public void FastaFormatterValidateFormat()
{
FastaFormatter formatter = new FastaFormatter();
// Gets the actual sequence and the alphabet from the Xml
string actualSequence = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
string alpName = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: Validating with Sequence '{0}' and Alphabet '{1}'.",
actualSequence, alpName));
Sequence seqOriginal = new Sequence(Utility.GetAlphabet(alpName),
actualSequence);
Assert.IsNotNull(seqOriginal);
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: Creating the Temp file '{0}'.", Constants.FastaTempFileName));
formatter.Format(seqOriginal, Constants.FastaTempFileName);
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
FastaParser parser = new FastaParser();
seqsNew = parser.Parse(Constants.FastaTempFileName);
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
// Now compare the sequences.
int countNew = seqsNew.Count();
Assert.AreEqual(1, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(seqOriginal.ID, seqsNew[0].ID);
string orgSeq = seqOriginal.ToString();
string newSeq = seqsNew[0].ToString();
Assert.AreEqual(orgSeq, newSeq);
Console.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method and is as expected.",
seqsNew[0].ToString()));
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method.",
seqsNew[0].ToString()));
// 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(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
public void FastaFormatter()
{
// Test with FASTA file from Simon
string filepathOriginal = @"testdata\FASTA\NC_005213.ffn";
Assert.IsTrue(File.Exists(filepathOriginal));
FastaParser 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);
}
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
if ((Sequence == null) && (SequenceList != null))
{
FastaFormatter formatter = new FastaFormatter();
formatter.Format(SequenceList, OutputFile);
}
else if ((Sequence != null) && (SequenceList == null))
{
FastaFormatter formatter = new FastaFormatter();
formatter.Format(Sequence, OutputFile);
}
else if ((Sequence != null) && (SequenceList != null))
{
SequenceList.Add(Sequence);
FastaFormatter formatter = new FastaFormatter();
formatter.Format(SequenceList, OutputFile);
SequenceList.Remove(Sequence);
}
return(ActivityExecutionStatus.Closed);
}
public void FastaFormatterWithParseValidateFormat()
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: File Exists in the Path '{0}'.", filePath));
FastaParser parser = new FastaParser();
FastaFormatter formatter = new FastaFormatter();
// Read the original file
IList <ISequence> seqsOriginal = null;
parser = new FastaParser();
seqsOriginal = parser.Parse(filePath);
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: Creating the Temp file '{0}'.",
Constants.FastaTempFileName));
using (TextWriter writer = new StreamWriter(Constants.FastaTempFileName))
{
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(Constants.FastaTempFileName);
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
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);
Console.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method and is as expected.",
seqsNew[i].ID));
ApplicationLog.WriteLine(string.Format(null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method.",
seqsNew[i].ID));
}
// 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(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
/// <summary>
/// Does the logic behind the sequence simulation
/// </summary>
internal void DoSimulation(SimulatorWindow window, string outputFileName, SimulatorSettings settings)
{
FileInfo file = new FileInfo(outputFileName);
if (!file.Directory.Exists)
{
throw new ArgumentException("Could not write to the output directory for " + outputFileName);
}
if (settings.OutputSequenceCount <= 0)
{
throw new ArgumentException("'Max Output Sequences Per File' should be greater than zero.");
}
if (settings.SequenceLength <= 0)
{
throw new ArgumentException("'Mean Output Length' should be greater than zero.");
}
string filePrefix;
if (String.IsNullOrEmpty(file.Extension))
{
filePrefix = file.FullName;
}
else
{
filePrefix = file.FullName.Substring(0, file.FullName.IndexOf(file.Extension));
}
string filePostfix = "_{0}.fa";
int seqCount = (settings.DepthOfCoverage * Sequence.Count) / settings.SequenceLength;
int fileCount = seqCount / settings.OutputSequenceCount;
if (seqCount % settings.OutputSequenceCount != 0)
{
fileCount++;
}
window.UpdateSimulationStats(seqCount, fileCount);
if (results == null)
{
results = new List <ISequence>();
}
else
{
results.Clear();
}
int fileIndex = 1;
FastaFormatter formatter = new FastaFormatter();
for (int i = 0; i < seqCount; i++)
{
results.Add(CreateSubsequence(settings, i));
if (results.Count >= settings.OutputSequenceCount)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
results.Clear();
}
}
if (results.Count > 0)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
}
window.NotifySimulationComplete(formatter.Name);
}