alg/test/test_nway.cpp

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