public double GetDeltaScore(SQTScan2 scn, bool training)
{
double primaryScoreFirstMatch = scn.Matches[0].PrimaryScore;
double deltaScore = -1;
//Now find the same peptide with a different fosfosite asignment
//Not cleaning appropriately
string pepSeq = PatternTools.pTools.CleanPeptide(scn.Matches[0].IDs[0].PeptideSequence, true);
List <PatternTools.SQTParser2.Match> matches = scn.Matches.FindAll(a => PatternTools.pTools.CleanPeptide(a.IDs[0].PeptideSequence, true).Equals(pepSeq) && a.PrimaryRank > 1);
double second = -1;
if (matches.Count > 0)
{
second = matches[0].PrimaryScore;
}
else
{
//Lets get the greatest delta
if (training)
{
return(double.NegativeInfinity);
}
else
{
scn.Matches.Sort((a, b) => a.PrimaryRank.CompareTo(b.PrimaryRank));
second = scn.Matches.Last().PrimaryScore;
}
}
if (primaryScoreFirstMatch - second == 0)
{
return(double.NegativeInfinity);
}
if (Log)
{
deltaScore = Math.Log(primaryScoreFirstMatch - second);
}
else
{
deltaScore = (primaryScoreFirstMatch - second);
}
return(deltaScore);
}
public double RetrievePValueForScanNumber(int scanNo, double xdPrime)
{
SQTScan2 thisSQT = scans.Find(a => a.ScanNumber == scanNo);
if (thisSQT == null)
{
return(-1);
}
else
{
double xdscore = GetDeltaScore(thisSQT, false);
return(ProbabilityGaussianIntersect(xdPrime, xdscore));
}
}
public XDScore(List <string> SQTFiles, bool log)
{
Log = log;
scans = Parse(SQTFiles);
int totalScans = scans.Count;
//Now select only those scans of which the first peptide is a phosphp
int scansRemoved = scans.RemoveAll(a => a.Matches.Count == 0);
SQTScan2 theS = scans.Find(a => a.ScanNumber == 14202);
scansRemoved += scans.RemoveAll(a => !a.Matches[0].PeptideSequence.Contains("79"));
Console.WriteLine("Scans removed for not being fosfo peptides = " + scansRemoved);
int scansRemovedDelta0 = scans.RemoveAll(a => GetDeltaScore(a, true) == double.NegativeInfinity);
Console.WriteLine("Scans removed for Delta 0 or not having the isobaric counterpart = " + scansRemovedDelta0);
Console.WriteLine("Scans removed = " + (scansRemoved + scansRemovedDelta0) + "/" + totalScans);
}
static void Main(string[] args)
{
// Generate DTA
string dtaDir = @"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\out";
string inputSQT = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\20140410_JF_HAP50mmmS2.sqt";
string inputMS2 = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\20140410_jf_hap50mmms2.ms2";
if (true) //Remove MSMS from a file
{
int targetNoSpectra = 9917;
List <MSLight> theMS = PatternTools.MSParserLight.ParserLight.ParseLightMS2(inputMS2);
string outputMS2 = @"C:\Users\pcarvalho\Desktop\Colaborations\Juli_fosfo\DTA\Removed3_20140410_jf_hap50mmms2.ms2";
while (theMS.Count > targetNoSpectra)
{
int scnRemove = PatternTools.pTools.getRandomNumber(theMS.Count - 1);
theMS.RemoveAt(scnRemove);
}
PatternTools.MSParser.MSPrinter.PrintMSListToFile(theMS, outputMS2, "", MSFileFormat.ms2);
Console.WriteLine("Done!");
}
//Generate a side by side table of XDScores and AScores
if (false) //Generate a side by side table of XDScores and AScores
{
XDScore.XDScore xdScore = new XDScore.XDScore(new List <string>()
{
inputSQT
}, true);
SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> theSQT = sqtParser.Parse(inputSQT);
//Parse the aScore File
StreamReader sr = new StreamReader(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\AllResults.txt");
string line;
StreamWriter sw = new StreamWriter(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\AScoreXDScoreGoodScores.txt");
while ((line = sr.ReadLine()) != null)
{
string[] cols = Regex.Split(line, "[-|\t]");
double aScore = double.Parse(cols[2]);
int scanNo = int.Parse(cols[0]);
SQTScan2 theScan = theSQT.Find(a => a.ScanNumber == scanNo);
if (theScan.Matches[0].PrimaryScore > 2 && theScan.ChargeState == 2)
{
double xd = xdScore.GetDeltaScore(theScan, false);
sw.WriteLine(scanNo + "\t" + aScore + "\t" + xd);
}
}
sr.Close();
sw.Close();
}
if (false)
{
SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> myScans = sqtParser.Parse(inputSQT);
List <MSLight> theMS2 = PatternTools.MSParserLight.ParserLight.ParseLightMS2(inputMS2);
myScans.RemoveAll(a => a.Matches.Count == 0);
myScans.RemoveAll(a => !a.Matches[0].PeptideSequence.Contains("79"));
foreach (SQTScan2 scn in myScans)
{
try
{
Console.Write(".");
MSLight thems = theMS2.Find(a => a.ScanNumber == (int)scn.ScanNumber);
string pepSeq = scn.Matches[0].PeptideSequence;
pepSeq = Regex.Replace(pepSeq, @"\(\+79\.966300\)", "Z");
StreamWriter sw = new StreamWriter(dtaDir + "/" + scn.ScanNumber + "-" + pepSeq + ".dta");
sw.WriteLine(thems.MHPrecursor[0] + " " + thems.Zs[0].ToString());
foreach (Ion i in thems.Ions)
{
sw.WriteLine(i.MZ + " " + i.Intensity);
}
sw.Close();
} catch
{
Console.Write("P");
}
}
}
if (false)
{
DirectoryInfo di = new DirectoryInfo(dtaDir);
FileInfo[] theFiles = di.GetFiles("*.dta");
StreamWriter sw = new StreamWriter(@"C:\Users\pcarvalho\Desktop\Juli_fosfo\DTA\result.txt");
foreach (FileInfo fi in theFiles)
{
// Read file data
FileStream fs = new FileStream(fi.FullName, FileMode.Open, FileAccess.Read);
byte[] data = new byte[fs.Length];
fs.Read(data, 0, data.Length);
fs.Close();
// Generate post objects
Dictionary <string, object> postParameters = new Dictionary <string, object>();
postParameters.Add("fileformat", "txt");
postParameters.Add("userfile", new FormUpload.FileParameter(data, fi.Name, "application/msword"));
postParameters.Add("mods", "1"); //Cystein
postParameters.Add("MAX_FILE_SIZE", "40000");
string [] cols = Regex.Split(fi.Name, "[-|.]");
string pepS = Regex.Replace(cols[1], "Z", "*");
postParameters.Add("sequence", pepS);
postParameters.Add("submit", "Calculate Ascore");
HttpWebResponse webResponse = FormUpload.MultipartFormDataPost(@"http://ascore.med.harvard.edu/trim/trim-single.php", "PhosphoPeptide", postParameters);
// Process response
StreamReader responseReader = new StreamReader(webResponse.GetResponseStream());
string fullResponse = responseReader.ReadToEnd();
webResponse.Close();
string[] cols2 = Regex.Split(fullResponse, "\n");
Regex getNo = new Regex("[0-9]+.[0-9]+");
try
{
foreach (var m in getNo.Matches(cols2[39]))
{
sw.WriteLine(fi.Name + "\t" + m.ToString());
Console.WriteLine(m.ToString());
sw.Flush();
}
}
catch { Console.Write("f"); }
fi.Delete();
}
sw.Close();
}
if (false)
{
// Read file data
string file = @"C:\Users\pcarvalho\Desktop\Juli_fosfo\ToMSAorNotToMSA\test.txt";
FileStream fs = new FileStream(file, FileMode.Open, FileAccess.Read);
byte[] data = new byte[fs.Length];
fs.Read(data, 0, data.Length);
fs.Close();
// Generate post objects
Dictionary <string, object> postParameters = new Dictionary <string, object>();
//postParameters.Add("fileformat", "txt");
postParameters.Add("userfile", new FormUpload.FileParameter(data, file, "application/msword"));
postParameters.Add("mods", "1"); //Cystein
postParameters.Add("MAX_FILE_SIZE", "40000");
postParameters.Add("sequence", "IEDVGS*DEEDDSGK");
postParameters.Add("submit", "Calculate Ascore");
HttpWebResponse webResponse = FormUpload.MultipartFormDataPost(@"http://ascore.med.harvard.edu/trim/trim-single.php", "PhosphoPeptide", postParameters);
// Process response
StreamReader responseReader = new StreamReader(webResponse.GetResponseStream());
string fullResponse = responseReader.ReadToEnd();
webResponse.Close();
string[] cols = Regex.Split(fullResponse, "\n");
Regex getNo = new Regex("[0-9]+.[0-9]+");
foreach (var m in getNo.Matches(cols[39]))
{
Console.WriteLine(m.ToString());
}
Console.WriteLine("Done");
}
}
