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;
5 #include <boost/assign/list_of.hpp>
6 #include <boost/assign/list_inserter.hpp>
7 #include <boost/assign.hpp>
8 namespace assign = boost::assign;
14 #include "alg/mussa.hpp"
15 #include "mussa_exceptions.hpp"
19 //! can we initialize a mussa object?
20 BOOST_AUTO_TEST_CASE( mussa_simple )
23 BOOST_CHECK_EQUAL(m.empty(), true);
24 BOOST_CHECK_EQUAL(m.get_name(), "" );
25 BOOST_CHECK_EQUAL(m.get_window(), 0);
26 BOOST_CHECK_EQUAL(m.get_threshold(), 0);
27 BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
28 m.set_name( "hello" );
29 BOOST_CHECK_EQUAL(m.get_name(), "hello" );
31 BOOST_CHECK_EQUAL(m.get_window(), 30);
33 BOOST_CHECK_EQUAL(m.get_threshold(), 21);
34 BOOST_CHECK_EQUAL(m.get_soft_threshold(), 21);
35 m.set_soft_threshold(19);
36 BOOST_CHECK_EQUAL(m.get_soft_threshold(), 21);
37 m.set_soft_threshold(35);
38 BOOST_CHECK_EQUAL(m.get_soft_threshold(), 30);
39 m.set_soft_threshold(25);
40 BOOST_CHECK_EQUAL(m.get_soft_threshold(), 25);
41 m.set_analysis_mode(Mussa::RadialNway);
42 BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::RadialNway);
43 // make sure our path is empty
44 BOOST_CHECK_EQUAL(m.get_analysis_path().string(), fs::path().string() );
47 BOOST_CHECK_EQUAL(m.get_name(), "" );
48 BOOST_CHECK_EQUAL(m.get_window(), 0);
49 BOOST_CHECK_EQUAL(m.get_threshold(), 0);
50 BOOST_CHECK_EQUAL(m.get_analysis_mode(), Mussa::TransitiveNway);
53 BOOST_AUTO_TEST_CASE ( mussa_title )
57 BOOST_CHECK_EQUAL( m.get_title(), "Unnamed");
60 BOOST_CHECK_EQUAL( m.get_title(), foo);
61 string foopath_name("/my/silly/path");
62 fs::path foopath(foopath_name);
63 m.set_analysis_path(foopath);
64 BOOST_CHECK_EQUAL( m.get_title().size(), 14);
67 BOOST_AUTO_TEST_CASE( mussa_analysis_name )
70 m.set_analysis_mode( Mussa::TransitiveNway );
71 BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Transitive" );
72 m.set_analysis_mode( Mussa::RadialNway );
73 BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Radial" );
74 m.set_analysis_mode( Mussa::EntropyNway );
75 BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "Entropy" );
76 m.set_analysis_mode( Mussa::RecursiveNway);
77 BOOST_CHECK_EQUAL( m.get_analysis_mode_name(), "[deprecated] Recursive" );
80 BOOST_AUTO_TEST_CASE( mussa_sequences )
82 std::string s0("AAAANNNN");
83 std::string s1("GGGGNNNN");
84 std::string s2("TTTTNNNN");
87 BOOST_CHECK_EQUAL(analysis.empty(), true);
88 analysis.append_sequence(s0);
89 analysis.append_sequence(s1);
90 analysis.append_sequence(s2);
92 BOOST_CHECK_EQUAL( analysis.empty(), false);
93 BOOST_CHECK_EQUAL( analysis.sequences().size(), 3 );
94 BOOST_CHECK_EQUAL( *(analysis.sequences()[0]), s0);
95 BOOST_CHECK_EQUAL( *(analysis.sequences()[1]), s1);
96 BOOST_CHECK_EQUAL( *(analysis.sequences()[2]), s2);
99 // for some reason we can call nway once safely but it
100 // somehow changed things and caused a segfault
101 // fixed by adding a return statement in trans_path_search
102 BOOST_AUTO_TEST_CASE ( empty_mussa_set_threshold )
105 m.set_soft_threshold(15);
108 m.set_soft_threshold(25);
112 BOOST_AUTO_TEST_CASE( mussa_load_mupa )
114 fs::path mupa_path(EXAMPLE_DIR, fs::native);
115 fs::path result_path = fs::initial_path() / "mck3test_w30_t20";
116 mupa_path /= "mck3test.mupa";
119 m1.load_mupa_file( mupa_path );
121 m1.save( result_path );
122 BOOST_CHECK_EQUAL( m1.empty(), false);
123 BOOST_CHECK_EQUAL( m1.get_name(), std::string("mck3test") );
124 BOOST_CHECK( m1.size() > 0 );
125 BOOST_CHECK_EQUAL( m1.get_analysis_path().string(), result_path.string());
128 m2.load( result_path );
129 BOOST_CHECK_EQUAL( m2.empty(), false);
130 BOOST_CHECK_EQUAL( m2.get_name(), result_path.leaf() );
131 BOOST_CHECK_EQUAL( m1.size(), m2.size() );
132 BOOST_CHECK_EQUAL( result_path.string(), m2.get_analysis_path().string() );
136 BOOST_CHECK_EQUAL( m2.empty(), true);
137 BOOST_CHECK_EQUAL( m2.is_dirty(), false );
138 BOOST_CHECK_EQUAL( m2.get_analysis_path().string(), fs::path().string());
141 BOOST_AUTO_TEST_CASE( mussa_load_full_path )
144 fs::path full_path(fs::path(EXAMPLE_DIR, fs::native) / "mck3test.mupa");
145 m1.load_mupa_file( full_path );
148 BOOST_CHECK( m1.size() > 0);
149 BOOST_CHECK_EQUAL( m1.get_window(), 30 );
150 BOOST_CHECK_EQUAL( m1.get_threshold(), 20);
151 BOOST_CHECK_EQUAL( m1.is_dirty(), true);
152 BOOST_CHECK_EQUAL( m1.get_analysis_path().string(), "");
155 // make sure we know that mupa files cannot be directories
156 BOOST_AUTO_TEST_CASE( mussa_mupa_is_file_not_directory )
158 fs::path curdir(".");
160 BOOST_CHECK_THROW(m1.load_mupa_file( curdir ), mussa_load_error );
163 BOOST_AUTO_TEST_CASE( mussa_load_analysis )
165 fs::path example_dir(EXAMPLE_DIR, fs::native);
167 m1.load_mupa_file( example_dir / "mck3test.mupa" );
171 fs::path analysis_path = fs::initial_path() / "mck3test_w30_t20";
172 m2.load( analysis_path );
174 BOOST_CHECK_EQUAL( m1.size(), m2.size() );
175 BOOST_CHECK_EQUAL( m1.get_window(), m2.get_window() );
176 BOOST_CHECK_EQUAL( m1.get_threshold(), m2.get_threshold() );
177 BOOST_CHECK_EQUAL( m2.get_analysis_path().string(), analysis_path.string());
180 BOOST_AUTO_TEST_CASE( mussa_load_motif )
182 string data = "AAGG 1.0 1.0 0.0\n"
183 "GGTT 0.0 0.1 1.0\n";
185 istringstream test_istream(data);
188 m1.append_sequence("AAAAGGGGTTTT");
189 m1.append_sequence("GGGCCCCTTCCAATT");
190 m1.load_motifs(test_istream);
192 BOOST_CHECK_EQUAL( m1.motifs().size(), 2);
193 for (Mussa::vector_sequence_type::const_iterator seq_i = m1.sequences().begin();
194 seq_i != m1.sequences().end();
197 BOOST_CHECK( (*seq_i)->motifs().size() > 0 );
201 BOOST_AUTO_TEST_CASE( mussa_load_broken_motif )
203 string data = "AAGG 1.0 1.0 0.0\n"
204 "GGTT 0.0 0.1 1.0 1.0\n"
205 "ZZCTA 0.1 0.0 1.0\n";
207 istringstream test_istream(data);
210 m1.append_sequence("AAAAGGGGTTTT");
211 m1.append_sequence("GGGCCCCTTCCAATT");
212 BOOST_CHECK_THROW(m1.load_motifs(test_istream), motif_load_error);
214 BOOST_CHECK_EQUAL( m1.motifs().size(), 0);
217 BOOST_AUTO_TEST_CASE( mussa_named_motif )
219 string data = "CCAATT cat 0.1 0.2 0.3\n";
220 istringstream test_istream(data);
223 m1.append_sequence("AAAAGGGGTTTT");
224 m1.append_sequence("GGGCCCCTTCCAATT");
225 m1.load_motifs(test_istream);
227 std::set<Sequence> motifs = m1.motifs();
228 BOOST_REQUIRE_EQUAL(motifs.size(), 1);
229 BOOST_CHECK_EQUAL(motifs.begin()->get_name(), "cat");
232 BOOST_AUTO_TEST_CASE( mussa_weirdly_spaced_named_motif )
234 string data = "CCAATT cat_meow123 0.1 0.2 0.3\n";
235 istringstream test_istream(data);
238 m1.append_sequence("AAAAGGGGTTTT");
239 m1.append_sequence("GGGCCCCTTCCAATT");
240 m1.load_motifs(test_istream);
242 std::set<Sequence> motifs = m1.motifs();
243 BOOST_REQUIRE_EQUAL(motifs.size(), 1);
244 BOOST_CHECK_EQUAL(motifs.begin()->get_name(), "cat_meow123");
246 BOOST_AUTO_TEST_CASE( mussa_add_motif )
248 vector<Sequence> motifs;
249 motifs.push_back("AAGG");
250 vector<Color> colors;
251 colors.push_back(Color(1.0, 0.0, 0.0));
254 m1.append_sequence("AAAAGGGGTTTT");
255 m1.append_sequence("GGGCCCCTTGGTT");
256 m1.set_motifs(motifs, colors);
257 int first_size = m1.motifs().size();
258 BOOST_CHECK_EQUAL( first_size, 1 );
259 BOOST_REQUIRE(first_size > 0);
260 BOOST_CHECK_EQUAL(*(m1.motifs().begin()), motifs.front());
261 // make sure that our sequences have the right number of motifs
262 BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 1);
263 BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1); // because of rc
265 // verify that setting the motif clears the arrays
266 m1.set_motifs(motifs, colors);
267 BOOST_CHECK_EQUAL( first_size, m1.motifs().size() );
268 // make sure that our sequences have the right number of motifs
269 BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 1);
270 BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
272 // add a different motif
274 motifs.push_back("CCTTGG");
275 BOOST_CHECK_EQUAL(motifs.size(), 1);
276 m1.set_motifs(motifs, colors);
277 BOOST_CHECK_EQUAL(m1.motifs().size(), 1);
278 BOOST_REQUIRE(m1.motifs().size() > 0);
279 BOOST_CHECK_EQUAL(*(m1.motifs().begin()), motifs.front());
280 BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 0);
281 BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
283 // try a motif that doesn't exist
285 motifs.push_back("CCTTGG");
286 BOOST_CHECK_EQUAL(motifs.size(), 1);
287 m1.set_motifs(motifs, colors);
288 BOOST_CHECK_EQUAL(m1.motifs().size(), 1);
289 BOOST_CHECK_EQUAL(m1.sequences()[0]->motifs().size(), 0);
290 BOOST_CHECK_EQUAL(m1.sequences()[1]->motifs().size(), 1);
295 local_align_test(const Mussa::vector_sequence_type &seqs,
296 const list<ConservedPath::path_type>& result,
297 const list<vector<bool> >& reversed)
299 map<char, vector <char> > m;
300 assign::insert(m)('A', assign::list_of('A')('T') )
301 ('T', assign::list_of('T')('A') )
302 ('G', assign::list_of('G')('C') )
303 ('C', assign::list_of('C')('G') );
304 list<vector<bool> >::const_iterator rc_i = reversed.begin();
306 for(list<ConservedPath::path_type>::const_iterator base_i = result.begin();
307 base_i != result.end();
310 // since the reverse compliment flag is relative to the first sequence
311 // the first one should always be false
312 BOOST_CHECK_EQUAL( (*rc_i)[0], false );
313 const int first_path_basepair_index = (*base_i)[0];
314 const int second_path_basepair_index = (*base_i)[1];
315 const char first_basepair = (*seqs[0])[first_path_basepair_index];
316 const char second_basepair = (*seqs[1])[second_path_basepair_index];
317 // get our index into our reverse compliment map m
318 const int second_compliment_index = (*rc_i)[1];
319 // lookup the forward or reverse compliment depending on our rc flag
320 const char complimented_second = m[second_basepair][second_compliment_index];
322 BOOST_CHECK_EQUAL( first_basepair, complimented_second) ;
327 BOOST_AUTO_TEST_CASE( local_alignment )
329 string s0("GCGCATAT");
330 string s1("AAAAAAAT");
334 analysis.append_sequence(s0);
335 analysis.append_sequence(s1);
336 analysis.set_threshold(3);
337 analysis.set_window(4);
339 NwayPaths npath = analysis.paths();
340 list<ConservedPath::path_type> result;
341 list<vector<bool> > reversed;
342 list<ConservedPath>::iterator pathz_i = npath.pathz.begin();
344 list<ConservedPath> selected_paths;
345 selected_paths.push_back(*pathz_i);
346 analysis.createLocalAlignment(selected_paths.begin(),
347 selected_paths.end(),
351 local_align_test(analysis.sequences(), result, reversed);
356 selected_paths.clear();
357 selected_paths.push_back(*pathz_i);
358 analysis.createLocalAlignment(selected_paths.begin(),
359 selected_paths.end(),
362 local_align_test(analysis.sequences(), result, reversed);
367 BOOST_AUTO_TEST_CASE( subanalysis )
369 Sequence s1("AATGAAGATTTTAATGCTTTAATTTTGTTTTGTAAACTTCGAATTTCCAAAATTTGAAA");
370 Sequence s2("AGGAGCAAGTTCGCTTCATCGAGAATTTTTAATTTTTAGTCAAATTTTCCAATGTCTGA");
373 analysis.append_sequence(s1);
374 analysis.append_sequence(s2);
375 analysis.set_threshold(8);
376 analysis.set_window(8);
379 NwayPaths perfect_path = analysis.paths();
380 int perfect_match_count = perfect_path.pathz.size();
382 Sequence sub1 = s1.subseq(2, s1.size()-4);
383 Sequence sub2 = s2.subseq(2, s2.size()-4);
385 subanalysis.append_sequence(sub1);
386 subanalysis.append_sequence(sub2);
387 subanalysis.set_threshold(7);
388 subanalysis.set_window(8);
389 subanalysis.analyze();
390 NwayPaths one_mismatch_path = subanalysis.paths();
391 int one_mismatch_count = one_mismatch_path.pathz.size();
393 BOOST_CHECK( perfect_match_count < one_mismatch_count );
396 BOOST_AUTO_TEST_CASE( dirty_flag )
399 BOOST_CHECK_EQUAL(m.is_dirty(), false);
401 BOOST_CHECK_EQUAL(m.is_dirty(), true);
404 BOOST_CHECK_EQUAL(m.is_dirty(), true);
407 BOOST_CHECK_EQUAL(m.is_dirty(), true);
409 m.set_soft_threshold(1);
410 BOOST_CHECK_EQUAL(m.is_dirty(), false);
412 m.append_sequence("AAGGCCTT");
413 BOOST_CHECK_EQUAL(m.is_dirty(), true);