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 "alg/sequence.hpp"
11 #include "mussa_exceptions.hpp"
15 //! when we try to load a missing file, do we get an error?
16 BOOST_AUTO_TEST_CASE( sequence_load_exception )
19 // there should be errors when we try to load something that doesn't exist
20 BOOST_CHECK_THROW( s.load_fasta("alkejralk", 1, 0, 0), mussa_load_error);
21 BOOST_CHECK_THROW( s.load_annot("alkejralk", 0, 0), mussa_load_error);
24 BOOST_AUTO_TEST_CASE( sequence_eol_conventions )
26 string header(">Header");
27 string line1("AAAAGGGGCCCCTTTTT");
28 string line2("AAAAGGGGCCCCTTTTT");
29 int seq_len = line1.size() + line2.size();
32 cr << header << "\015" << line1 << "\015" << line2 << "\015";
34 seq_cr.load_fasta(cr);
37 crlf << header << "\015\012" << line1 << "\015\012" << line2 << "\015\012";
39 seq_crlf.load_fasta(crlf);
42 lf << header << "\012" << line1 << "\012" << line2 << "\012";
44 seq_lf.load_fasta(lf);
46 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
47 BOOST_CHECK_EQUAL(seq_crlf.size(), seq_len);
48 BOOST_CHECK_EQUAL(seq_cr.size(), seq_len);
52 //! Do simple operations work correctly?
53 BOOST_AUTO_TEST_CASE( sequence_filter )
55 const char *core_seq = "AATTGGCC";
56 Sequence s1(core_seq);
57 BOOST_CHECK_EQUAL(s1, core_seq);
59 Sequence s2("aattggcc");
60 BOOST_CHECK_EQUAL(s2, "AATTGGCC");
61 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
62 BOOST_CHECK_EQUAL(s2.size(), s2.size());
63 BOOST_CHECK_EQUAL(s2.c_str(), core_seq);
66 BOOST_CHECK_EQUAL(s3, "ANNNG");
67 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
69 s3.set_filtered_sequence("AAGGCCTT", 0, 2);
70 BOOST_CHECK_EQUAL(s3, "AA");
71 s3.set_filtered_sequence("AAGGCCTT", 2, 2);
72 BOOST_CHECK_EQUAL( s3, "GG");
73 s3.set_filtered_sequence("AAGGCCTT", 4);
74 BOOST_CHECK_EQUAL( s3, "CCTT");
77 BOOST_CHECK_EQUAL(s3, "");
80 BOOST_CHECK_EQUAL(s3, "AAGGNN");
83 BOOST_AUTO_TEST_CASE( subseq_names )
85 Sequence s1("AAGGCCTT");
86 s1.set_species("species");
87 s1.set_fasta_header("a fasta header");
88 Sequence s2 = s1.subseq(2,2);
89 BOOST_CHECK_EQUAL(s2, "GG");
90 BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
91 BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
94 //! Can we load data from a file
95 BOOST_AUTO_TEST_CASE( sequence_load )
97 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
98 seq_path /= "human_mck_pro.fa";
100 s.load_fasta(seq_path);
101 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
102 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
103 BOOST_CHECK_EQUAL(s.get_fasta_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
104 "muscle creatine kinase gene (CKMM), "
108 BOOST_AUTO_TEST_CASE( annotation_load )
110 string annot_data = "human\n"
114 "50\t55 anothername\n"
119 "75\t90\tname2\ttype2\n"
120 "100 120 name-asdf type!@#$%\n"
126 //istringstream annot_stream(annot_data);
127 seq.parse_annot(annot_data, 0, 0);
128 std::list<annot> annots_list = seq.annotations();
129 std::vector<annot> annots(annots_list.begin(), annots_list.end());
130 BOOST_REQUIRE_EQUAL( annots.size(), 8);
131 BOOST_CHECK_EQUAL( annots[0].start, 0 );
132 BOOST_CHECK_EQUAL( annots[0].end, 10 );
133 BOOST_CHECK_EQUAL( annots[0].type, "type");
134 BOOST_CHECK_EQUAL( annots[0].name, "name");
135 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
136 BOOST_CHECK_EQUAL( annots[2].name, "myod");
137 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
138 BOOST_CHECK_EQUAL( annots[4].name, "backward");
139 BOOST_CHECK_EQUAL( annots[5].name, "name2");
140 BOOST_CHECK_EQUAL( annots[5].end, 90);
141 BOOST_CHECK_EQUAL( annots[6].start, 100);
142 BOOST_CHECK_EQUAL( annots[6].end, 120);
143 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
144 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
145 // sequence defined annotations will always be after the
146 // absolute positions
147 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
148 BOOST_CHECK_EQUAL( annots[7].start, 100);
150 //BOOST_CHECK_EQUAL( annots
153 BOOST_AUTO_TEST_CASE( annotation_load_no_species_name )
155 string annot_data = "0 10 name type\n"
158 "50\t55 anothername\n"
163 "75\t90\tname2\ttype2\n"
164 "100 120 name-asdf type!@#$%\n"
170 //istringstream annot_stream(annot_data);
171 seq.parse_annot(annot_data, 0, 0);
172 std::list<annot> annots_list = seq.annotations();
173 std::vector<annot> annots(annots_list.begin(), annots_list.end());
174 BOOST_REQUIRE_EQUAL( annots.size(), 8);
175 BOOST_CHECK_EQUAL( annots[0].start, 0 );
176 BOOST_CHECK_EQUAL( annots[0].end, 10 );
177 BOOST_CHECK_EQUAL( annots[0].type, "type");
180 // ticket:83 when you try to load a sequence from a file that doesn't
181 // have fasta headers it crashes.
182 BOOST_AUTO_TEST_CASE( sequence_past_end )
184 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
185 seq_path /= "misformated_seq.fa";
187 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
190 BOOST_AUTO_TEST_CASE ( sequence_empty )
193 BOOST_CHECK_EQUAL( s.empty(), true );
195 BOOST_CHECK_EQUAL( s.empty(), false );
198 BOOST_AUTO_TEST_CASE ( sequence_iterators )
200 std::string seq_string = "AAGGCCTTNNTATA";
201 Sequence s(seq_string);
202 const Sequence cs(s);
203 std::string::size_type count = 0;
205 std::string::iterator str_itor;
206 Sequence::iterator s_itor;
207 Sequence::const_iterator cs_itor;
209 for( str_itor = seq_string.begin(),
211 cs_itor = cs.begin();
212 str_itor != seq_string.end() and
213 s_itor != s.end() and
215 ++str_itor, ++s_itor, ++cs_itor, ++count)
217 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
218 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
219 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
221 BOOST_CHECK_EQUAL( seq_string.size(), count );
222 BOOST_CHECK_EQUAL( s.size(), count );
223 BOOST_CHECK_EQUAL( cs.size(), count );
226 BOOST_AUTO_TEST_CASE( sequence_motifs )
229 string bogus("AATTGGAA");
230 Sequence s1("AAAAGGGGCCCCTTTT");
232 list<motif>::const_iterator motif_i = s1.motifs().begin();
233 list<motif>::const_iterator motif_end = s1.motifs().end();
235 // do our iterators work?
236 BOOST_CHECK( motif_i == s1.motifs().begin() );
237 BOOST_CHECK( motif_end == s1.motifs().end() );
238 BOOST_CHECK( motif_i == motif_end );
240 // this shouldn't show up
242 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
243 BOOST_CHECK_EQUAL( s1.motifs().size(), 0 );
246 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
247 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
249 for(motif_i = s1.motifs().begin();
250 motif_i != s1.motifs().end();
253 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
254 BOOST_CHECK_EQUAL( motif_i->name, m);
255 BOOST_CHECK_EQUAL( motif_i->sequence, m);
259 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
261 /* FIXME: enable this when i find a way of passing storing the motif name
262 // does our annotation travel?
263 Sequence motif_seq(m);
264 motif_seq.set_fasta_header("hi");
265 s1.add_motif(motif_seq);
267 BOOST_CHECK_EQUAL(s1.motifs().size(), 2);
268 for(motif_i = s1.motifs().begin();
269 motif_i != s1.motifs().end();
272 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
273 BOOST_CHECK_EQUAL( motif_i->name, "hi");
274 BOOST_CHECK_EQUAL( motif_i->sequence, m);
279 BOOST_AUTO_TEST_CASE( annot_test )
281 annot a(0, 10, "test", "thing");
283 BOOST_CHECK_EQUAL( a.start, 0 );
284 BOOST_CHECK_EQUAL( a.end, 10 );
285 BOOST_CHECK_EQUAL( a.type, "test" );
286 BOOST_CHECK_EQUAL( a.name, "thing" );
288 motif m(10, "AAGGCC");
289 BOOST_CHECK_EQUAL( m.start, 10 );
290 BOOST_CHECK_EQUAL( m.type, "motif" );
291 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
292 BOOST_CHECK_EQUAL( m.end, 10+6 );
295 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
297 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
298 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
299 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
300 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
301 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
302 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
303 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
304 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
306 string gga("GGACACCTC");
309 std::list<Sequence> query_list;
310 std::list<string> string_list;
311 query_list.push_back(Sequence(gc));
312 string_list.push_back(gc);
313 query_list.push_back(Sequence(gga));
314 string_list.push_back(gga);
316 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
317 seq.find_sequences(query_list.begin(), query_list.end());
320 for(list<string>::iterator string_i = string_list.begin();
321 string_i != string_list.end();
324 string::size_type pos=0;
325 while(pos != string::npos) {
326 pos = s.find(*string_i, pos);
327 if (pos != string::npos) {
333 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
336 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
338 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
339 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
340 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
341 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
342 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
343 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
344 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
345 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
349 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
350 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
351 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
352 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
353 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
355 Sequence subseq = seq.subseq(5, 10);
356 const list<annot> annots = subseq.annotations();
357 // generate some ground truth
359 correct.push_back(annot(0, 5, "0-10", "0-10"));
360 correct.push_back(annot(5,10, "10-20", "10-20"));
361 correct.push_back(annot(0,10, "0-20", "0-20"));
362 correct.push_back(annot(3, 7, "8-12", "8-12"));
363 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
365 list<annot>::iterator correct_i = correct.begin();
366 list<annot>::const_iterator annot_i = annots.begin();
367 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
369 BOOST_CHECK( *annot_i == *correct_i );
373 BOOST_AUTO_TEST_CASE( motif_annotation_update )
375 string s("CCGTCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
376 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
377 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
378 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
379 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
380 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
381 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
382 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
385 // starting conditions
386 BOOST_CHECK_EQUAL(seq.annotations().size(), 0);
387 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
388 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
389 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
390 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
391 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
392 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
393 seq.add_motif("CCGTCCC");
394 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
395 BOOST_CHECK_EQUAL(seq.motifs().size(), 1);
397 BOOST_CHECK_EQUAL(seq.annotations().size(), 3);
398 BOOST_CHECK_EQUAL(seq.motifs().size(), 0);
401 BOOST_AUTO_TEST_CASE( out_operator )
403 string s("AAGGCCTT");
408 BOOST_CHECK_EQUAL( s, buf.str() );
411 BOOST_AUTO_TEST_CASE( get_name )
413 Sequence seq("AAGGCCTT");
415 BOOST_CHECK_EQUAL( seq.get_name(), "" );
416 seq.set_species("hooman"); // anyone remember tradewars?
417 BOOST_CHECK_EQUAL( seq.get_name(), "hooman");
418 seq.set_fasta_header("fasta human");
419 BOOST_CHECK_EQUAL( seq.get_name(), "fasta human");