alg/test/test_nway.cpp

   1 #define BOOST_TEST_DYN_LINK
   2 #define BOOST_TEST_MODULE test_nway
   3 #include <boost/test/unit_test.hpp>
   4
   5 #include <boost/filesystem/path.hpp>
   6 namespace fs = boost::filesystem;
   7
   8 #include <string>
   9 #include <iostream>
  10
  11 #include "alg/mussa.hpp"
  12 #include "alg/nway_paths.hpp"
  13 #include "alg/sequence.hpp"
  14
  15 using namespace std;
  16
  17 //! there should be no matches
  18 BOOST_AUTO_TEST_CASE( nway_null )
  19 {
  20   string s0("AAAANNNN");
  21   string s1("GGGGNNNN");
  22   string s2("TTTTNNNN");
  23
  24   Mussa analysis;
  25   analysis.append_sequence(s0);
  26   analysis.append_sequence(s1);
  27   analysis.append_sequence(s2);
  28   analysis.set_window(4);
  29   analysis.set_threshold(3);
  30   analysis.analyze();
  31   NwayPaths npath = analysis.paths();
  32   // we added 3 sequences, but none-matched
  33   BOOST_CHECK_EQUAL( npath.sequence_count(), 0);
  34   BOOST_CHECK_EQUAL( npath.size(), 0 );
  35   BOOST_CHECK_EQUAL( npath.path_size(), 0 );
  36   BOOST_CHECK_EQUAL( npath.refined_path_size(), 0 );
  37   // there should be no paths for these sequences
  38   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
  39        pathz_i != npath.pathz.end();
  40        ++pathz_i)
  41   {
  42     BOOST_CHECK_EQUAL( pathz_i->size(), 0);
  43   }
  44 }
  45
  46 BOOST_AUTO_TEST_CASE( nway_test )
  47 {
  48   string s0("ATATGCGC");
  49   string s1("GGGGGGGC");
  50   Sequence seq1(s1);
  51
  52   Mussa analysis;
  53   analysis.append_sequence(s0);
  54   analysis.append_sequence(s1);
  55   analysis.set_window(4);
  56   analysis.set_threshold(3);
  57   analysis.analyze();
  58   NwayPaths npath = analysis.paths();
  59   BOOST_CHECK_EQUAL( npath.sequence_count(), 2);
  60   BOOST_CHECK_EQUAL( npath.size(), 2 );
  61   BOOST_CHECK_EQUAL( npath.path_size(), 2 );
  62   BOOST_CHECK_EQUAL( npath.refined_path_size(), 2 );
  63   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
  64        pathz_i != npath.pathz.end();
  65        ++pathz_i)
  66   {
  67     for( ConservedPath::iterator path_i = pathz_i->begin();
  68          path_i != pathz_i->end();
  69          ++path_i)
  70     {
  71       BOOST_CHECK( *path_i == 4 || *path_i == -4);
  72     }
  73   }
  74 }
  75
  76 BOOST_AUTO_TEST_CASE( nway_refine )
  77 {
  78   fs::path mupa_path( EXAMPLE_DIR, fs::native );
  79   mupa_path /= "mck3test.mupa";
  80   Mussa m1;
  81   m1.load_mupa_file( mupa_path );
  82   m1.analyze();
  83   const NwayPaths& npath = m1.paths();
  84   //BOOST_CHECK_EQUAL (npath.path_size(), npath.refined_path_size());
  85   // FIXME: shouldn't these be equal to start with?
  86   BOOST_CHECK(npath.path_size() > npath.refined_path_size());
  87   size_t first_refined_size = npath.refined_path_size();
  88   BOOST_CHECK( first_refined_size > 0 );
  89
  90   // we're using a window size 30 (threshold 20) example
  91   m1.set_soft_threshold(22);
  92   m1.nway();
  93   BOOST_CHECK_EQUAL( npath.path_size(), npath.size() );
  94   BOOST_CHECK( npath.path_size() > 0 );
  95   BOOST_CHECK( npath.refined_path_size() > 0);
  96   BOOST_CHECK( npath.refined_path_size() < first_refined_size);
  97
  98   m1.set_soft_threshold(20);
  99   m1.nway();
 100   BOOST_CHECK_EQUAL(npath.refined_path_size(), first_refined_size);
 101 }
 102
 103 // The following data causes a crash...
 104 // ticket:85 is the user report
 105 // ticket:83 provided the sample data
 106 // ticket:64 was my version where I didn't have a consistent way of
 107 // duplicating.
 108 BOOST_AUTO_TEST_CASE( nway_threshold_crash )
 109 {
 110   string seq1 = "CACTCCCTCGAAGCTGCTGT\
 111 TCTCTTGTCTGTCTGTCTCTGTCTTGAAGCTCAGCCAAGAAACTTTCCCGTGTCACGCCT\
 112 GCGTCCCACCGTGGGGCTCTCTTGGAGCACCCAGGGACACCCAGCGTGCAACAGCCACGG\
 113 GAAGCCTTTCTGCCGCCCAGGCCCACAGGTCTCGAGACGCACATGCACGCCTGGGCGTGG\
 114 CAGCCTCACAGGGAACACGGGACAGACGCCGGCGACGCGCAGACACACGGACACGCGGAA\
 115 GCCAAGCACACTCTGGCGGGTCCCGCAAGGGACGCCGTGGAAGAAAGGAGCCTGTGGCAA\
 116 CAGGCGGCCGAGCTGCCGAATTCAGTTGACACGAGGCACAGAAAACAAATATCAAAGATC\
 117 TAATAATACAAAACAAACTTGATTAAAACTGGTGCTTAAAGTTTATTACCCACAACTCCA\
 118 CAGTCTCTGTGTAAACCACTCGACTCATCTTGTAGCTTATTTTTTTTTAAAGAGGACGTT\
 119 TTCTACGGCTGTGGCCCGCCTCTGTGAACCATAGCGGTGTGCGGCGGGGGGTCTGCACCC\
 120 GGGTGGGGGACAGAGGGACCTTTAAAGAAAACAAAACTGGACAGAAACAGGAATGTGAGC\
 121 TGGGGGAGCTGGCTTGAGTTTCTCAAAAGCCATCGGAAGATGCGAGTTTGTGCCTTTTTT\
 122 TTTATTGCTCTGGTGGATTTTTGTGGCTGGGTTTTCTGAAGTCTGAGGAACAATGCCTTA\
 123 AGAAAAAACAAACAGCAGGAATCGGTGGGACAGTTTCCTGTGGCCAGCCGAGCCTGGCAG\
 124 TGCTGGCACCGCGAGCTGGCCTGACGCCTCAAGCACGGGCACCAGCCGTCATCTCCGGGG\
 125 CCAGGGGCTGCAGCCCGGCGGTCCCTGTTTTGCTTTATTGCTGTTTAAGAAAAATGGAGG\
 126 TAGTTCCAAAAAAGTGGCAAATCCCGTTGGAGGTTTTGAAGTCCAACAAATTTTAAACGA\
 127 ATCCAAAGTGTTCTCACACGTCACATACGATTGAGCATCTCCATCTGGTCGTGAAGCATG\
 128 TGGTAGGCACACTTGCAGTGTTACGATCGGAATGCTTTTTATTAAAAGCAAGTAGCATGA\
 129 AGTATTGCTTAAATTTTAGGTATAAATAAATATATATATGTATAATATATATTCCAATGT\
 130 ATTCCAAGCTAAGAAACTTACTTGATTCTTATGAAATCTTGATAAAATATTTATAATGCA\
 131 TTTATAGAAAAAGTATATATATATATATAAAATGAATGCAGATTGCGAAGGTCCCTGCAA\
 132 ATGGATGGCTTGTGAATTTGCTCTCAAGGTGCTTATGGAAAGGGATCCTGATTGATTGAA\
 133 ATTCATGTTTTCTCAAGCTCCAGATTGGCTAGATTTCAGATCGCCAACACATTCGCCACT\
 134 GGGCAACTACCCTACAAGTTTGTACTTTCATTTTAATTATTTTCTAACAGAACCGCTCCC\
 135 GTCTCCAAGCCTTCATGCACATATGTACCTAATGAGTTTTTATAGCAAAGAATATAAATT\
 136 TGCTGTTGATTTTTGTATGAATTTTTTCACAAAAAGATCCTGAATAAGCATTGTTTTATG\
 137 AATTTTACATTTTTCCTCACCATTTAGCAATTTTCTGAATGGTAATAATGTCTAAATCTT\
 138 TTTCCTTTCTGAATTCTTGCTTGTACATTTTTTTTTACCTTTCAAAGGTTTTTAATTATT\
 139 TTTGTTTTTATTTTTGTACGATGAGTTTTCTGCAGCGTACAGAATTGTTGCTGTCAGATT\
 140 CTATTTTCAGAAAGTGAGAGGAGGGACCGTAGGTCTTTTCGGAGTGACACCAACGATTGT\
 141 GTCTTTCCTGGTCTGTCCTAGGAGCTGTATAAAGAAGCCCAGGGGCTCTTTTTAACTTTC\
 142 AACACTAGTAGTATTACGAGGGGTGGTGTGTTTTTCCCCTCCGTGGCAAGGGCAGGGAGG\
 143 GTTGCTTAGGATGCCCGGCCACCCTGGGAGGCTTGCCAGATGCCGGGGGCAGTCAGCATT\
 144 AATGAAACTCATGTTTAAACTTCTCTGACCACATCGTCAGGATAGAATTCTAACTTGAGT\
 145 TTTCCAAAGACCTTTTGAGCATGTCAGCAATGCATGGGGCACACGTGGGGCTCTTTACCC\
 146 ACTTGGGTTTTTCCACTGCAGCCACGTGGCCAGCCCTGGATTTTGGAGCCTGTGGCTGCA\
 147 AGGAACCCAGGGACCCTTGTTGCCTGGTGAACCTGCAGGGAGGGTATGATTGCCTGACCA\
 148 GGACAGCCAGTCTTTACTCTTTTTCTCTTCAACAGTAACTGACAGTCACGTTTTACTGGT\
 149 AACTTATTTTCCAGCACATGAAGCCACCAGTTTCATTCCAAAGTGTATATTGGGTTCAGA\
 150 CTTGGGGGCAGAAGTTCAGACACACCGTGCTCAGGAGGGACCCAGAGCCGAGTTTCGGAG\
 151 TTTGGTAAAGTTTACAGGGTAGCTTCTGAAATTAACTCAAACTTTTGACCAAATGAGTGC\
 152 AGATTCTTGGATTCACTTGGTCACTGGGCTGCTGATGGTCAGCTCTGAGACAGTGGTTTG\
 153 AGAGCAGGCAGAACGGTCTTGGGACTTGTTTGACTTTCCCCTCCCTGGTGGCCACTCTTT\
 154 GCTCTGAAGCCCAGATTGGCAAGAGGAGCTGGTCCATTCCCCATTCATGGCACAGAGCAG\
 155 TGGCAGGGCCCAGCTAGCAGGCTCTTCTGGCCTCCTTGGCCTCATTCTCTGCATAGCCCT\
 156 CTGGGGATCCTGCCACCTGCCCTCTTACCCCGCCGTGGCTTATGGGGAGGAATGCATCAT\
 157 CTCACTTTTTTTTTTTAAGCAGATGATGGGATAACATGGACTGCTCAGTGGCCAGGTTAT\
 158 CAGTGGGGGGACTTAATTCTAATCTCATTCAAATGGAGACGCCCTCTGCAAAGGCCTGGC\
 159 AGGGGGAGGCACGTTTCATCTGTCAGCTCACTCCAGCTTCACAAATGTGCTGAGAGCATT\
 160 ACTGTGTAGCCTTTTCTTTGAAGACACACTCGGCTCTTCTCCACAGCAAGCGTCCAGGGC\
 161 AGATGGCAGAGGATCTGCCTCGGCGTCTGCAGGCGGGACCACGTCAGGGAGGGTTCCTTC\
 162 ATGTGTTCTCCCTGTGGGTCCTTGGACCTTTAGCCTTTTTCTTCCTTTGCAAAGGCCTTG\
 163 GGGGCACTGGCTGGGAGTCAGCAAGCGAGCACTTTATATCCCTTTGAGGGAAACCCTGAT\
 164 GACGCCACTGGGCCTCTTGGCGTCTGCCCTGCCCTCGCGGCTTCCCGCCGTGCCGCAGCG\
 165 TGCCCACGTGCCCACGCCCCACCAGCAGGCGGCTGTCCCGGAGGCCGTGGCCCGCTGGGA\
 166 CTGGCCGCCCCTCCCCAGCGTCCCAGGGCTCTGGTTCTGGAGGGCCACTTTGTCAAGGTG\
 167 TTTCAGTTTTTCTTTACTTCTTTTGAAAATCTGTTTGCAAGGGGAAGGACCATTTCGTAA\
 168 TGGTCTGACACAAAAGCAAGTTTGATTTTTGCAGCACTAGCAATGGACTTTGTTGTTTTT\
 169 CTTTTTGATCAGAACATTCCTTCTTTACTGGTCACAGCCACGTGCTCATTCCATTCTTCT\
 170 TTTTGTAGACTTTGGGCCCACGTGTTTTATGGGCATTGATACATATATAAATATATAGAT\
 171 ATAAATATATATGAATATATTTTTTTAAGTTTCCTACACCTGGAGGTTGCATGGACTGTA\
 172 CGACCGGCATGACTTTATATTGTATACAGATTTTGCACGCCAAACTCGGCAGCTTTGGGG\
 173 AAGAAGAAAAATGCCTTTCTGTTCCCCTCTCATGACATTTGCAGATACAAAAGATGGAAA\
 174 TTTTTCTGTAAAACAAAACCTTGAAGGAGAGGAGGGCGGGGAAGTTTGCGTCTTATTGAA\
 175 CTTATTCTTAAGAAATTGTACTTTTTATTGTAAGAAAAATAAAAAGGACTACTTAAACAT\
 176 TTGTCATATTAAGAAAAAAAGTTTATCTAGCACTTGTGACATACCAATAATAGAGTTTAT\
 177 TGTATTTATGTGGAAACAGTGTTTTAGGGAAACTACTCAGAATTCACAGTGAACTGCCTG\
 178 TCTCTCTCGAGTTGATTTGGAGGAATTTTGTTTTGTTTTGTTTTGTTTGTTTCCTTTTAT\
 179 CTCCTTCCACGGGCCAGGCGAGCGCCGCCCGCCCTCACTGGCCTTGTGACGGTTTATTCT\
 180 GATTGAGAACTGGGCGGACTCGAAAGAGTCCCCTTTTCCGCACAGCTGTGTTGACTTTTT\
 181 AATTACTTTTAGGTGATGTATGGCTAAGATTTCACTTTAAGCAGTCGTGAACTGTGCGAG\
 182 CACTGTGGTTTACAATTATACTTTGCATCGAAAGGAAACCATTTCTTCATTGTAACGAAG\
 183 CTGAGCGTGTTCTTAGCTCGGCCTCACTTTGTCTCTGGCATTGATTAAAAGTCTGCTATT";
 184   string seq2="ATCCCAGCACATGACAACACTTCAGAAGGG\
 185 TCCCCCTGCTGACTGGAGAGCTGGGAATATGGCATTTGGACACTTCATTTGTAAATAGTG\
 186 TACATTTTAAACATTGGCTCGAAACTTCAGAGATAAGTCATGGAGAGGACATTGGAGGGG\
 187 AGAAATGCAGTTGCTGACTGGGAATTTAAGAATGTGAACTTCTCACTAGAATTGGTATGG\
 188 AAAAGCAAAATACTGTAAATAAACTTTTTTTCTAACAATTTGCC";
 189   string seq3="GGAGCTGGATGAATGAGAGGCCCCCAGATGCAGAGAGACTGGAGAGGGT\
 190 GGGGAGGGGCCCAGCGGCCTTGGTGACAGGCCCAGGGTGGGAGGGGTCGGGGCCCCTGGA\
 191 GGGGCAATGGGGAGGTGATGTCTTCTCTCTGCTCAGAGAGCAGGGACTAGGGTAGGACCC\
 192 TCACCGCTGCGTCCAGCAGACACTGAACCAGAATTGGAAACGTGCTTGAAACAATCACAC\
 193 AGGACACTTTTCTACATTGGTGCAAAATGGAATATTTTGTACATTTTTAAAATGTGATTT\
 194 TTGTATATACTTGTATATGTATGCCAATTTGGTGCTTTTTGTAAAGGAACTTTTGTATAA\
 195 TAATGCCTGGTCGTTGGGTGACCTGCGATTGTCAGAAAGAGGGGAAGGAAGCCAGGTTGA\
 196 TACAGCTGCCCACTTCCTTTCCTGAGCAGGAGGATGGGGTAGCACTCACAGGGACGATGT\
 197 GCTGTATTTCAGTGCCTATCCCAGACATACGGGGTGGTAACTGAGTTTGTGTTATATGTT\
 198 GTTTTAATAAATGCACAATGCTCTCTTCCTGTTCTTC";
 199
 200   // now that we've got some data lets see if it crashes
 201   Mussa m1;
 202   m1.append_sequence(seq1);
 203   m1.append_sequence(seq2);
 204   m1.append_sequence(seq3);
 205
 206   m1.set_window(10);
 207   m1.set_threshold(8);
 208   m1.analyze();
 209   m1.set_soft_threshold(10);
 210   m1.nway();
 211 }