TEST(IupacAlignmentTests, BasicTest)
{
PairwiseAlignment* a;
a = AlignAffineIupac("GATTTT", "GMTTT");
ASSERT_EQ("GATTTT", a->Target());
ASSERT_EQ("GM-TTT", a->Query());
delete a;
a = AlignAffineIupac("TTTTAG", "TTTMG");
ASSERT_EQ("TTTTAG", a->Target());
ASSERT_EQ("-TTTMG", a->Query());
delete a;
}
TEST(PairwiseAlignmentTests, GlobalAlignmentTests)
{
PairwiseAlignment* a = Align("GATT", "GATT");
EXPECT_FLOAT_EQ(1.0, a->Accuracy());
EXPECT_EQ("GATT", a->Target());
EXPECT_EQ("GATT", a->Query());
EXPECT_EQ("MMMM", a->Transcript());
delete a;
a = Align("GATT", "GAT");
EXPECT_FLOAT_EQ(0.75, a->Accuracy());
EXPECT_EQ("GATT", a->Target());
EXPECT_EQ("GA-T", a->Query());
EXPECT_EQ("MMDM", a->Transcript());
delete a;
a = Align("GATTACA", "TT");
EXPECT_EQ("GATTACA", a->Target());
EXPECT_EQ("--TT---", a->Query());
EXPECT_FLOAT_EQ(2./7, a->Accuracy());
delete a;
}
TEST(AffineAlignmentTests, LargeGapTest)
{
// Test a real-world large insertion, found in an E. Coli
// experiment
const char* target = \
"AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
"AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
"GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
"CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
"CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
"TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
"TCTCATCCCCCCGGTGTGTGCAATACACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCT"
"TCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCG"
"CTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGC"
"TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
"TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
"GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
"CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
"CTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACA"
"CTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTG"
"CTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAAA"
"TCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
const char* query = \
"AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
"AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
"GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
"CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
"CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
"TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
"TCTCATCCCCCCGGTGTGTGCAATACACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCT"
"TCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCG"
"CTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGC"
"TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
"TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
"GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
"CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
"CTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCC"
"CGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGG"
"GCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGC"
"TCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC"
"ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTT"
"GCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA"
"ATCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
const char* expectedAlignedTarget = \
"AACGATTTTATGATGGCATGTGACATGTATTTCCGTTGGGGGCATTTTAATAAGTGAGGA"
"AGTGATAGGAAGTGACCAGATAATACATATATGTTCTGTACTCTCTTGCGCATTTTGATT"
"GTTGACTGAGTAACCAGACAGTTGATGTGCACGATTTCCCCTCGCCCTAACAGACGTGGG"
"CGGGGGCACCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTT"
"CTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCCGC"
"TCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGACCCCCGGTCGGGGCT"
"TCTCATCCCCCCGGTGTGTGCAATAC----------------------------------"
"------------------------------------------------------------"
"------------------------------------------------------------"
"---------------------------ACGAAAAAAAAGCCCGTACTTTCGTACGAGCTC"
"TTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCCC"
"GCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGG"
"CTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCT"
"CTTCTTTAAATATGGCGGTGAGGGGGGGATTGACTCGCTTCGCTCGCCCTGCGGGCAGCC"
"CGCTCACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGG"
"GCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGC"
"TCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACAC"
"ACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTT"
"GCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAAAAA"
"ATCGCGCGTTTATTCAAACTTCAATCAATGTGTGGTTTTAATAAGCGAAAT";
PairwiseAlignment* a = AlignWithAffineGapPenalty(target, query);
ASSERT_EQ(expectedAlignedTarget, a->Target());
}
TEST(AffineAlignmentTests, BasicTests)
{
PairwiseAlignment* a = AlignWithAffineGapPenalty("ATT", "ATT");
EXPECT_EQ("ATT", a->Target());
EXPECT_EQ("ATT", a->Query());
delete a;
a = AlignWithAffineGapPenalty("AT", "ATT");
EXPECT_EQ("A-T", a->Target());
EXPECT_EQ("ATT", a->Query());
delete a;
a = AlignWithAffineGapPenalty("GA", "GAT");
EXPECT_EQ("GA-", a->Target());
EXPECT_EQ("GAT", a->Query());
delete a;
a = AlignWithAffineGapPenalty("GAT", "GA");
EXPECT_EQ("GAT", a->Target());
EXPECT_EQ("GA-", a->Query());
delete a;
a = AlignWithAffineGapPenalty("GA", "TGA");
EXPECT_EQ("-GA", a->Target());
EXPECT_EQ("TGA", a->Query());
delete a;
a = AlignWithAffineGapPenalty("TGA", "GA");
EXPECT_EQ("TGA", a->Target());
EXPECT_EQ("-GA", a->Query());
delete a;
a = AlignWithAffineGapPenalty("GATTACA", "GATTTACA");
EXPECT_EQ("GA-TTACA", a->Target());
EXPECT_EQ("GATTTACA", a->Query());
delete a;
}
TEST(PairwiseAlignmentTests, JustifyTest)
{
// deletion
{
PairwiseAlignment a = PairwiseAlignment("AAAAAA", "AAA-AA");
a.Justify(LRType::LEFT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("-AAAAA", a.Query());
EXPECT_EQ("DMMMMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("AAAAA-", a.Query());
EXPECT_EQ("MMMMMD", a.Transcript());
}
// insertion
{
PairwiseAlignment a = PairwiseAlignment("A-AAAA", "AAAAAA");
a.Justify(LRType::LEFT);
EXPECT_EQ("-AAAAA", a.Target());
EXPECT_EQ("AAAAAA", a.Query());
EXPECT_EQ("IMMMMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("AAAAA-", a.Target());
EXPECT_EQ("AAAAAA", a.Query());
EXPECT_EQ("MMMMMI", a.Transcript());
}
// interruption in homopolymer
{
PairwiseAlignment a = PairwiseAlignment("GATTTACA", "GAGT-ACA");
a.Justify(LRType::LEFT);
EXPECT_EQ("GATTTACA", a.Target());
EXPECT_EQ("GAG-TACA", a.Query());
EXPECT_EQ("MMRDMMMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("GATTTACA", a.Target());
EXPECT_EQ("GAGT-ACA", a.Query());
EXPECT_EQ("MMRMDMMM", a.Transcript());
}
// double bases, adjacent
{
PairwiseAlignment a = PairwiseAlignment("AAAAAA", "AAA--A");
a.Justify(LRType::LEFT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("--AAAA", a.Query());
EXPECT_EQ("DDMMMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("AAAA--", a.Query());
EXPECT_EQ("MMMMDD", a.Transcript());
}
// double bases, separated
{
PairwiseAlignment a = PairwiseAlignment("AAAAAA", "A-AA-A");
a.Justify(LRType::LEFT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("--AAAA", a.Query());
EXPECT_EQ("DDMMMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("AAAAAA", a.Target());
EXPECT_EQ("AAAA--", a.Query());
EXPECT_EQ("MMMMDD", a.Transcript());
}
// intervening insertion
{
PairwiseAlignment a = PairwiseAlignment("A----A", "AATAAA");
a.Justify(LRType::LEFT);
EXPECT_EQ("----AA", a.Target());
EXPECT_EQ("AATAAA", a.Query());
EXPECT_EQ("IIIIMM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("AA----", a.Target());
EXPECT_EQ("AATAAA", a.Query());
EXPECT_EQ("MMIIII", a.Transcript());
}
// intervening match
{
PairwiseAlignment a = PairwiseAlignment("A-T--A", "AATAAA");
a.Justify(LRType::LEFT);
EXPECT_EQ("-AT--A", a.Target());
EXPECT_EQ("AATAAA", a.Query());
EXPECT_EQ("IMMIIM", a.Transcript());
a.Justify(LRType::RIGHT);
EXPECT_EQ("A-TA--", a.Target());
EXPECT_EQ("AATAAA", a.Query());
EXPECT_EQ("MIMMII", a.Transcript());
}
}
std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln)
{
return TargetToQueryPositions(aln.Transcript());
}
