public void Test_AlignMatrix()
{
string Q8I2J3 = "MDKKAREYAQDALKFIQRSGSNFLACKNLKERLENNGFINLSEGETWNLNKNEGYVLCKE" +
"NRNICGFFVGKNFNIDTGSILISIGHIDSCALKISPNNNVIKKKIHQINVECYGSGLWHT" +
"WFDRSLGLSGQVLYKKGNKLVEKLIQINKSVLFLPSLAIHLQNRTRYDFSVKINYENHIK" +
"PIISTTLFNQLNKCKRNNVHHDTILTTDTKFSHKENSQNKRDDQMCHSFNDKDVSNHNLD" +
"KNTIEHLTNQQNEEKNKHTKDNPNSKDIVEHINTDNSYPLLYLLSKELNCKEEDILDFEL" +
"CLMDTQEPCFTGVYEEFIEGARFDNLLGSFCVFEGFIELVNSIKNHTSNENTNHTNNITN" +
"DINDNIHNNLYISIGYDHEEIGSLSEVGARSYCTKNFIDRIISSVFKKEIHEKNLSVQEI" +
"YGNLVNRSFILNVDMAHCSHPNYPETVQDNHQLFFHEGIAIKYNTNKNYVTSPLHASLIK" +
"RTFELYYNKYKQQIKYQNFMVKNDTPCGSTVGSMVAANLSMPGIDIGIPQLAMHSIREIA" +
"AVHDVFFLIKGVFAFYTYYNQVLSTCVHDK";
string protein = DataBaseManipulation.DegenerateSequence(Q8I2J3);
string query = "LGGKYLLLLGGYPLYXGYGL";
int gap = 32767;
MatrixAlignment ma = new MatrixAlignment(protein, query);
MatrixAlignment.AlignMatrix(ma, gap, MatrixAlignment.ScoreTable);
var path = MatrixAlignment.Traceback(ma);
var seqCom = MatrixAlignment.SequenceComparison(ma, path);
}
public void Test_AlignMatrix2()
{
string O77390 = "MNKMASTHNEIIPRLGFEEMRNEMNKYGVEINQSTLKNPSTEDIQGIYSLCIKYILNKDI" +
"QNIRIEEYTGDLKSSLPTVDGLQILPNEGKNHLQAIGNLRFLRHCEKINKILNLDNILSY" +
"IFKPVGSHMTKLINAFIHFMKYRDQLYNENGEKIKSIQEKKNEYDVLENEYDALENELNK" +
"LLLKHEDIRNNIINEKNIKRNYEEDIIKNQNLLNSQQSLIISLNSTKDKIVNETNELIFQ" +
"YSRYRQKKEDLEDQIVPSPEKLQKYNEELKDHLYEHIAQFEDDRKKNEDIKNKINIADIC" +
"IKKLVDLLTALNEHIEHTIKLHIEKKNNLQTIEKQYKSLTNEKQNFITKNTEQDKIIKET" +
"KEFLQQEQTKWNQKIKQEQHNTILIQQKVKDIYQNVDDLNIKTNREINQINNIIKHIQDI" +
"INHYNKNILLITELIQNTKNSHSILTHKVLNNIQKDISANM";
string protein = DataBaseManipulation.DegenerateSequence(O77390);
string protein_select = "YGGLGYKGLLLGLKLGGG";
//string query = "KGKGYGLLGGXYGXKGGGPYLGGLGLKGK";
string query = "GGGKGYGGLLYXLKLGGGGY";
int gap = 32767; //Default in Blastp gapopen
MatrixAlignment ma = new MatrixAlignment(protein, query);
MatrixAlignment.AlignMatrix(ma, gap, MatrixAlignment.ScoreTable);
var path = MatrixAlignment.Traceback(ma);
var seqCom = MatrixAlignment.SequenceComparison(ma, path);
Assert.That(new string(seqCom[0]) == "GGKGYGGLLYXLKLGGG");
Assert.That(new string(seqCom[1]) == "GGLGYKGLLLGLKLGGG");
//MatrixAlignment.PrintMatrix(ma, Path.Combine(TestContext.CurrentContext.TestDirectory, @"matrix_alignment_debug.txt"));
}
public void Test_LoadQueryMap()
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\UnkwnPro_queries_optimized.pdb");
var queries = DataBaseManipulation.LoadQueryMap(filePath);
Assert.That(queries.Count == 3);
var dQueries = DataBaseManipulation.DegenerateQueryMap(queries);
//Assert.That(dQueries.First() == "ZGGMYZZZZGGYPZYXGYGZ");
Assert.That(dQueries.First() == "LGGKYLLLLGGYPLYXGYGL");
}
