public static List <DetectabilityEntry> ReadFromDirectory(string dir)
{
List <string> peptides = FileUtils.ReadFile(dir + "\\peppro.txt", true);
List <string> detectability = FileUtils.ReadFile(dir + "\\detectabilityres.txt", true);
List <string> positions = FileUtils.ReadFile(dir + "\\positions.txt", true);
var deList = new List <DetectabilityEntry>();
for (int iPep = 0; iPep < peptides.Count; iPep++)
{
string pep = peptides[iPep];
string[] pp = Regex.Split(pep, "\\s+");
if (pp.Length < 2)
{
throw new Exception("Wrong peptide/protein line : " + pep);
}
double d = MyConvert.ToDouble(detectability[iPep].Trim());
int position = int.Parse(positions[iPep].Trim());
var de = new DetectabilityEntry();
de.Protein = pp[1];
de.Peptide = pp[0];
de.Detectability = d;
de.Position = position;
deList.Add(de);
}
return(deList);
}
public void TestReadFromFile()
{
List <DetectabilityEntry> deList = DetectabilityEntry.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/IPI00206171.detectability");
Assert.AreEqual(135, deList.Count);
Assert.AreEqual("APHWTSASLTEAAAHPHSPEMK", deList[1].Peptide);
Assert.AreEqual("IPI:IPI00206171.1|", deList[1].Protein);
Assert.AreEqual(0.4483, deList[1].Detectability, 0.0001);
Assert.AreEqual(10, deList[1].Position);
}
public IEnumerable <string> Process(string fastaFilename)
{
var fi = new FileInfo(fastaFilename).FullName;
SystemUtils.Execute(this.predictorExeFilePath, "-F \"" + fi + "\"");
DirectoryInfo di = new FileInfo(fastaFilename).Directory;
List <DetectabilityEntry> deList = DetectabilityEntry.ReadFromDirectory(di.FullName);
string detectabilityFilename = FileUtils.ChangeExtension(fastaFilename, "detectability");
DetectabilityEntry.WriteToFile(detectabilityFilename, deList);
DetectabilityEntry.DeleteFromDirectory(di.FullName);
return(new[] { detectabilityFilename });
}
public static List <DetectabilityEntry> ReadFromFile(string filename)
{
var result = new List <DetectabilityEntry>();
List <string> lines = FileUtils.ReadFile(filename, true);
for (int i = 1; i < lines.Count; i++)
{
String[] parts = Regex.Split(lines[i], "\t");
if (4 == parts.Length)
{
var de = new DetectabilityEntry();
de.Protein = parts[0];
de.Peptide = parts[1];
de.Detectability = MyConvert.ToDouble(parts[2].Trim());
de.Position = int.Parse(parts[3].Trim());
result.Add(de);
}
}
return(result);
}
