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 //! Do simple operations work correctly?
25 BOOST_AUTO_TEST_CASE( sequence_filter )
27 Sequence s1("AATTGGCC");
28 BOOST_CHECK_EQUAL(s1.get_seq(), "AATTGGCC");
30 Sequence s2("aattggcc");
31 BOOST_CHECK_EQUAL(s2.get_seq(), "AATTGGCC");
32 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
33 BOOST_CHECK_EQUAL(s2.size(), s2.get_seq().size());
34 BOOST_CHECK_EQUAL(s2.c_seq(), s2.get_seq().c_str());
37 BOOST_CHECK_EQUAL(s3.get_seq(), "ANNNG");
38 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
40 s3.set_filtered_sequence("AAGGCCTT", 0, 2);
41 BOOST_CHECK_EQUAL(s3.get_seq(), "AA");
42 s3.set_filtered_sequence("AAGGCCTT", 2, 2);
43 BOOST_CHECK_EQUAL( s3.get_seq(), "GG");
44 s3.set_filtered_sequence("AAGGCCTT", 4);
45 BOOST_CHECK_EQUAL( s3.get_seq(), "CCTT");
48 BOOST_CHECK_EQUAL(s3.get_seq(), "");
51 BOOST_CHECK_EQUAL(s3.get_seq(), "AAGGNN");
54 //! Can we load data from a file
55 BOOST_AUTO_TEST_CASE( sequence_load )
57 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
58 seq_path /= "human_mck_pro.fa";
60 s.load_fasta(seq_path);
61 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
62 BOOST_CHECK_EQUAL(s.get_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
63 "muscle creatine kinase gene (CKMM), "
67 BOOST_AUTO_TEST_CASE( annotation_load )
69 string annot_data = "human\n"
73 "50\t55 anothername\n"
78 "75\t90\tname2\ttype2\n"
84 //istringstream annot_stream(annot_data);
85 seq.parse_annot(annot_data, 0, 0);
86 std::list<annot> annots_list = seq.annotations();
87 std::vector<annot> annots(annots_list.begin(), annots_list.end());
88 BOOST_REQUIRE_EQUAL( annots.size(), 7);
89 BOOST_CHECK_EQUAL( annots[0].start, 0 );
90 BOOST_CHECK_EQUAL( annots[0].end, 10 );
91 BOOST_CHECK_EQUAL( annots[0].type, "type");
92 BOOST_CHECK_EQUAL( annots[0].name, "name");
93 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
94 BOOST_CHECK_EQUAL( annots[2].name, "myod");
95 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
96 BOOST_CHECK_EQUAL( annots[4].name, "backward");
97 BOOST_CHECK_EQUAL( annots[5].name, "name2");
98 BOOST_CHECK_EQUAL( annots[5].end, 90);
99 // sequence defined annotations will always be after the
100 // absolute positions
101 BOOST_CHECK_EQUAL( annots[6].name, "ident3 asdf");
102 BOOST_CHECK_EQUAL( annots[6].start, 100);
104 //BOOST_CHECK_EQUAL( annots
107 // ticket:83 when you try to load a sequence from a file that doesn't
108 // have fasta headers it crashes.
109 BOOST_AUTO_TEST_CASE( sequence_past_end )
111 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
112 seq_path /= "misformated_seq.fa";
114 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
117 BOOST_AUTO_TEST_CASE ( sequence_empty )
120 BOOST_CHECK_EQUAL( s.empty(), true );
122 BOOST_CHECK_EQUAL( s.empty(), false );
125 BOOST_AUTO_TEST_CASE ( sequence_iterators )
127 std::string seq_string = "AAGGCCTTNNTATA";
128 Sequence s(seq_string);
129 const Sequence cs(s);
130 std::string::size_type count = 0;
132 std::string::iterator str_itor;
133 Sequence::iterator s_itor;
134 Sequence::const_iterator cs_itor;
136 for( str_itor = seq_string.begin(),
138 cs_itor = cs.begin();
139 str_itor != seq_string.end() and
140 s_itor != s.end() and
142 ++str_itor, ++s_itor, ++cs_itor, ++count)
144 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
145 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
146 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
148 BOOST_CHECK_EQUAL( seq_string.size(), count );
149 BOOST_CHECK_EQUAL( s.size(), count );
150 BOOST_CHECK_EQUAL( cs.size(), count );
153 BOOST_AUTO_TEST_CASE( sequence_motifs )
156 string bogus("AATTGGAA");
157 Sequence s1("AAAAGGGGCCCCTTTT");
159 list<motif>::const_iterator motif_i = s1.motifs().begin();
160 list<motif>::const_iterator motif_end = s1.motifs().end();
162 // do our iterators work?
163 BOOST_CHECK( motif_i == s1.motifs().begin() );
164 BOOST_CHECK( motif_end == s1.motifs().end() );
165 BOOST_CHECK( motif_i == motif_end );
169 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
171 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
172 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
174 for(motif_i = s1.motifs().begin();
175 motif_i != s1.motifs().end();
178 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
179 BOOST_CHECK_EQUAL( motif_i->name, m);
180 BOOST_CHECK_EQUAL( motif_i->sequence, m);
184 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
187 BOOST_AUTO_TEST_CASE( annot_test )
189 annot a(0, 10, "test", "thing");
191 BOOST_CHECK_EQUAL( a.start, 0 );
192 BOOST_CHECK_EQUAL( a.end, 10 );
193 BOOST_CHECK_EQUAL( a.type, "test" );
194 BOOST_CHECK_EQUAL( a.name, "thing" );
196 motif m(10, "AAGGCC");
197 BOOST_CHECK_EQUAL( m.start, 10 );
198 BOOST_CHECK_EQUAL( m.type, "motif" );
199 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
200 BOOST_CHECK_EQUAL( m.end, 10+6 );
203 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
205 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
206 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
207 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
208 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
209 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
210 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
211 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
212 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
214 string gga("GGACACCTC");
217 std::list<Sequence> query_list;
218 std::list<string> string_list;
219 query_list.push_back(Sequence(gc));
220 string_list.push_back(gc);
221 query_list.push_back(Sequence(gga));
222 string_list.push_back(gga);
224 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
225 seq.find_sequences(query_list.begin(), query_list.end());
228 for(list<string>::iterator string_i = string_list.begin();
229 string_i != string_list.end();
232 string::size_type pos=0;
233 while(pos != string::npos) {
234 pos = s.find(*string_i, pos);
235 if (pos != string::npos) {
241 BOOST_CHECK_EQUAL(seq.annotations().size(), count);