public void BadContent()
{
StringBuilder s = new StringBuilder();
s.AppendLine("AAAA");
FastaParser parser = null;
try
{
parser = new FastaParser();
bool exception = false;
IList <ISequence> sequences = null;
try
{
sequences = parser.Parse(new StringReader(s.ToString()));
}
catch (Exception ex)
{
exception = true;
Assert.AreEqual(ex.Message, "Bad input in file [Fasta]");
}
Assert.IsTrue(exception);
}
finally
{
if (parser != null)
{
parser.Dispose();
}
}
}
public void FastaFor186972391()
{
string expectedSequence =
"IFYEPVEILGYDNKSSLVLVKRLITRMYQQKSLISSLNDSNQNEFWGHKNSFSSHFSSQMVSEGFGVILE" +
"IPFSSRLVSSLEEKRIPKSQNLRSIHSIFPFLEDKLSHLNYVSDLLIPHPIHLEILVQILQCWIKDVPSL" +
"HLLRLFFHEYHNLNSLITLNKSIYVFSKRKKRFFGFLHNSYVYECEYLFLFIRKKSSYLRSISSGVFLER" +
"THFYGKIKYLLVVCCNSFQRILWFLKDTFIHYVRYQGKAIMASKGTLILMKKWKFHLVNFWQSYFHFWFQ" +
"PYRINIKQLPNYSFSFLGYFSSVRKNPLVVRNQMLENSFLINTLTQKLDTIVPAISLIGSLSKAQFCTVL" +
"GHPISKPIWTDLSDSDILDRFCRICRNLCRYHSGSSKKQVLYRIKYIFRLSCARTLARKHKSTVRTFMRR" +
"LGSGFLEEFFLEEE";
string filepath = @"TestUtils\FASTA\186972391.fasta";
Assert.IsTrue(File.Exists(filepath));
IList <ISequence> seqs = null;
FastaParser parser = null;
try
{
parser = new FastaParser();
using (StreamReader reader = File.OpenText(filepath))
{
seqs = parser.Parse(reader);
}
Assert.IsNotNull(seqs);
Assert.AreEqual(1, seqs.Count);
Sequence seq = (Sequence)seqs[0];
Assert.IsNotNull(seq);
Assert.AreEqual(expectedSequence, seq.ToString());
Assert.AreEqual(expectedSequence.Length, seq.EncodedValues.Length);
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
Assert.AreEqual("gi|186972391|gb|ACC99454.1| maturase K [Scaphosepalum rapax]", seq.ID);
// Try it again with ParseOne, from reader and from filename
using (StreamReader reader = File.OpenText(filepath))
{
seq = (Sequence)parser.ParseOne(reader);
}
Assert.IsNotNull(seq);
Assert.AreEqual(expectedSequence, seq.ToString());
Assert.AreEqual(expectedSequence.Length, seq.EncodedValues.Length);
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
Assert.AreEqual("gi|186972391|gb|ACC99454.1| maturase K [Scaphosepalum rapax]", seq.ID);
seq = (Sequence)parser.ParseOne(filepath);
Assert.IsNotNull(seq);
Assert.AreEqual(expectedSequence, seq.ToString());
Assert.AreEqual(expectedSequence.Length, seq.EncodedValues.Length);
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
Assert.AreEqual("gi|186972391|gb|ACC99454.1| maturase K [Scaphosepalum rapax]", seq.ID);
}
finally
{
if (parser != null)
{
parser.Dispose();
}
}
}
public void AllEditableScenarios()
{
string filepathOriginal = @"TestUtils\Fasta\5_sequences.fasta";
Assert.IsTrue(File.Exists(filepathOriginal));
FastaParser fastaParser = null;
try
{
fastaParser = new FastaParser();
IList <ISequence> sequences;
string[] expectedSequences = new string[] {
"KRIPKSQNLRSIHSIFPFLEDKLSHLN",
"LNIPSLITLNKSIYVFSKRKKRLSGFLHN",
"HEAGAWGHEEHEAGAWGHEEHEAGAWGHEE",
"PAWHEAEPAWHEAEPAWHEAEPAWHEAEPAWHEAE",
"CGGUCCCGCGGUCCCGCGGUCCCGCGGUCCCG"
};
fastaParser.EnforceDataVirtualization = true;
sequences = fastaParser.Parse(filepathOriginal, true);
int sequenceCount = sequences.Count;
for (int i = 0; i < sequenceCount; i++)
{
Sequence actualSequence = sequences[i] as Sequence;
actualSequence.IsReadOnly = false;
ISequenceItem item = actualSequence[1];
actualSequence.Add(item);
expectedSequences[i] += item.Symbol;
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Remove(item);
int indexOfItem = expectedSequences[i].IndexOf(item.Symbol);
expectedSequences[i] = expectedSequences[i].Remove(indexOfItem, 1);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.RemoveAt(0);
expectedSequences[i] = expectedSequences[i].Remove(0, 1);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.RemoveRange(2, 5);
expectedSequences[i] = expectedSequences[i].Remove(2, 5);
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Replace(0, 'C');
expectedSequences[i] = expectedSequences[i].Remove(0, 1);
expectedSequences[i] = expectedSequences[i].Insert(0, "C");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.ReplaceRange(3, "GG");
expectedSequences[i] = expectedSequences[i].Remove(3, 2);
expectedSequences[i] = expectedSequences[i].Insert(3, "GG");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.Insert(3, item);
expectedSequences[i] = expectedSequences[i].Insert(3, item.Symbol.ToString());
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
actualSequence.InsertRange(2, "CC");
expectedSequences[i] = expectedSequences[i].Insert(2, "CC");
Assert.AreEqual(expectedSequences[i], actualSequence.ToString());
bool actualContainsValue = actualSequence.Contains(actualSequence[3]);
bool expectedContainsValue = expectedSequences[i].Contains(actualSequence[3].Symbol.ToString());
Assert.AreEqual(actualContainsValue, expectedContainsValue);
}
}
finally
{
if (fastaParser != null)
{
fastaParser.Dispose();
}
}
}
public void FastaFormatter()
{
// Test with FASTA file from Simon
string filepathOriginal = @"TestUtils\FASTA\NC_005213.ffn";
Assert.IsTrue(File.Exists(filepathOriginal));
FastaParser parser = null;
try
{
parser = new FastaParser();
FastaFormatter formatter = new FastaFormatter();
// Read the original file
IList <ISequence> seqsOriginal = null;
parser = new FastaParser();
seqsOriginal = parser.Parse(filepathOriginal);
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
string filepathTmp = Path.GetTempFileName();
using (TextWriter writer = new StreamWriter(filepathTmp))
{
foreach (Sequence s in seqsOriginal)
{
formatter.Format(s, writer);
}
}
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
parser = new FastaParser();
seqsNew = parser.Parse(filepathTmp);
Assert.IsNotNull(seqsOriginal);
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
int i;
for (i = 0; i < countOriginal; i++)
{
Assert.AreEqual(seqsOriginal[i].ID, seqsNew[i].ID);
string orgSeq = seqsOriginal[i].ToString();
string newSeq = seqsNew[i].ToString();
Assert.AreEqual(orgSeq, newSeq);
}
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
File.Delete(filepathTmp);
}
finally
{
if (parser != null)
{
parser.Dispose();
}
}
}