public override IEnumerable <string> Process(string filename)
{
CensusResultFormat crFormat = new CensusResultFormat(false);
CensusResult cr = crFormat.ReadFromFile(filename);
cr.Recalculate();
CensusResult result = new CensusResult();
result.Headers.AddRange(cr.Headers);
foreach (CensusProteinItem cpi in cr.Proteins)
{
if (cpi.PeptideNumber >= uniqueCount)
{
result.Proteins.Add(cpi);
}
}
string resultFilename = FileUtils.ChangeExtension(filename, "." + uniqueCount + new FileInfo(filename).Extension);
crFormat.WriteToFile(resultFilename, result);
return(new[] { resultFilename });
}
public void Test()
{
CensusResult cr;
cr = new CensusResultFormat(true).ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/census-g1-out.txt");
Assert.AreEqual(3, cr.Proteins.Count);
Assert.AreEqual(271, cr.Proteins[0].Peptides.Count);
cr = new CensusResultFormat(false).ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/census-g1-out.txt");
Assert.AreEqual(2, cr.Proteins.Count);
}
public void Test()
{
CensusResult cr;
cr = new CensusResultFormat(true).ReadFromFile(@"../../../data/census-g1-out.txt");
Assert.AreEqual(3, cr.Proteins.Count);
Assert.AreEqual(271, cr.Proteins[0].Peptides.Count);
cr = new CensusResultFormat(false).ReadFromFile(@"../../../data/census-g1-out.txt");
Assert.AreEqual(2, cr.Proteins.Count);
}
public override IEnumerable <string> Process(string targetFilename)
{
Dictionary <string, List <CensusPeptideItem> > peptideMap = new Dictionary <string, List <CensusPeptideItem> >();
CensusResultFormat crf = new CensusResultFormat(true, isLabelFree);
Progress.SetRange(1, sourceFilenames.Length + 1);
for (int i = 0; i < sourceFilenames.Length; i++)
{
string f = sourceFilenames[i];
Progress.SetMessage("Reading from " + f + "...");
Progress.SetPosition(i + 1);
List <CensusPeptideItem> peptides = crf.ReadPeptides(f);
foreach (CensusPeptideItem cpi in peptides)
{
if (!peptideMap.ContainsKey(cpi.Sequence))
{
peptideMap[cpi.Sequence] = new List <CensusPeptideItem>();
}
peptideMap[cpi.Sequence].Add(cpi);
}
}
List <string> sequences = new List <string>(peptideMap.Keys);
sequences.Sort(delegate(string seq1, string seq2)
{
int result = peptideMap[seq2].Count - peptideMap[seq1].Count;
if (0 == result)
{
result = seq1.CompareTo(seq2);
}
return(result);
});
Progress.SetMessage("Writing to " + targetFilename + "...");
using (var sw = new StreamWriter(targetFilename))
{
sw.WriteLine("PLINE\tSEQUENCE\tS_INT/R_INT\tINT(S)\tINT(R)");
sw.WriteLine(crf.PeptideFormat.GetHeader());
foreach (string seq in sequences)
{
List <CensusPeptideItem> items = peptideMap[seq];
double sInt = 0.0;
double rInt = 0.0;
foreach (CensusPeptideItem item in items)
{
sInt += item.SampleIntensity;
rInt += item.ReferenceIntensity;
}
double ratio;
if (rInt != 0.0)
{
ratio = sInt / rInt;
}
else
{
ratio = 0.0;
}
sw.WriteLine(MyConvert.Format("P\t{0}\t{1:0.00}\t{2:0.0}\t{3:0.0}", seq, ratio, sInt, rInt));
foreach (CensusPeptideItem item in items)
{
sw.WriteLine(crf.PeptideFormat.GetString(item));
}
}
}
Progress.SetMessage("Write to " + targetFilename + " finished.");
Progress.SetPosition(sourceFilenames.Length + 1);
return(new[] { targetFilename });
}
public override IEnumerable <string> Process(string targetFilename)
{
Dictionary <string, CensusProteinItem> proteinMap = new Dictionary <string, CensusProteinItem>();
CensusResultFormat crf = new CensusResultFormat(true, isLabelFree);
Progress.SetRange(1, sourceFilenames.Length + 1);
for (int i = 0; i < sourceFilenames.Length; i++)
{
string f = sourceFilenames[i];
Progress.SetMessage("Reading from " + f + "...");
Progress.SetPosition(i + 1);
CensusResult cr = crf.ReadFromFile(f);
foreach (CensusProteinItem cpi in cr.Proteins)
{
if (!proteinMap.ContainsKey(cpi.Locus))
{
proteinMap[cpi.Locus] = cpi;
}
else
{
proteinMap[cpi.Locus].Peptides.AddRange(cpi.Peptides);
}
}
}
List <CensusProteinItem> proteins = new List <CensusProteinItem>(proteinMap.Values);
foreach (CensusProteinItem cpi in proteins)
{
cpi.Recalculate();
cpi.Peptides.Sort(delegate(CensusPeptideItem a, CensusPeptideItem b)
{
int result = a.Sequence.CompareTo(b.Sequence);
if (0 == result)
{
result = a.Filename.Charge.CompareTo(b.Filename.Charge);
}
if (0 == result)
{
result = a.Filename.LongFileName.CompareTo(b.Filename.LongFileName);
}
return(result);
});
}
proteins.Sort(delegate(CensusProteinItem a, CensusProteinItem b)
{
int result = b.PeptideNumber - a.PeptideNumber;
if (0 == result)
{
result = b.SpectraCount - a.SpectraCount;
}
if (0 == result)
{
result = a.Locus.CompareTo(b.Locus);
}
return(result);
});
CensusResult target = new CensusResult();
target.Headers = CensusUtils.ReadHeaders(sourceFilenames[0]);
target.Proteins = proteins;
Progress.SetMessage("Writing to " + targetFilename + "...");
crf.WriteToFile(targetFilename, target);
Progress.SetMessage("Write to " + targetFilename + " finished.");
Progress.SetPosition(sourceFilenames.Length + 1);
return(new[] { targetFilename });
}