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 //! Can we load data from a file
84 BOOST_AUTO_TEST_CASE( sequence_load )
86 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
87 seq_path /= "human_mck_pro.fa";
89 s.load_fasta(seq_path);
90 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
91 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
92 BOOST_CHECK_EQUAL(s.get_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
93 "muscle creatine kinase gene (CKMM), "
97 BOOST_AUTO_TEST_CASE( annotation_load )
99 string annot_data = "human\n"
103 "50\t55 anothername\n"
108 "75\t90\tname2\ttype2\n"
109 "100 120 name-asdf type!@#$%\n"
115 //istringstream annot_stream(annot_data);
116 seq.parse_annot(annot_data, 0, 0);
117 std::list<annot> annots_list = seq.annotations();
118 std::vector<annot> annots(annots_list.begin(), annots_list.end());
119 BOOST_REQUIRE_EQUAL( annots.size(), 8);
120 BOOST_CHECK_EQUAL( annots[0].start, 0 );
121 BOOST_CHECK_EQUAL( annots[0].end, 10 );
122 BOOST_CHECK_EQUAL( annots[0].type, "type");
123 BOOST_CHECK_EQUAL( annots[0].name, "name");
124 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
125 BOOST_CHECK_EQUAL( annots[2].name, "myod");
126 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
127 BOOST_CHECK_EQUAL( annots[4].name, "backward");
128 BOOST_CHECK_EQUAL( annots[5].name, "name2");
129 BOOST_CHECK_EQUAL( annots[5].end, 90);
130 BOOST_CHECK_EQUAL( annots[6].start, 100);
131 BOOST_CHECK_EQUAL( annots[6].end, 120);
132 BOOST_CHECK_EQUAL( annots[6].name, "name-asdf");
133 BOOST_CHECK_EQUAL( annots[6].type, "type!@#$%");
134 // sequence defined annotations will always be after the
135 // absolute positions
136 BOOST_CHECK_EQUAL( annots[7].name, "ident3 asdf");
137 BOOST_CHECK_EQUAL( annots[7].start, 100);
139 //BOOST_CHECK_EQUAL( annots
142 // ticket:83 when you try to load a sequence from a file that doesn't
143 // have fasta headers it crashes.
144 BOOST_AUTO_TEST_CASE( sequence_past_end )
146 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
147 seq_path /= "misformated_seq.fa";
149 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
152 BOOST_AUTO_TEST_CASE ( sequence_empty )
155 BOOST_CHECK_EQUAL( s.empty(), true );
157 BOOST_CHECK_EQUAL( s.empty(), false );
160 BOOST_AUTO_TEST_CASE ( sequence_iterators )
162 std::string seq_string = "AAGGCCTTNNTATA";
163 Sequence s(seq_string);
164 const Sequence cs(s);
165 std::string::size_type count = 0;
167 std::string::iterator str_itor;
168 Sequence::iterator s_itor;
169 Sequence::const_iterator cs_itor;
171 for( str_itor = seq_string.begin(),
173 cs_itor = cs.begin();
174 str_itor != seq_string.end() and
175 s_itor != s.end() and
177 ++str_itor, ++s_itor, ++cs_itor, ++count)
179 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
180 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
181 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
183 BOOST_CHECK_EQUAL( seq_string.size(), count );
184 BOOST_CHECK_EQUAL( s.size(), count );
185 BOOST_CHECK_EQUAL( cs.size(), count );
188 BOOST_AUTO_TEST_CASE( sequence_motifs )
191 string bogus("AATTGGAA");
192 Sequence s1("AAAAGGGGCCCCTTTT");
194 list<motif>::const_iterator motif_i = s1.motifs().begin();
195 list<motif>::const_iterator motif_end = s1.motifs().end();
197 // do our iterators work?
198 BOOST_CHECK( motif_i == s1.motifs().begin() );
199 BOOST_CHECK( motif_end == s1.motifs().end() );
200 BOOST_CHECK( motif_i == motif_end );
204 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
206 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
207 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
209 for(motif_i = s1.motifs().begin();
210 motif_i != s1.motifs().end();
213 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
214 BOOST_CHECK_EQUAL( motif_i->name, m);
215 BOOST_CHECK_EQUAL( motif_i->sequence, m);
219 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
222 BOOST_AUTO_TEST_CASE( annot_test )
224 annot a(0, 10, "test", "thing");
226 BOOST_CHECK_EQUAL( a.start, 0 );
227 BOOST_CHECK_EQUAL( a.end, 10 );
228 BOOST_CHECK_EQUAL( a.type, "test" );
229 BOOST_CHECK_EQUAL( a.name, "thing" );
231 motif m(10, "AAGGCC");
232 BOOST_CHECK_EQUAL( m.start, 10 );
233 BOOST_CHECK_EQUAL( m.type, "motif" );
234 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
235 BOOST_CHECK_EQUAL( m.end, 10+6 );
238 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
240 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
241 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
242 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
243 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
244 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
245 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
246 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
247 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
249 string gga("GGACACCTC");
252 std::list<Sequence> query_list;
253 std::list<string> string_list;
254 query_list.push_back(Sequence(gc));
255 string_list.push_back(gc);
256 query_list.push_back(Sequence(gga));
257 string_list.push_back(gga);
259 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
260 seq.find_sequences(query_list.begin(), query_list.end());
263 for(list<string>::iterator string_i = string_list.begin();
264 string_i != string_list.end();
267 string::size_type pos=0;
268 while(pos != string::npos) {
269 pos = s.find(*string_i, pos);
270 if (pos != string::npos) {
276 BOOST_CHECK_EQUAL(seq.annotations().size(), count);
279 BOOST_AUTO_TEST_CASE( subseq_annotation_test )
281 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
282 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
283 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
284 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
285 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
286 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
287 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
288 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
292 seq.add_annotation(annot(0, 10, "0-10", "0-10"));
293 seq.add_annotation(annot(10, 20, "10-20", "10-20"));
294 seq.add_annotation(annot(0, 20, "0-20", "0-20"));
295 seq.add_annotation(annot(8, 12, "8-12", "8-12"));
296 seq.add_annotation(annot(100, 5000, "100-5000", "100-5000"));
298 Sequence subseq = seq.subseq(5, 10);
299 const list<annot> annots = subseq.annotations();
300 // generate some ground truth
302 correct.push_back(annot(0, 5, "0-10", "0-10"));
303 correct.push_back(annot(5,10, "10-20", "10-20"));
304 correct.push_back(annot(0,10, "0-20", "0-20"));
305 correct.push_back(annot(3, 7, "8-12", "8-12"));
306 BOOST_REQUIRE_EQUAL( annots.size(), correct.size() );
308 list<annot>::iterator correct_i = correct.begin();
309 list<annot>::const_iterator annot_i = annots.begin();
310 for(; annot_i != annots.end(); ++annot_i, ++correct_i)
312 BOOST_CHECK( *annot_i == *correct_i );
316 BOOST_AUTO_TEST_CASE( out_operator )
318 string s("AAGGCCTT");
323 BOOST_CHECK_EQUAL( s, buf.str() );