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 Sequence s1("AATTGGCC");
56 BOOST_CHECK_EQUAL(s1.get_seq(), "AATTGGCC");
58 Sequence s2("aattggcc");
59 BOOST_CHECK_EQUAL(s2.get_seq(), "AATTGGCC");
60 BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
61 BOOST_CHECK_EQUAL(s2.size(), s2.get_seq().size());
62 BOOST_CHECK_EQUAL(s2.c_seq(), s2.get_seq().c_str());
65 BOOST_CHECK_EQUAL(s3.get_seq(), "ANNNG");
66 BOOST_CHECK_EQUAL(s3.subseq(0,2), "AN");
68 s3.set_filtered_sequence("AAGGCCTT", 0, 2);
69 BOOST_CHECK_EQUAL(s3.get_seq(), "AA");
70 s3.set_filtered_sequence("AAGGCCTT", 2, 2);
71 BOOST_CHECK_EQUAL( s3.get_seq(), "GG");
72 s3.set_filtered_sequence("AAGGCCTT", 4);
73 BOOST_CHECK_EQUAL( s3.get_seq(), "CCTT");
76 BOOST_CHECK_EQUAL(s3.get_seq(), "");
79 BOOST_CHECK_EQUAL(s3.get_seq(), "AAGGNN");
82 //! Can we load data from a file
83 BOOST_AUTO_TEST_CASE( sequence_load )
85 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
86 seq_path /= "human_mck_pro.fa";
88 s.load_fasta(seq_path);
89 BOOST_CHECK_EQUAL(s.subseq(0, 5), "GGATC"); // first few chars of fasta file
90 BOOST_CHECK_EQUAL(s.subseq(2, 3), "ATC");
91 BOOST_CHECK_EQUAL(s.get_header(), "gi|180579|gb|M21487.1|HUMCKMM1 Human "
92 "muscle creatine kinase gene (CKMM), "
96 BOOST_AUTO_TEST_CASE( annotation_load )
98 string annot_data = "human\n"
102 "50\t55 anothername\n"
107 "75\t90\tname2\ttype2\n"
113 //istringstream annot_stream(annot_data);
114 seq.parse_annot(annot_data, 0, 0);
115 std::list<annot> annots_list = seq.annotations();
116 std::vector<annot> annots(annots_list.begin(), annots_list.end());
117 BOOST_REQUIRE_EQUAL( annots.size(), 7);
118 BOOST_CHECK_EQUAL( annots[0].start, 0 );
119 BOOST_CHECK_EQUAL( annots[0].end, 10 );
120 BOOST_CHECK_EQUAL( annots[0].type, "type");
121 BOOST_CHECK_EQUAL( annots[0].name, "name");
122 BOOST_CHECK_EQUAL( annots[1].name, "myf7");
123 BOOST_CHECK_EQUAL( annots[2].name, "myod");
124 BOOST_CHECK_EQUAL( annots[3].name, "anothername");
125 BOOST_CHECK_EQUAL( annots[4].name, "backward");
126 BOOST_CHECK_EQUAL( annots[5].name, "name2");
127 BOOST_CHECK_EQUAL( annots[5].end, 90);
128 // sequence defined annotations will always be after the
129 // absolute positions
130 BOOST_CHECK_EQUAL( annots[6].name, "ident3 asdf");
131 BOOST_CHECK_EQUAL( annots[6].start, 100);
133 //BOOST_CHECK_EQUAL( annots
136 // ticket:83 when you try to load a sequence from a file that doesn't
137 // have fasta headers it crashes.
138 BOOST_AUTO_TEST_CASE( sequence_past_end )
140 fs::path seq_path(fs::path(EXAMPLE_DIR)/ "seq" );
141 seq_path /= "misformated_seq.fa";
143 BOOST_CHECK_THROW( s.load_fasta(seq_path), mussa_load_error );
146 BOOST_AUTO_TEST_CASE ( sequence_empty )
149 BOOST_CHECK_EQUAL( s.empty(), true );
151 BOOST_CHECK_EQUAL( s.empty(), false );
154 BOOST_AUTO_TEST_CASE ( sequence_iterators )
156 std::string seq_string = "AAGGCCTTNNTATA";
157 Sequence s(seq_string);
158 const Sequence cs(s);
159 std::string::size_type count = 0;
161 std::string::iterator str_itor;
162 Sequence::iterator s_itor;
163 Sequence::const_iterator cs_itor;
165 for( str_itor = seq_string.begin(),
167 cs_itor = cs.begin();
168 str_itor != seq_string.end() and
169 s_itor != s.end() and
171 ++str_itor, ++s_itor, ++cs_itor, ++count)
173 BOOST_CHECK_EQUAL ( *str_itor, *s_itor );
174 BOOST_CHECK_EQUAL ( *s_itor, *cs_itor );
175 BOOST_CHECK_EQUAL ( *cs_itor, *str_itor );
177 BOOST_CHECK_EQUAL( seq_string.size(), count );
178 BOOST_CHECK_EQUAL( s.size(), count );
179 BOOST_CHECK_EQUAL( cs.size(), count );
182 BOOST_AUTO_TEST_CASE( sequence_motifs )
185 string bogus("AATTGGAA");
186 Sequence s1("AAAAGGGGCCCCTTTT");
188 list<motif>::const_iterator motif_i = s1.motifs().begin();
189 list<motif>::const_iterator motif_end = s1.motifs().end();
191 // do our iterators work?
192 BOOST_CHECK( motif_i == s1.motifs().begin() );
193 BOOST_CHECK( motif_end == s1.motifs().end() );
194 BOOST_CHECK( motif_i == motif_end );
198 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
200 BOOST_CHECK( s1.motifs().begin() != s1.motifs().end() );
201 BOOST_CHECK_EQUAL( s1.motifs().size(), 2 );
203 for(motif_i = s1.motifs().begin();
204 motif_i != s1.motifs().end();
207 BOOST_CHECK_EQUAL( motif_i->type, "motif" );
208 BOOST_CHECK_EQUAL( motif_i->name, m);
209 BOOST_CHECK_EQUAL( motif_i->sequence, m);
213 BOOST_CHECK( s1.motifs().begin() == s1.motifs().end() );
216 BOOST_AUTO_TEST_CASE( annot_test )
218 annot a(0, 10, "test", "thing");
220 BOOST_CHECK_EQUAL( a.start, 0 );
221 BOOST_CHECK_EQUAL( a.end, 10 );
222 BOOST_CHECK_EQUAL( a.type, "test" );
223 BOOST_CHECK_EQUAL( a.name, "thing" );
225 motif m(10, "AAGGCC");
226 BOOST_CHECK_EQUAL( m.start, 10 );
227 BOOST_CHECK_EQUAL( m.type, "motif" );
228 BOOST_CHECK_EQUAL( m.name, "AAGGCC" );
229 BOOST_CHECK_EQUAL( m.end, 10+6 );
232 BOOST_AUTO_TEST_CASE( annotate_from_sequence )
234 string s("CCGCCCCCCATCATCGCGGCTCTCCGAGAGTCCCGCGCCCCACTCCCGGC"
235 "ACCCACCTGACCGCGGGCGGCTCCGGCCCCGCTTCGCCCCACTGCGATCA"
236 "GTCGCGTCCCGCAGGCCAGGCACGCCCCGCCGCTCCCGCTGCGCCGGGCG"
237 "TCTGGGACCTCGGGCGGCTCCTCCGAGGGGCGGGGCAGCCGGGAGCCACG"
238 "CCCCCGCAGGTGAGCCGGCCACGCCCACCGCCCGTGGGAAGTTCAGCCTC"
239 "GGGGCTCCAGCCCCGCGGGAATGGCAGAACTTCGCACGCGGAACTGGTAA"
240 "CCTCCAGGACACCTCGAATCAGGGTGATTGTAGCGCAGGGGCCTTGGCCA"
241 "AGCTAAAACTTTGGAAACTTTAGATCCCAGACAGGTGGCTTTCTTGCAGT");
243 string gga("GGACACCTC");
246 std::list<Sequence> query_list;
247 std::list<string> string_list;
248 query_list.push_back(Sequence(gc));
249 string_list.push_back(gc);
250 query_list.push_back(Sequence(gga));
251 string_list.push_back(gga);
253 BOOST_CHECK_EQUAL( seq.annotations().size(), 0 );
254 seq.find_sequences(query_list.begin(), query_list.end());
257 for(list<string>::iterator string_i = string_list.begin();
258 string_i != string_list.end();
261 string::size_type pos=0;
262 while(pos != string::npos) {
263 pos = s.find(*string_i, pos);
264 if (pos != string::npos) {
270 BOOST_CHECK_EQUAL(seq.annotations().size(), count);