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   // there should be no paths for these sequences
  30   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
  31        pathz_i != npath.pathz.end();
  32        ++pathz_i)
  33   {
  34     BOOST_CHECK_EQUAL( pathz_i->size(), 0);
  35   }
  36 }
  37
  38 BOOST_AUTO_TEST_CASE( nway_test )
  39 {
  40   string s0("ATATGCGC");
  41   string s1("GGGGGGGC");
  42   Sequence seq1(s1);
  43
  44   Mussa analysis;
  45   analysis.append_sequence(s0);
  46   analysis.append_sequence(s1);
  47   analysis.set_window(4);
  48   analysis.set_threshold(3);
  49   analysis.analyze();
  50   NwayPaths npath = analysis.paths();
  51   for (std::list<ConservedPath >::iterator pathz_i = npath.pathz.begin();
  52        pathz_i != npath.pathz.end();
  53        ++pathz_i)
  54   {
  55     for( ConservedPath::iterator path_i = pathz_i->begin();
  56          path_i != pathz_i->end();
  57          ++path_i)
  58     {
  59       BOOST_CHECK( *path_i == 4 || *path_i == -4);
  60     }
  61   }
  62 }
  63
  64 BOOST_AUTO_TEST_CASE( nway_refine )
  65 {
  66   fs::path mupa_path( EXAMPLE_DIR, fs::native );
  67   mupa_path /= "mck3test.mupa";
  68   Mussa m1;
  69   m1.load_mupa_file( mupa_path );
  70   m1.analyze();
  71   const NwayPaths& npath = m1.paths();
  72   BOOST_CHECK_EQUAL (npath.path_size(), npath.refined_path_size());
  73   size_t first_refined_size = npath.refined_path_size();
  74   BOOST_CHECK( first_refined_size > 0 );
  75
  76   // we're using a window size 30 (threshold 20) example
  77   m1.set_soft_threshold(22);
  78   m1.nway();
  79   BOOST_CHECK( npath.refined_path_size() > 0);
  80   BOOST_CHECK( npath.refined_path_size() < first_refined_size);
  81
  82   m1.set_soft_threshold(20);
  83   m1.nway();
  84   BOOST_CHECK_EQUAL(npath.refined_path_size(), first_refined_size);
  85 }
  86
  87 // The following data causes a crash...
  88 // ticket:85 is the user report
  89 // ticket:83 provided the sample data
  90 // ticket:64 was my version where I didn't have a consistent way of
  91 // duplicating.
  92 BOOST_AUTO_TEST_CASE( nway_threshold_crash )
  93 {
  94   string seq1 = "CACTCCCTCGAAGCTGCTGT\
  95 TCTCTTGTCTGTCTGTCTCTGTCTTGAAGCTCAGCCAAGAAACTTTCCCGTGTCACGCCT\
  96 GCGTCCCACCGTGGGGCTCTCTTGGAGCACCCAGGGACACCCAGCGTGCAACAGCCACGG\
  97 GAAGCCTTTCTGCCGCCCAGGCCCACAGGTCTCGAGACGCACATGCACGCCTGGGCGTGG\
  98 CAGCCTCACAGGGAACACGGGACAGACGCCGGCGACGCGCAGACACACGGACACGCGGAA\
  99 GCCAAGCACACTCTGGCGGGTCCCGCAAGGGACGCCGTGGAAGAAAGGAGCCTGTGGCAA\
 100 CAGGCGGCCGAGCTGCCGAATTCAGTTGACACGAGGCACAGAAAACAAATATCAAAGATC\
 101 TAATAATACAAAACAAACTTGATTAAAACTGGTGCTTAAAGTTTATTACCCACAACTCCA\
 102 CAGTCTCTGTGTAAACCACTCGACTCATCTTGTAGCTTATTTTTTTTTAAAGAGGACGTT\
 103 TTCTACGGCTGTGGCCCGCCTCTGTGAACCATAGCGGTGTGCGGCGGGGGGTCTGCACCC\
 104 GGGTGGGGGACAGAGGGACCTTTAAAGAAAACAAAACTGGACAGAAACAGGAATGTGAGC\
 105 TGGGGGAGCTGGCTTGAGTTTCTCAAAAGCCATCGGAAGATGCGAGTTTGTGCCTTTTTT\
 106 TTTATTGCTCTGGTGGATTTTTGTGGCTGGGTTTTCTGAAGTCTGAGGAACAATGCCTTA\
 107 AGAAAAAACAAACAGCAGGAATCGGTGGGACAGTTTCCTGTGGCCAGCCGAGCCTGGCAG\
 108 TGCTGGCACCGCGAGCTGGCCTGACGCCTCAAGCACGGGCACCAGCCGTCATCTCCGGGG\
 109 CCAGGGGCTGCAGCCCGGCGGTCCCTGTTTTGCTTTATTGCTGTTTAAGAAAAATGGAGG\
 110 TAGTTCCAAAAAAGTGGCAAATCCCGTTGGAGGTTTTGAAGTCCAACAAATTTTAAACGA\
 111 ATCCAAAGTGTTCTCACACGTCACATACGATTGAGCATCTCCATCTGGTCGTGAAGCATG\
 112 TGGTAGGCACACTTGCAGTGTTACGATCGGAATGCTTTTTATTAAAAGCAAGTAGCATGA\
 113 AGTATTGCTTAAATTTTAGGTATAAATAAATATATATATGTATAATATATATTCCAATGT\
 114 ATTCCAAGCTAAGAAACTTACTTGATTCTTATGAAATCTTGATAAAATATTTATAATGCA\
 115 TTTATAGAAAAAGTATATATATATATATAAAATGAATGCAGATTGCGAAGGTCCCTGCAA\
 116 ATGGATGGCTTGTGAATTTGCTCTCAAGGTGCTTATGGAAAGGGATCCTGATTGATTGAA\
 117 ATTCATGTTTTCTCAAGCTCCAGATTGGCTAGATTTCAGATCGCCAACACATTCGCCACT\
 118 GGGCAACTACCCTACAAGTTTGTACTTTCATTTTAATTATTTTCTAACAGAACCGCTCCC\
 119 GTCTCCAAGCCTTCATGCACATATGTACCTAATGAGTTTTTATAGCAAAGAATATAAATT\
 120 TGCTGTTGATTTTTGTATGAATTTTTTCACAAAAAGATCCTGAATAAGCATTGTTTTATG\
 121 AATTTTACATTTTTCCTCACCATTTAGCAATTTTCTGAATGGTAATAATGTCTAAATCTT\
 122 TTTCCTTTCTGAATTCTTGCTTGTACATTTTTTTTTACCTTTCAAAGGTTTTTAATTATT\
 123 TTTGTTTTTATTTTTGTACGATGAGTTTTCTGCAGCGTACAGAATTGTTGCTGTCAGATT\
 124 CTATTTTCAGAAAGTGAGAGGAGGGACCGTAGGTCTTTTCGGAGTGACACCAACGATTGT\
 125 GTCTTTCCTGGTCTGTCCTAGGAGCTGTATAAAGAAGCCCAGGGGCTCTTTTTAACTTTC\
 126 AACACTAGTAGTATTACGAGGGGTGGTGTGTTTTTCCCCTCCGTGGCAAGGGCAGGGAGG\
 127 GTTGCTTAGGATGCCCGGCCACCCTGGGAGGCTTGCCAGATGCCGGGGGCAGTCAGCATT\
 128 AATGAAACTCATGTTTAAACTTCTCTGACCACATCGTCAGGATAGAATTCTAACTTGAGT\
 129 TTTCCAAAGACCTTTTGAGCATGTCAGCAATGCATGGGGCACACGTGGGGCTCTTTACCC\
 130 ACTTGGGTTTTTCCACTGCAGCCACGTGGCCAGCCCTGGATTTTGGAGCCTGTGGCTGCA\
 131 AGGAACCCAGGGACCCTTGTTGCCTGGTGAACCTGCAGGGAGGGTATGATTGCCTGACCA\
 132 GGACAGCCAGTCTTTACTCTTTTTCTCTTCAACAGTAACTGACAGTCACGTTTTACTGGT\
 133 AACTTATTTTCCAGCACATGAAGCCACCAGTTTCATTCCAAAGTGTATATTGGGTTCAGA\
 134 CTTGGGGGCAGAAGTTCAGACACACCGTGCTCAGGAGGGACCCAGAGCCGAGTTTCGGAG\
 135 TTTGGTAAAGTTTACAGGGTAGCTTCTGAAATTAACTCAAACTTTTGACCAAATGAGTGC\
 136 AGATTCTTGGATTCACTTGGTCACTGGGCTGCTGATGGTCAGCTCTGAGACAGTGGTTTG\
 137 AGAGCAGGCAGAACGGTCTTGGGACTTGTTTGACTTTCCCCTCCCTGGTGGCCACTCTTT\
 138 GCTCTGAAGCCCAGATTGGCAAGAGGAGCTGGTCCATTCCCCATTCATGGCACAGAGCAG\
 139 TGGCAGGGCCCAGCTAGCAGGCTCTTCTGGCCTCCTTGGCCTCATTCTCTGCATAGCCCT\
 140 CTGGGGATCCTGCCACCTGCCCTCTTACCCCGCCGTGGCTTATGGGGAGGAATGCATCAT\
 141 CTCACTTTTTTTTTTTAAGCAGATGATGGGATAACATGGACTGCTCAGTGGCCAGGTTAT\
 142 CAGTGGGGGGACTTAATTCTAATCTCATTCAAATGGAGACGCCCTCTGCAAAGGCCTGGC\
 143 AGGGGGAGGCACGTTTCATCTGTCAGCTCACTCCAGCTTCACAAATGTGCTGAGAGCATT\
 144 ACTGTGTAGCCTTTTCTTTGAAGACACACTCGGCTCTTCTCCACAGCAAGCGTCCAGGGC\
 145 AGATGGCAGAGGATCTGCCTCGGCGTCTGCAGGCGGGACCACGTCAGGGAGGGTTCCTTC\
 146 ATGTGTTCTCCCTGTGGGTCCTTGGACCTTTAGCCTTTTTCTTCCTTTGCAAAGGCCTTG\
 147 GGGGCACTGGCTGGGAGTCAGCAAGCGAGCACTTTATATCCCTTTGAGGGAAACCCTGAT\
 148 GACGCCACTGGGCCTCTTGGCGTCTGCCCTGCCCTCGCGGCTTCCCGCCGTGCCGCAGCG\
 149 TGCCCACGTGCCCACGCCCCACCAGCAGGCGGCTGTCCCGGAGGCCGTGGCCCGCTGGGA\
 150 CTGGCCGCCCCTCCCCAGCGTCCCAGGGCTCTGGTTCTGGAGGGCCACTTTGTCAAGGTG\
 151 TTTCAGTTTTTCTTTACTTCTTTTGAAAATCTGTTTGCAAGGGGAAGGACCATTTCGTAA\
 152 TGGTCTGACACAAAAGCAAGTTTGATTTTTGCAGCACTAGCAATGGACTTTGTTGTTTTT\
 153 CTTTTTGATCAGAACATTCCTTCTTTACTGGTCACAGCCACGTGCTCATTCCATTCTTCT\
 154 TTTTGTAGACTTTGGGCCCACGTGTTTTATGGGCATTGATACATATATAAATATATAGAT\
 155 ATAAATATATATGAATATATTTTTTTAAGTTTCCTACACCTGGAGGTTGCATGGACTGTA\
 156 CGACCGGCATGACTTTATATTGTATACAGATTTTGCACGCCAAACTCGGCAGCTTTGGGG\
 157 AAGAAGAAAAATGCCTTTCTGTTCCCCTCTCATGACATTTGCAGATACAAAAGATGGAAA\
 158 TTTTTCTGTAAAACAAAACCTTGAAGGAGAGGAGGGCGGGGAAGTTTGCGTCTTATTGAA\
 159 CTTATTCTTAAGAAATTGTACTTTTTATTGTAAGAAAAATAAAAAGGACTACTTAAACAT\
 160 TTGTCATATTAAGAAAAAAAGTTTATCTAGCACTTGTGACATACCAATAATAGAGTTTAT\
 161 TGTATTTATGTGGAAACAGTGTTTTAGGGAAACTACTCAGAATTCACAGTGAACTGCCTG\
 162 TCTCTCTCGAGTTGATTTGGAGGAATTTTGTTTTGTTTTGTTTTGTTTGTTTCCTTTTAT\
 163 CTCCTTCCACGGGCCAGGCGAGCGCCGCCCGCCCTCACTGGCCTTGTGACGGTTTATTCT\
 164 GATTGAGAACTGGGCGGACTCGAAAGAGTCCCCTTTTCCGCACAGCTGTGTTGACTTTTT\
 165 AATTACTTTTAGGTGATGTATGGCTAAGATTTCACTTTAAGCAGTCGTGAACTGTGCGAG\
 166 CACTGTGGTTTACAATTATACTTTGCATCGAAAGGAAACCATTTCTTCATTGTAACGAAG\
 167 CTGAGCGTGTTCTTAGCTCGGCCTCACTTTGTCTCTGGCATTGATTAAAAGTCTGCTATT";
 168   string seq2="ATCCCAGCACATGACAACACTTCAGAAGGG\
 169 TCCCCCTGCTGACTGGAGAGCTGGGAATATGGCATTTGGACACTTCATTTGTAAATAGTG\
 170 TACATTTTAAACATTGGCTCGAAACTTCAGAGATAAGTCATGGAGAGGACATTGGAGGGG\
 171 AGAAATGCAGTTGCTGACTGGGAATTTAAGAATGTGAACTTCTCACTAGAATTGGTATGG\
 172 AAAAGCAAAATACTGTAAATAAACTTTTTTTCTAACAATTTGCC";
 173   string seq3="GGAGCTGGATGAATGAGAGGCCCCCAGATGCAGAGAGACTGGAGAGGGT\
 174 GGGGAGGGGCCCAGCGGCCTTGGTGACAGGCCCAGGGTGGGAGGGGTCGGGGCCCCTGGA\
 175 GGGGCAATGGGGAGGTGATGTCTTCTCTCTGCTCAGAGAGCAGGGACTAGGGTAGGACCC\
 176 TCACCGCTGCGTCCAGCAGACACTGAACCAGAATTGGAAACGTGCTTGAAACAATCACAC\
 177 AGGACACTTTTCTACATTGGTGCAAAATGGAATATTTTGTACATTTTTAAAATGTGATTT\
 178 TTGTATATACTTGTATATGTATGCCAATTTGGTGCTTTTTGTAAAGGAACTTTTGTATAA\
 179 TAATGCCTGGTCGTTGGGTGACCTGCGATTGTCAGAAAGAGGGGAAGGAAGCCAGGTTGA\
 180 TACAGCTGCCCACTTCCTTTCCTGAGCAGGAGGATGGGGTAGCACTCACAGGGACGATGT\
 181 GCTGTATTTCAGTGCCTATCCCAGACATACGGGGTGGTAACTGAGTTTGTGTTATATGTT\
 182 GTTTTAATAAATGCACAATGCTCTCTTCCTGTTCTTC";
 183
 184   // now that we've got some data lets see if it crashes
 185   Mussa m1;
 186   m1.append_sequence(seq1);
 187   m1.append_sequence(seq2);
 188   m1.append_sequence(seq3);
 189
 190   m1.set_window(10);
 191   m1.set_threshold(8);
 192   m1.analyze();
 193   m1.set_soft_threshold(10);
 194   m1.nway();
 195 }