/// <summary>
/// Write out a set of contigs to the given file.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="contig">Contig to write</param>
/// <param name="filename">Filename</param>
public static void Format(this XsvContigFormatter formatter, Contig contig, string filename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (contig == null)
{
throw new ArgumentNullException("contig");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
using (var fs = File.Create(filename))
{
formatter.Write(fs, contig);
}
}
/// <summary>
/// Write out a set of contigs to the given file.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="contig">Contig to write</param>
public static void Format(this XsvContigFormatter formatter, Contig contig)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (contig == null)
{
throw new ArgumentNullException("contig");
}
var fs = ParserFormatterExtensions <ISequenceFormatter> .GetOpenStream(formatter, true);
if (fs != null)
{
formatter.Write(fs, contig);
}
else
{
throw new Exception("You must open a formatter before calling Write.");
}
}
public void XsvSparseContigFormatterWrite()
{
// Gets the expected sequence from the Xml
string filePathObj = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Xsv Contig Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
Contig expectedContig;
XsvContigParser parserObj = new XsvContigParser(Alphabets.DNA, ',', '#');
Contig contig = parserObj.ParseContig(filePathObj);
string seqId = contig.Sequences.Aggregate(string.Empty, (current, seq) => current + (seq.Sequence.ID + ","));
// Write Xsv file.
XsvContigFormatter formatObj = new XsvContigFormatter(',', '#');
formatObj.Format(contig, Constants.XsvTempFileName);
XsvContigParser parserObjNew = new XsvContigParser(Alphabets.DNA, ',', '#');
expectedContig = parserObjNew.ParseContig(Constants.XsvTempFileName);
string expectedseqId = expectedContig.Sequences.Aggregate(string.Empty, (current, seq) => current + (seq.Sequence.ID + ","));
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(contig.Length, expectedContig.Length);
Assert.AreEqual(contig.Consensus.Count, expectedContig.Consensus.Count);
Assert.AreEqual(contig.Consensus.ID, expectedContig.Consensus.ID);
Assert.AreEqual(contig.Sequences.Count, expectedContig.Sequences.Count);
Assert.AreEqual(seqId.Length, expectedseqId.Length);
Assert.AreEqual(seqId, expectedseqId);
File.Delete(Constants.XsvTempFileName);
ApplicationLog.WriteLine("Successfully validated the Write Xsv file");
}
