public static List <SQTScan2> CallComet(cometParams cp, string searchFile)
{
FileInfo fi = new FileInfo(searchFile);
string cpf = CometWrapper.GenerateTheSearchParamsString(cp);
//Write the comet result to the directory
StreamWriter sw = new StreamWriter(fi.DirectoryName + "/" + "comet.params");
sw.WriteLine(cpf);
sw.Close();
string cometCall = CometWrapper.GetCometPath();
CometWrapper.CallComet(fi, cometCall, cpf);
string sqtFileTmp = fi.Name.Replace(fi.Extension, ".sqt");
string sqtFile = fi.Directory.FullName + "/" + sqtFileTmp;
PatternTools.SQTParser2.SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> theResult = sqtParser.Parse(sqtFile);
int removedNoMatch = theResult.RemoveAll(a => a.Matches.Count == 0);
return(theResult);
}
private static List <SQTScan2> Parse(List <string> SQTFiles)
{
List <SQTScan2> scans = new List <SQTScan2>();
//Parse the files
foreach (string file in SQTFiles)
{
Console.WriteLine("Parsing file " + file);
SQTParser2 sqtParser2 = new SQTParser2();
scans.AddRange(sqtParser2.Parse(file, 50));
Console.Write(".");
}
return(scans);
}
static void Main()
{
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
//Parse AScore result
string inputAscore = @"C:\Users\pcarvalho\Desktop\SyntheticLib\10\phosphoRS_HCD_10.csv";
string inputXDScore = @"C:\Users\pcarvalho\Desktop\SyntheticLib\10\10.sqt";
List <PhosphoAnalysis> phosfo = new List <PhosphoAnalysis>();
Console.WriteLine("Parsing PhosphoScores");
string line;
StreamReader sr = new StreamReader(inputAscore);
Regex pSplitter = new Regex(Regex.Escape("."));
int counter = 0;
while ((line = sr.ReadLine()) != null)
{
counter++;
if (counter <= 1)
{
continue;
}
string[] cols = Regex.Split(line, ",");
string confidence = cols[0];
string sequence = cols[1];
int scanNo = int.Parse(cols[25]);
PhosphoAnalysis p = new PhosphoAnalysis(sequence, scanNo, confidence, cols[12]);
phosfo.Add(p);
}
//Remove all non-fosfo hits
int removed = phosfo.RemoveAll(a => !Regex.IsMatch(a.Sequence, "[a-z]"));
sr.Close();
Console.WriteLine("Parsing sqt file");
SQTParser2 sqtParser2 = new SQTParser2();
List <SQTScan2> sqts = sqtParser2.Parse(inputXDScore, 50);
List <double> goodScores = new List <double>();
List <double> badScores = new List <double>();
foreach (PhosphoAnalysis p in phosfo)
{
int index = sqts.FindIndex(a => a.ScanNumber == p.ScanNo);
if (index > -1)
{
double xdScore = XDScore.XDScore.GetDeltaScore(sqts[index], true);
if (!double.IsNegativeInfinity(xdScore))
{
if (p.Confidence.Equals("High") || p.Confidence.Equals("Medium"))
{
int noSites = Regex.Matches(p.Sequence, "[a-z]").Count;
int NoConfidenceAssignments = Regex.Matches(p.FosfoScores, "100").Count;
if (NoConfidenceAssignments == noSites)
{
goodScores.Add(xdScore);
}
else
{
badScores.Add(xdScore);
}
}
}
}
}
double avgGood = goodScores.Average();
double avgBad = badScores.Average();
double goodSTD = PatternTools.pTools.Stdev(goodScores, true);
double badSTD = PatternTools.pTools.Stdev(badScores, true);
double bothTails;
double leftTail;
double rightTail;
alglib.studentttest2(goodScores.ToArray(), goodScores.Count, badScores.ToArray(), badScores.Count, out bothTails, out leftTail, out rightTail);
Console.WriteLine("Done!");
//Application.Run(new Form1());
}
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");
}
}
