public void TestGffForManyFiles()
{
// parser and formatter will be used for all files in input dir
GffFormatter formatter = new GffFormatter();
// iterate through the files in input dir, parsing and formatting each; write results
// to log file
DirectoryInfo inputDirInfo = new DirectoryInfo(_gffDataPath);
foreach (FileInfo fileInfo in inputDirInfo.GetFiles("*.gff"))
{
ApplicationLog.WriteLine("Parsing file {0}...{1}", fileInfo.FullName, Environment.NewLine);
ISequenceParser parser = new GffParser();
foreach (ISequence sequence in parser.Parse(fileInfo.FullName))
{
// don't do anything with it; just make sure it doesn't crash
formatter.FormatString(sequence);
}
ApplicationLog.WriteLine("Parse completed successfully." + Environment.NewLine);
}
}
public void GffFormatterValidateFormatString()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleGffNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
IList<ISequence> seqs = null;
GffParser parserObj = new GffParser();
seqs = parserObj.Parse(filePath).ToList();
ISequence originalSequence = seqs[0];
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: Creating the Temp file '{0}'.", Constants.GffTempFileName));
GffFormatter formatter = new GffFormatter();
formatter.ShouldWriteSequenceData = true;
string formatString = formatter.FormatString(originalSequence);
string expectedString = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGffNodeName, Constants.FormatStringNode);
expectedString = expectedString.Replace("current-date",
DateTime.Today.ToString("yyyy-MM-dd", null));
expectedString =
expectedString.Replace("\r", "").Replace("\n", "").Replace(" ", "").Replace("\t", "").ToUpper(CultureInfo.CurrentCulture);
string modifedformatString =
formatString.Replace("\r", "").Replace("\n", "").Replace(" ", "").Replace("\t", "").ToUpper(CultureInfo.CurrentCulture);
Assert.AreEqual(modifedformatString, expectedString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: The Gff Format String '{0}' are matching with FormatString() method and is as expected.",
formatString));
// 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.GffTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
public void TestGffWhenParsingOne()
{
// parse
GffParser parser = new GffParser();
ISequence seq = parser.Parse(_singleSeqGffFilename).FirstOrDefault();
// test the non-metadata properties
Assert.AreEqual(Alphabets.DNA, seq.Alphabet);
Assert.AreEqual("NC_001133.7", seq.ID);
// just test the formatting; if that's good, the parsing was good
GffFormatter formatter = new GffFormatter();
string actual = formatter.FormatString(seq);
Assert.AreEqual(_singleSeqGffFileExpectedOutput.Replace("\r\n", Environment.NewLine), actual);
}
/// <summary>
/// General method to invalidate Argument Null exceptions generated from different methods.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Gff Parse method parameters</param>
void InvalidateGffWriteMethod(ArgumentNullExceptions method)
{
ISequence sequence=null;
List<ISequence> collection = new List<ISequence>();
string sequenceData = null;
GffFormatter gffFormatter = null;
try
{
switch (method)
{
case ArgumentNullExceptions.writeWithEmptyFile:
sequenceData = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGffDnaNodeName, Constants.ExpectedSequenceNode);
gffFormatter = new GffFormatter();
{
gffFormatter.Format(new Sequence(DnaAlphabet.Instance, sequenceData));
}
break;
case ArgumentNullExceptions.writeWithEmptySequence:
gffFormatter = new GffFormatter();
{
gffFormatter.Format(sequence);
}
break;
case ArgumentNullExceptions.FormatString:
gffFormatter = new GffFormatter();
{
gffFormatter.FormatString(sequence);
}
break;
case ArgumentNullExceptions.writeCollectionWithEmptyFile:
sequenceData = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGffDnaNodeName, Constants.ExpectedSequenceNode);
collection.Add(new Sequence(DnaAlphabet.Instance, sequenceData));
gffFormatter = new GffFormatter();
{
gffFormatter.Format(collection);
}
break;
case ArgumentNullExceptions.writeCollectionWithEmptySequence:
gffFormatter = new GffFormatter();
{
gffFormatter.Format(collection);
}
break;
default:
break;
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine("GFF P2 : Exception is validated successfully.");
}
catch (Exception)
{
ApplicationLog.WriteLine("GFF P2 : Exception is validated successfully.");
}
}
