134 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
135 BOOST_CHECK_EQUAL( annots[0].end, 10 );
136 BOOST_CHECK_EQUAL( annots[0].type, "type");
137 BOOST_CHECK_EQUAL( annots[0].name, "name");
138 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
139 BOOST_CHECK_EQUAL( annots[2].name, "myod");
140 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
141 BOOST_CHECK_EQUAL( annots[4].name, "backward");
142 BOOST_CHECK_EQUAL( annots[5].name, "name2");
143 BOOST_CHECK_EQUAL( annots[5].end, 90);
144 BOOST_CHECK_EQUAL( annots[6].begin, 100);
145 BOOST_CHECK_EQUAL( annots[6].end, 120);
146 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
147 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
148 // sequence defined annotations will always be after the
149 // absolute positions
150 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
151 BOOST_CHECK_EQUAL( annots[7].begin, 100);
153 //BOOST_CHECK_EQUAL( annots
157 BOOST_AUTO_TEST_CASE(annotation_ucsc_html_load)
159 // this actually is basically what's returned by UCSC
160 // (well actually with some of the sequence and copies of fasta blocks
161 // removed to make the example shorter
162 string annot_data = "\n"
164 ">hg17_knownGene_NM_001824_0 range=chr19:50517919-50517974 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
165 "GGGTCAGTGTCACCTCCAGGATACAGACAG\n"
166 ">hg17_knownGene_NM_001824_3 range=chr19:50510563-50510695 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none\n"
167 "GGTGGAGACGACCTGGACCCTAACTACGT\n"
175 "TGGGTCAGTGTCACCTCCAGGATACAGACAGCCCCCCTTCAGCCCAGCCCAGCCAG"
177 "GGTGGAGACGACCTGGACCCTAACTACGTGCTCAGCAGCCGCGTCCGCAC";
179 seq.parse_annot(annot_data);
180 std::list<annot> annots = seq.annotations();
181 BOOST_CHECK_EQUAL( annots.size(), 2);
184 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
186 string annot_data = "0 10 name type\n"
189 "50\t55 anothername\n"
194 "75\t90\tname2\ttype2\n"
195 "100 120 name-asdf type!@#$%\n"
201 //istringstream annot_stream(annot_data);
202 seq.parse_annot(annot_data, 0, 0);
203 std::list<annot> annots_list = seq.annotations();
204 std::vector<annot> annots(annots_list.begin(), annots_list.end());
205 BOOST_REQUIRE_EQUAL( annots.size(), 8);
206 BOOST_CHECK_EQUAL( annots[0].begin, 0 );
207 BOOST_CHECK_EQUAL( annots[0].end, 10 );
208 BOOST_CHECK_EQUAL( annots[0].type, "type");
211 // ticket:83 when you try to load a sequence from a file that doesn't
212 // have fasta headers it crashes.
213 BOOST_AUTO_TEST_CASE( sequence_past_end )
215 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
216 seq_path /= "misformated_seq.fa";
218 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
221 BOOST_AUTO_TEST_CASE ( sequence_empty )
224 BOOST_CHECK_EQUAL( s.empty(), true );
226 BOOST_CHECK_EQUAL( s.empty(), false );
229 BOOST_AUTO_TEST_CASE ( sequence_iterators )
231 std::string seq_string = "AAGGCCTTNNTATA";
232 Sequence s(seq_string);
233 const Sequence cs(s);
234 std::string::size_type count = 0;
236 std::string::iterator str_itor;
237 Sequence::iterator s_itor;
238 Sequence::const_iterator cs_itor;
240 for( str_itor = seq_string.begin(),
242 cs_itor = cs.begin();
243 str_itor != seq_string.end() and
244 s_itor != s.end() and
246 ++str_itor, ++s_itor, ++cs_itor, ++count)
248 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
249 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
250 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
252 BOOST_CHECK_EQUAL( seq_string.size(), count );
253 BOOST_CHECK_EQUAL( s.size(), count );
254 BOOST_CHECK_EQUAL( cs.size(), count );
257 BOOST_AUTO_TEST_CASE( sequence_motifs )
260 string bogus("AATTGGAA");
261 Sequence s1("AAAAGGGGCCCCTTTT");
263 list<motif>::const_iterator motif_i = s1.motifs().begin();
264 list<motif>::const_iterator motif_end = s1.motifs().end();
266 // do our iterators work?
267 BOOST_CHECK( motif_i == s1.motifs().begin() );
268 BOOST_CHECK( motif_end == s1.motifs().end() );
269 BOOST_CHECK( motif_i == motif_end );
271 // this shouldn't show up
273 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
274 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
277 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
278 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
280 for(motif_i = s1.motifs().begin();
281 motif_i != s1.motifs().end();
284 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
285 BOOST_CHECK_EQUAL( motif_i->name, m);
286 BOOST_CHECK_EQUAL( motif_i->sequence, m);
290 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
292 /* FIXME: enable this when i find a way of passing storing the motif name
293 // does our annotation travel?
294 Sequence motif_seq(m);
295 motif_seq.set_fasta_header("hi");
296 s1.add_motif(motif_seq);
298 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
299 for(motif_i = s1.motifs().begin();
300 motif_i != s1.motifs().end();
303 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
304 BOOST_CHECK_EQUAL( motif_i->name, "hi");
305 BOOST_CHECK_EQUAL( motif_i->sequence, m);
310 BOOST_AUTO_TEST_CASE( annot_test )
312 annot a(0, 10, "test", "thing");
314 BOOST_CHECK_EQUAL( a.begin, 0 );
315 BOOST_CHECK_EQUAL( a.end, 10 );
316 BOOST_CHECK_EQUAL( a.type, "test" );
317 BOOST_CHECK_EQUAL( a.name, "thing" );
319 motif m(10, "AAGGCC");
320 BOOST_CHECK_EQUAL( m.begin, 10 );
321 BOOST_CHECK_EQUAL( m.type, "motif" );
322 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
323 BOOST_CHECK_EQUAL( m.end, 10+6 );
326 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
328 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
329 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
330 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
331 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
332 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
333 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
334 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
335 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
337 string gga("GGACACCTC");
340 std::list<Sequence> query_list;
341 std::list<string> string_list;
342 query_list.push_back(Sequence(gc));
343 string_list.push_back(gc);
344 query_list.push_back(Sequence(gga));
345 string_list.push_back(gga);
347 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
348 seq.find_sequences(query_list.begin(), query_list.end());
351 for(list<string>::iterator string_i = string_list.begin();
352 string_i != string_list.end();
355 string::size_type pos=0;
356 while(pos != string::npos) {
357 pos = s.find(*string_i, pos);
358 if (pos != string::npos) {
364 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
367 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
369 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
370 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
371 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
372 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
373 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
374 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
375 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
376 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
380 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
381 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
382 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
383 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
384 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
386 Sequence subseq = seq.subseq(5, 10);
387 const list<annot> annots = subseq.annotations();
388 // generate some ground truth
390 correct.push_back(annot(0, 5, "0-10", "0-10"));
391 correct.push_back(annot(5,10, "10-20", "10-20"));
392 correct.push_back(annot(0,10, "0-20", "0-20"));
393 correct.push_back(annot(3, 7, "8-12", "8-12"));
394 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
396 list<annot>::iterator correct_i = correct.begin();
397 list<annot>::const_iterator annot_i = annots.begin();
398 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
400 BOOST_CHECK( *annot_i == *correct_i );
404 BOOST_AUTO_TEST_CASE( motif_annotation_update )
406 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
407 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
408 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
409 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
410 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
411 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
412 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
413 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
416 // starting conditions
417 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
418 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
419 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
420 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
421 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
422 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
423 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
424 seq.add_motif("CCGTCCC");
425 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
426 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
428 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
429 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
432 BOOST_AUTO_TEST_CASE( out_operator )
434 string s("AAGGCCTT");
439 BOOST_CHECK_EQUAL( s, buf.str() );
442 BOOST_AUTO_TEST_CASE( get_name )
444 Sequence seq("AAGGCCTT");
446 BOOST_CHECK_EQUAL( seq.get_name(), "" );
447 seq.set_species("hooman"); // anyone remember tradewars?
448 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
449 seq.set_fasta_header("fasta human");
450 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");
453 BOOST_AUTO_TEST_CASE( serialize_simple )
455 std::string seq_string = "AAGGCCTT";
456 Sequence seq(seq_string);
458 std::ostringstream oss;
459 // allocate/deallocate serialization components
461 boost::archive::text_oarchive oarchive(oss);
462 const Sequence& const_seq(seq);
463 BOOST_CHECK_EQUAL(seq, const_seq);
464 oarchive << const_seq;
469 std::istringstream iss(oss.str());
470 boost::archive::text_iarchive iarchive(iss);
471 iarchive >> seq_loaded;