public void TestGetDatabaseComposition()
{
Dictionary <char, double> actual = SequenceUtils.GetDatabaseComposition(TestContext.CurrentContext.TestDirectory + "/../../../data//test.fasta");
Assert.AreEqual(0.5, actual['A']);
Assert.AreEqual(0.5, actual['B']);
}
public void TestGetReversedSequence4()
{
Sequence seq = SequenceUtils.GetReversedSequence("ABCDE", "REV_", 2, 5);
Assert.AreEqual("REV_05", seq.Name);
Assert.AreEqual("EDCBA", seq.SeqString);
}
public void TestReadFromFasta()
{
FastaFormat ff = new FastaFormat();
List <Sequence> seqs = SequenceUtils.Read(ff, @TestContext.CurrentContext.TestDirectory + "/../../../data//Standard_Protein_FIT_060222.noredundant.fasta");
Assert.AreEqual(43, seqs.Count);
}
public void TestRead()
{
List <Sequence> seqs = SequenceUtils.Read(new FastaFormat(), TestContext.CurrentContext.TestDirectory + "/../../../data//test.fasta");
Assert.AreEqual(2, seqs.Count);
Assert.AreEqual("test1 description of test1", seqs[0].Reference);
Assert.AreEqual("AAAAA", seqs[0].SeqString);
Assert.AreEqual("test2 description of test2", seqs[1].Reference);
Assert.AreEqual("BBBBB", seqs[1].SeqString);
}
private void ProcessFile(ref int index, StreamWriter sw, string fastaFile, bool isContaminant)
{
FastaFormat ff = new FastaFormat();
using (StreamReader sr = new StreamReader(fastaFile))
{
Progress.SetRange(0, sr.BaseStream.Length);
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
if (isContaminant)
{
if (!seq.Reference.StartsWith("CON_"))
{
seq.Reference = "CON_" + seq.Reference;
}
}
if (combined)
{
ff.WriteSequence(sw, seq);
}
if (pseudoAminoacid)
{
builder.Build(seq);
}
index++;
Sequence reversedSeq = SequenceUtils.GetReversedSequence(seq.SeqString, index);
ff.WriteSequence(sw, reversedSeq);
}
}
}
public void TestGetReversedSequence1()
{
Assert.AreEqual("EDCBA", SequenceUtils.GetReversedSequence("ABCDE"));
}
