alg/test/test_nway.cpp

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