public override GenericFastqInputs perform(GenericFastqInputs inputs)
{
StreamWriter writer;
String extension = Path.GetExtension(inputs.SaveFileName);
String fileName = Path.GetFileNameWithoutExtension(inputs.SaveFileName);
String[] part = Path.GetFileNameWithoutExtension(inputs.FastqFile.getFileName()).Split('_');
String directory = Path.GetDirectoryName(inputs.SaveFileName);
String number = part[part.Length - 1];
String FullName = String.Format(@"{0}{1}{2}_{3}{4}", directory, Path.DirectorySeparatorChar, fileName, number, extension);
string COMMA_DELIMITER = ",";
string[] output;
IFqFile fqFile = inputs.FastqFile;
writer = new StreamWriter(FullName);
output = new string[] { "Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
Console.WriteLine("Saving CSV TO: {0}", FullName);
writer.Flush();
writer.Close();
return(inputs);
}
/// <summary>
/// Outputs the data for a FastqFile to the console, keeping code clean in other classes
/// </summary>
/// <param name="fqFile"></param>
public void OutputFileDataToConsole(IFqFile fqFile)
{
Console.WriteLine("Joint Test Results Completed on " + fqFile.getTotalNucleotides() + " Nucleotides");
Console.WriteLine("Joint Test Results: " + fqFile.getGCount() + "G " + Math.Round(fqFile.gContents(), 2) + "% " + fqFile.getCCount() + "C " + Math.Round(fqFile.cContents(), 2) + " %");
Console.WriteLine("Misreads: " + fqFile.getNCount());
Console.WriteLine("Nucleotides Cleaned: {0}", fqFile.getNucleotidesCleaned());
Console.WriteLine("Distribution: " + fqFile.getDistribution().Count);
Console.WriteLine("Stats Performed");
for (int i = 0; i < 20; i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
Console.WriteLine("-- -Stats for Sequence " + (i + 1) + ": LB: {0} 1Q: {1} Median: {2} Mean: {3} 3Q: {4} UB: {5}", fqSeq.getLowerThreshold(), fqSeq.getFirstQuartile(), fqSeq.getMedian(), Math.Round(fqSeq.getMean(), 2), fqSeq.getThirdQuartile(), fqSeq.getUpperThreshold());
}
for (int i = 0; i < fqFile.getDistribution().Count; i++)
{
Console.WriteLine("---> Quality Score: {0} Count: {1}", i, fqFile.getDistribution()[i]);
}
for (int i = 0; i < fqFile.GetPerBaseStatisticsArray().Length; i++)
{
Console.WriteLine("===> BaseStatistic: {0} \tCount: {1} LB: {2} 1Q: {3} Median: {4} Mean: {5} 3Q: {6} UB: {7}", i, fqFile.GetPerBaseStatisticsArray()[i].BaseCount, fqFile.GetPerBaseStatisticsArray()[i].LowerThreshold, fqFile.GetPerBaseStatisticsArray()[i].FirstQuartile, fqFile.GetPerBaseStatisticsArray()[i].Median, fqFile.GetPerBaseStatisticsArray()[i].Mean, fqFile.GetPerBaseStatisticsArray()[i].ThirdQuartile, fqFile.GetPerBaseStatisticsArray()[i].UpperThreshold);
}
}
private void SaveCSVAction(IFqFile fq, String fileName)
{
StreamWriter writer;
string COMMA_DELIMITER = ",";
string[] output;
try
{
writer = new StreamWriter(@fileName);
saveWorker.ReportProgress(30, "[CREATING CSV FORMAT]");
output = new string[] { "Sequence Index", "Header", "Total Nucleotides", "G Count", "C Count", "Misread Count", "Lower Threshold", "First Quartile",
"Median", "Mean", "Third Quartile", "Upper Threshold" };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
for (int i = 0; i < fqFile.getFastqArraySize(); i++)
{
FqSequence fqSeq = fqFile.getFastqSequenceByPosition(i);
output = new string[] { fqSeq.getSeqIndex().ToString(), fqSeq.getSequenceHeader(), fqSeq.getFastqSeqSize().ToString(), fqSeq.getGCount().ToString(),
fqSeq.getCCount().ToString(), fqSeq.getNCount().ToString(), fqSeq.getLowerThreshold().ToString(),
fqSeq.getFirstQuartile().ToString(), fqSeq.getMedian().ToString(), fqSeq.getMean().ToString(),
fqSeq.getThirdQuartile().ToString(), fqSeq.getUpperThreshold().ToString(),
fqSeq.createSequenceString(fqFile.getMap()) };
writer.WriteLine(string.Join(COMMA_DELIMITER, output));
}
saveWorker.ReportProgress(100, "[FASTQ FORMAT CREATED]");
writer.Flush();
writer.Close();
}
catch (IOException exception)
{
Console.WriteLine(exception.ToString());
UserResponse.ErrorResponse(exception.ToString());
}
}
