public static void ImportMasses()
{
AminoAcidMasses();
NeoFindAmbiguity.ReadMassDictionary();
}
public static void ExportCandidates(List <NeoPsm> psms, Ms2ScanWithSpecificMass[] spectra, string path, CommonParameters commonParameters)
{
using (StreamWriter file = new StreamWriter(path + folder + @"\" + folder + "ExportedFusionCandidatesAll.txt"))
{
file.WriteLine("Scan" + '\t' + "ExperimentalMass" + '\t' + "OriginalNSequence" + '\t' + "OriginalNScore" + '\t' + "OriginalCSequence" + '\t' + "OriginalCScore" + '\t' + "SampleSequence" + '\t' + "Ambiguity" + '\t' + "ProbableType" + '\t' + "MostProbableSequenceJunctions" + '\t' + "MostProbableSequence(s)" + '\t' + "MostProbableParents" + '\t' + "AllPossibleSequenceJunctions" + '\t' + "AllPossibleSequence(s)" + '\t' + "AllPossibleParent(s)" + '\t' + "NumberOfPossibleSequences" + '\t' + "PotentialFalsePositives" + '\t' + "TotalScore");
//double progress = 0;
Parallel.ForEach(psms, new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (psm) =>
{
Ms2ScanWithSpecificMass spectrum = spectra[psm.scanNumber];
//printout the scan, the mass, the sequences with and without junctions, the number of potential sequences
string allPossibleSequences = "";
string mostProbableSequences = "";
int indexOfFirstProbableSequence = -1;
string mostProbableParents = "";
string allPossibleParents = "";
FusionCandidate.FusionType probableType = psm.fusionType;
for (int fc = 0; fc < psm.candidates.Count(); fc++)
{
FusionCandidate fusionCandidate = psm.candidates[fc]; //need fc for indexOfFirstProbableSequence
char[] tempArray = fusionCandidate.seq.ToCharArray();
//if most probable, add to all and most
if (fusionCandidate.fusionType.Equals(probableType))
{
//record sequences
if (indexOfFirstProbableSequence < 0)
{
indexOfFirstProbableSequence = fc;
}
for (int i = 0; i < tempArray.Count(); i++)
{
mostProbableSequences += tempArray[i];
allPossibleSequences += tempArray[i];
foreach (int junction in fusionCandidate.junctionIndexes)
{
if (junction == i)
{
mostProbableSequences += "-";
allPossibleSequences += "-";
}
}
}
mostProbableSequences += "|";
allPossibleSequences += "|";
//record parents
string tempParents = "";
//switch (probableType)
//{
// case FusionCandidate.FusionType.TL:
// if (fusionCandidate.translatedParents.Count == 0)
// throw new Exception();
// tempParents += GenerateParentOutput(fusionCandidate.translatedParents, new List<CisParent>(), new List<TransParent>());
// break;
// case FusionCandidate.FusionType.NC:
// case FusionCandidate.FusionType.RC:
// if (fusionCandidate.cisParents.Count == 0)
// throw new Exception();
// tempParents += GenerateParentOutput(new List<TranslatedParent>(), fusionCandidate.cisParents, new List<TransParent>());
// break;
// default: //if trans
// if (fusionCandidate.transParents.Count == 0)
// throw new Exception();
// tempParents += GenerateParentOutput(new List<TranslatedParent>(), new List<CisParent>(), fusionCandidate.transParents);
// break;
//}
mostProbableParents += tempParents;
allPossibleParents += tempParents;
}
else //not most probable, only add it to allPossibleSequences
{
//record sequences
for (int i = 0; i < tempArray.Count(); i++)
{
allPossibleSequences += tempArray[i];
if (fusionCandidate.junctionIndexes.Contains(i))
{
allPossibleSequences += "-";
}
}
allPossibleSequences += "|";
//record parents
//UNCOMMENT allPossibleParents += GenerateParentOutput(fusionCandidate.translatedParents, fusionCandidate.cisParents, fusionCandidate.transParents);
}
/* foreach(ParentInfo PI in fusionCandidate.parentInfo)
* {
* parents += PI.accession + "_" + PI.parentType.ToString() + "_" + PI.seqFound + "|";
* }*/
}
allPossibleSequences = allPossibleSequences.Substring(0, allPossibleSequences.Length - 1); //remove last "|"
mostProbableSequences = mostProbableSequences.Substring(0, mostProbableSequences.Length - 1); //remove last "|"
string ambiguity = "";
NeoFindAmbiguity.FindIons(psm.candidates[indexOfFirstProbableSequence], psm, spectrum); //this should be carried over, but it's not...
// mutableError_message += e;
bool[] foundIons = psm.candidates[indexOfFirstProbableSequence].foundIons;
char[] firstSeq = psm.candidates[indexOfFirstProbableSequence].seq.ToCharArray();
// if(foundIons.Count()==firstSeq.Count()) //prevent crashing if something went wrong
// {
bool ambiguous = false;
for (int i = 1; i < foundIons.Length; i++)
{
if (foundIons[i]) //if found
{
ambiguity += firstSeq[i - 1]; //add aa
if (ambiguous) //if it is part of an ambiguous sequence
{
ambiguity += ")";
ambiguous = false; //no longer ambiguous
}
}
else
{
if (!ambiguous)
{
ambiguous = true;
ambiguity += "(";
}
ambiguity += firstSeq[i - 1];
}
}
ambiguity += firstSeq[foundIons.Length - 1];
if (ambiguous)
{
ambiguity += ")";
}
string potentialFalsePositives = "";
//foreach (Variant v in psm.variants)
//{
// potentialFalsePositives += v.id + "_" + v.start + "-" + (v.start + v.peptideLength - 1) + "(" + v.pepSeq + ")" + v.varType + "|";
//}
if (potentialFalsePositives.Length > 0)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, potentialFalsePositives.Length - 1); //remove last |
if (potentialFalsePositives.Length > 30000)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, 30000);
}
}
//workarounds for excel. Actual limit is 32767, but that doesn't seem to work
if (mostProbableParents.Length > 30000)
{
mostProbableParents = mostProbableParents.Substring(0, 30000);
}
if (allPossibleParents.Length > 30000)
{
allPossibleParents = allPossibleParents.Substring(0, 30000);
}
int score = 0;
foreach (bool b in psm.candidates[indexOfFirstProbableSequence].foundIons)
{
if (b)
{
score++;
}
}
lock (file)
{
file.WriteLine(psm.scanNumber.ToString() + '\t' + psm.expMass.ToString() + '\t' + psm.nInfo.seq + '\t' + psm.nInfo.score + '\t' + psm.cInfo.seq + '\t' + psm.cInfo.score + '\t' + psm.candidates[indexOfFirstProbableSequence].seq + '\t' + ambiguity + '\t' + psm.fusionType.ToString() + '\t' + mostProbableSequences + '\t' + mostProbableSequences.Replace("-", "") + '\t' + mostProbableParents + '\t' + allPossibleSequences + '\t' + allPossibleSequences.Replace("-", "") + '\t' + allPossibleParents + '\t' + psm.candidates.Count().ToString() + '\t' + potentialFalsePositives + '\t' + score);
//progress++;
//this.worker.ReportProgress((int)(progress / psms.Count() * 100));
}
});
}
using (StreamWriter file = new StreamWriter(path + folder + @"\" + folder + "ExportedFusionCandidatesTL.txt"))
{
file.WriteLine("Scan" + '\t' + "ExperimentalMass" + '\t' + "OriginalNSequence" + '\t' + "OriginalNScore" + '\t' + "OriginalCSequence" + '\t' + "OriginalCScore" + '\t' + "SampleSequence" + '\t' + "Ambiguity" + '\t' + "ProbableType" + '\t' + "MostProbableSequenceJunctions" + '\t' + "MostProbableSequence(s)" + '\t' + "MostProbableParents" + '\t' + "AllPossibleSequenceJunctions" + '\t' + "AllPossibleSequence(s)" + '\t' + "AllPossibleParent(s)" + '\t' + "NumberOfPossibleSequences" + '\t' + "PotentialFalsePositives" + '\t' + "TotalScore");
Parallel.ForEach(psms, new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (psm) =>
{
if (psm.candidates.Any(x => x.fusionType == FusionCandidate.FusionType.TL))
{
Ms2ScanWithSpecificMass spectrum = spectra[psm.scanNumber];
//printout the scan, the mass, the sequences with and without junctions, the number of potential sequences
string allPossibleSequences = "";
string mostProbableSequences = "";
int indexOfFirstProbableSequence = -1;
string mostProbableParents = "";
string allPossibleParents = "";
FusionCandidate.FusionType probableType = psm.fusionType;
for (int fc = 0; fc < psm.candidates.Count(); fc++)
{
FusionCandidate fusionCandidate = psm.candidates[fc]; //need fc for indexOfFirstProbableSequence
if (fusionCandidate.fusionType != FusionCandidate.FusionType.TL)
{
continue;
}
char[] tempArray = fusionCandidate.seq.ToCharArray();
//if most probable, add to all and most
//record sequences
if (indexOfFirstProbableSequence < 0)
{
indexOfFirstProbableSequence = fc;
}
for (int i = 0; i < tempArray.Count(); i++)
{
mostProbableSequences += tempArray[i];
allPossibleSequences += tempArray[i];
foreach (int junction in fusionCandidate.junctionIndexes)
{
if (junction == i)
{
mostProbableSequences += "-";
allPossibleSequences += "-";
}
}
}
mostProbableSequences += "|";
allPossibleSequences += "|";
//record parents
string tempParents = "";
mostProbableParents += tempParents;
allPossibleParents += tempParents;
}
allPossibleSequences = allPossibleSequences.Substring(0, allPossibleSequences.Length - 1); //remove last "|"
mostProbableSequences = mostProbableSequences.Substring(0, mostProbableSequences.Length - 1); //remove last "|"
string ambiguity = "";
NeoFindAmbiguity.FindIons(psm.candidates[indexOfFirstProbableSequence], psm, spectrum); //this should be carried over, but it's not...
// mutableError_message += e;
bool[] foundIons = psm.candidates[indexOfFirstProbableSequence].foundIons;
char[] firstSeq = psm.candidates[indexOfFirstProbableSequence].seq.ToCharArray();
bool ambiguous = false;
for (int i = 1; i < foundIons.Length; i++)
{
if (foundIons[i]) //if found
{
ambiguity += firstSeq[i - 1]; //add aa
if (ambiguous) //if it is part of an ambiguous sequence
{
ambiguity += ")";
ambiguous = false; //no longer ambiguous
}
}
else
{
if (!ambiguous)
{
ambiguous = true;
ambiguity += "(";
}
ambiguity += firstSeq[i - 1];
}
}
ambiguity += firstSeq[foundIons.Length - 1];
if (ambiguous)
{
ambiguity += ")";
}
string potentialFalsePositives = "";
if (potentialFalsePositives.Length > 0)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, potentialFalsePositives.Length - 1); //remove last |
if (potentialFalsePositives.Length > 30000)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, 30000);
}
}
//workarounds for excel. Actual limit is 32767, but that doesn't seem to work
if (mostProbableParents.Length > 30000)
{
mostProbableParents = mostProbableParents.Substring(0, 30000);
}
if (allPossibleParents.Length > 30000)
{
allPossibleParents = allPossibleParents.Substring(0, 30000);
}
int score = 0;
foreach (bool b in psm.candidates[indexOfFirstProbableSequence].foundIons)
{
if (b)
{
score++;
}
}
lock (file)
{
file.WriteLine(psm.scanNumber.ToString() + '\t' + psm.expMass.ToString() + '\t' + psm.nInfo.seq + '\t' + psm.nInfo.score + '\t' + psm.cInfo.seq + '\t' + psm.cInfo.score + '\t' + psm.candidates[indexOfFirstProbableSequence].seq + '\t' + ambiguity + '\t' + psm.fusionType.ToString() + '\t' + mostProbableSequences + '\t' + mostProbableSequences.Replace("-", "") + '\t' + mostProbableParents + '\t' + allPossibleSequences + '\t' + allPossibleSequences.Replace("-", "") + '\t' + allPossibleParents + '\t' + psm.candidates.Count().ToString() + '\t' + potentialFalsePositives + '\t' + score);
//progress++;
//this.worker.ReportProgress((int)(progress / psms.Count() * 100));
}
}
});
}
using (StreamWriter file = new StreamWriter(path + folder + @"\" + folder + "ExportedFusionCandidatesNC.txt"))
{
file.WriteLine("Scan" + '\t' + "ExperimentalMass" + '\t' + "OriginalNSequence" + '\t' + "OriginalNScore" + '\t' + "OriginalCSequence" + '\t' + "OriginalCScore" + '\t' + "SampleSequence" + '\t' + "Ambiguity" + '\t' + "ProbableType" + '\t' + "MostProbableSequenceJunctions" + '\t' + "MostProbableSequence(s)" + '\t' + "MostProbableParents" + '\t' + "AllPossibleSequenceJunctions" + '\t' + "AllPossibleSequence(s)" + '\t' + "AllPossibleParent(s)" + '\t' + "NumberOfPossibleSequences" + '\t' + "PotentialFalsePositives" + '\t' + "TotalScore");
Parallel.ForEach(psms, new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (psm) =>
{
if (psm.candidates.Any(x => x.fusionType == FusionCandidate.FusionType.NC))
{
Ms2ScanWithSpecificMass spectrum = spectra[psm.scanNumber];
//printout the scan, the mass, the sequences with and without junctions, the number of potential sequences
string allPossibleSequences = "";
string mostProbableSequences = "";
int indexOfFirstProbableSequence = -1;
string mostProbableParents = "";
string allPossibleParents = "";
FusionCandidate.FusionType probableType = psm.fusionType;
for (int fc = 0; fc < psm.candidates.Count(); fc++)
{
FusionCandidate fusionCandidate = psm.candidates[fc]; //need fc for indexOfFirstProbableSequence
if (fusionCandidate.fusionType != FusionCandidate.FusionType.NC)
{
continue;
}
char[] tempArray = fusionCandidate.seq.ToCharArray();
//if most probable, add to all and most
//record sequences
if (indexOfFirstProbableSequence < 0)
{
indexOfFirstProbableSequence = fc;
}
for (int i = 0; i < tempArray.Count(); i++)
{
mostProbableSequences += tempArray[i];
allPossibleSequences += tempArray[i];
foreach (int junction in fusionCandidate.junctionIndexes)
{
if (junction == i)
{
mostProbableSequences += "-";
allPossibleSequences += "-";
}
}
}
mostProbableSequences += "|";
allPossibleSequences += "|";
//record parents
string tempParents = "";
mostProbableParents += tempParents;
allPossibleParents += tempParents;
}
allPossibleSequences = allPossibleSequences.Substring(0, allPossibleSequences.Length - 1); //remove last "|"
mostProbableSequences = mostProbableSequences.Substring(0, mostProbableSequences.Length - 1); //remove last "|"
string ambiguity = "";
NeoFindAmbiguity.FindIons(psm.candidates[indexOfFirstProbableSequence], psm, spectrum); //this should be carried over, but it's not...
// mutableError_message += e;
bool[] foundIons = psm.candidates[indexOfFirstProbableSequence].foundIons;
char[] firstSeq = psm.candidates[indexOfFirstProbableSequence].seq.ToCharArray();
bool ambiguous = false;
for (int i = 1; i < foundIons.Length; i++)
{
if (foundIons[i]) //if found
{
ambiguity += firstSeq[i - 1]; //add aa
if (ambiguous) //if it is part of an ambiguous sequence
{
ambiguity += ")";
ambiguous = false; //no longer ambiguous
}
}
else
{
if (!ambiguous)
{
ambiguous = true;
ambiguity += "(";
}
ambiguity += firstSeq[i - 1];
}
}
ambiguity += firstSeq[foundIons.Length - 1];
if (ambiguous)
{
ambiguity += ")";
}
string potentialFalsePositives = "";
if (potentialFalsePositives.Length > 0)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, potentialFalsePositives.Length - 1); //remove last |
if (potentialFalsePositives.Length > 30000)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, 30000);
}
}
//workarounds for excel. Actual limit is 32767, but that doesn't seem to work
if (mostProbableParents.Length > 30000)
{
mostProbableParents = mostProbableParents.Substring(0, 30000);
}
if (allPossibleParents.Length > 30000)
{
allPossibleParents = allPossibleParents.Substring(0, 30000);
}
int score = 0;
foreach (bool b in psm.candidates[indexOfFirstProbableSequence].foundIons)
{
if (b)
{
score++;
}
}
lock (file)
{
file.WriteLine(psm.scanNumber.ToString() + '\t' + psm.expMass.ToString() + '\t' + psm.nInfo.seq + '\t' + psm.nInfo.score + '\t' + psm.cInfo.seq + '\t' + psm.cInfo.score + '\t' + psm.candidates[indexOfFirstProbableSequence].seq + '\t' + ambiguity + '\t' + psm.fusionType.ToString() + '\t' + mostProbableSequences + '\t' + mostProbableSequences.Replace("-", "") + '\t' + mostProbableParents + '\t' + allPossibleSequences + '\t' + allPossibleSequences.Replace("-", "") + '\t' + allPossibleParents + '\t' + psm.candidates.Count().ToString() + '\t' + potentialFalsePositives + '\t' + score);
//progress++;
//this.worker.ReportProgress((int)(progress / psms.Count() * 100));
}
}
});
}
using (StreamWriter file = new StreamWriter(path + folder + @"\" + folder + "ExportedFusionCandidatesTS.txt"))
{
file.WriteLine("Scan" + '\t' + "ExperimentalMass" + '\t' + "OriginalNSequence" + '\t' + "OriginalNScore" + '\t' + "OriginalCSequence" + '\t' + "OriginalCScore" + '\t' + "SampleSequence" + '\t' + "Ambiguity" + '\t' + "ProbableType" + '\t' + "MostProbableSequenceJunctions" + '\t' + "MostProbableSequence(s)" + '\t' + "MostProbableParents" + '\t' + "AllPossibleSequenceJunctions" + '\t' + "AllPossibleSequence(s)" + '\t' + "AllPossibleParent(s)" + '\t' + "NumberOfPossibleSequences" + '\t' + "PotentialFalsePositives" + '\t' + "TotalScore");
Parallel.ForEach(psms, new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (psm) =>
{
if (psm.candidates.Any(x => x.fusionType == FusionCandidate.FusionType.TS))
{
Ms2ScanWithSpecificMass spectrum = spectra[psm.scanNumber];
//printout the scan, the mass, the sequences with and without junctions, the number of potential sequences
string allPossibleSequences = "";
string mostProbableSequences = "";
int indexOfFirstProbableSequence = -1;
string mostProbableParents = "";
string allPossibleParents = "";
FusionCandidate.FusionType probableType = psm.fusionType;
for (int fc = 0; fc < psm.candidates.Count(); fc++)
{
FusionCandidate fusionCandidate = psm.candidates[fc]; //need fc for indexOfFirstProbableSequence
if (fusionCandidate.fusionType != FusionCandidate.FusionType.TS)
{
continue;
}
char[] tempArray = fusionCandidate.seq.ToCharArray();
//if most probable, add to all and most
//record sequences
if (indexOfFirstProbableSequence < 0)
{
indexOfFirstProbableSequence = fc;
}
for (int i = 0; i < tempArray.Count(); i++)
{
mostProbableSequences += tempArray[i];
allPossibleSequences += tempArray[i];
foreach (int junction in fusionCandidate.junctionIndexes)
{
if (junction == i)
{
mostProbableSequences += "-";
allPossibleSequences += "-";
}
}
}
mostProbableSequences += "|";
allPossibleSequences += "|";
//record parents
string tempParents = "";
mostProbableParents += tempParents;
allPossibleParents += tempParents;
}
allPossibleSequences = allPossibleSequences.Substring(0, allPossibleSequences.Length - 1); //remove last "|"
mostProbableSequences = mostProbableSequences.Substring(0, mostProbableSequences.Length - 1); //remove last "|"
string ambiguity = "";
NeoFindAmbiguity.FindIons(psm.candidates[indexOfFirstProbableSequence], psm, spectrum); //this should be carried over, but it's not...
// mutableError_message += e;
bool[] foundIons = psm.candidates[indexOfFirstProbableSequence].foundIons;
char[] firstSeq = psm.candidates[indexOfFirstProbableSequence].seq.ToCharArray();
bool ambiguous = false;
for (int i = 1; i < foundIons.Length; i++)
{
if (foundIons[i]) //if found
{
ambiguity += firstSeq[i - 1]; //add aa
if (ambiguous) //if it is part of an ambiguous sequence
{
ambiguity += ")";
ambiguous = false; //no longer ambiguous
}
}
else
{
if (!ambiguous)
{
ambiguous = true;
ambiguity += "(";
}
ambiguity += firstSeq[i - 1];
}
}
ambiguity += firstSeq[foundIons.Length - 1];
if (ambiguous)
{
ambiguity += ")";
}
string potentialFalsePositives = "";
if (potentialFalsePositives.Length > 0)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, potentialFalsePositives.Length - 1); //remove last |
if (potentialFalsePositives.Length > 30000)
{
potentialFalsePositives = potentialFalsePositives.Substring(0, 30000);
}
}
//workarounds for excel. Actual limit is 32767, but that doesn't seem to work
if (mostProbableParents.Length > 30000)
{
mostProbableParents = mostProbableParents.Substring(0, 30000);
}
if (allPossibleParents.Length > 30000)
{
allPossibleParents = allPossibleParents.Substring(0, 30000);
}
int score = 0;
foreach (bool b in psm.candidates[indexOfFirstProbableSequence].foundIons)
{
if (b)
{
score++;
}
}
lock (file)
{
file.WriteLine(psm.scanNumber.ToString() + '\t' + psm.expMass.ToString() + '\t' + psm.nInfo.seq + '\t' + psm.nInfo.score + '\t' + psm.cInfo.seq + '\t' + psm.cInfo.score + '\t' + psm.candidates[indexOfFirstProbableSequence].seq + '\t' + ambiguity + '\t' + psm.fusionType.ToString() + '\t' + mostProbableSequences + '\t' + mostProbableSequences.Replace("-", "") + '\t' + mostProbableParents + '\t' + allPossibleSequences + '\t' + allPossibleSequences.Replace("-", "") + '\t' + allPossibleParents + '\t' + psm.candidates.Count().ToString() + '\t' + potentialFalsePositives + '\t' + score);
//progress++;
//this.worker.ReportProgress((int)(progress / psms.Count() * 100));
}
}
});
}
}
protected override MyTaskResults RunSpecific(string OutputFolder, List <DbForTask> dbFilenameList, List <string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList)
{
MyTaskResults = new MyTaskResults(this);
if (NeoType.Equals(NeoTaskType.AggregateTargetDecoyFiles))
{
//getfolders
if (NeoParameters.DecoyFilePath == null)
{
NeoParameters.DecoyFilePath = new DirectoryInfo(OutputFolder).Name;
string taskString = NeoParameters.DecoyFilePath.Split('-')[0];
int taskNum = Convert.ToInt32(taskString.Substring(4, taskString.Length - 4));
taskNum--;
NeoParameters.DecoyFilePath = OutputFolder.Substring(0, OutputFolder.Length - NeoParameters.DecoyFilePath.Length) + "Task" + taskNum + "-SearchTask\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
if (NeoParameters.TargetFilePath == null)
{
NeoParameters.TargetFilePath = new DirectoryInfo(OutputFolder).Name;
taskNum--;
NeoParameters.TargetFilePath = OutputFolder.Substring(0, OutputFolder.Length - NeoParameters.TargetFilePath.Length) + "Task" + taskNum + "-SearchTask\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
}
}
if (NeoParameters.TargetFilePath == null)
{
NeoParameters.TargetFilePath = new DirectoryInfo(OutputFolder).Name;
string taskString = NeoParameters.TargetFilePath.Split('-')[0];
int taskNum = Convert.ToInt32(taskString.Substring(4, taskString.Length - 4));
taskNum--;
NeoParameters.TargetFilePath = OutputFolder.Substring(0, OutputFolder.Length - NeoParameters.TargetFilePath.Length) + "Task" + taskNum + "-SearchTask\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
}
AggregateSearchFiles.Combine(NeoParameters.TargetFilePath, NeoParameters.DecoyFilePath, OutputFolder + "\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]));
}
else if (NeoType.Equals(NeoTaskType.AggregateNormalSplicedFiles))
{
//reset database
dbFilenameList = StoredDatabases;
string normalPath = "";
string cisPath = new DirectoryInfo(OutputFolder).Name;
string taskString = cisPath.Split('-')[0];
int taskNum = Convert.ToInt32(taskString.Substring(4, taskString.Length - 4));
taskNum -= 2;
string transPath = OutputFolder.Substring(0, OutputFolder.Length - cisPath.Length) + "Task" + (taskNum + 1) + "-SearchTask\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
cisPath = OutputFolder.Substring(0, OutputFolder.Length - cisPath.Length) + "Task" + taskNum + "-SearchTask\\" + Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
AggregateSearchFiles.RecursiveNeoAggregation(normalPath, cisPath, OutputFolder, "CisResults.psmtsv");
AggregateSearchFiles.RecursiveNeoAggregation(normalPath, transPath, OutputFolder, "TransResults.psmtsv");
}
else if (NeoType.Equals(NeoTaskType.GenerateSplicedPeptides))
{
NeoMassCalculator.ImportMasses();
MyFileManager myFileManager = new MyFileManager(true);
//Import Spectra
for (int spectraFileIndex = 0; spectraFileIndex < currentRawFileList.Count; spectraFileIndex++)
{
var origDataFile = currentRawFileList[spectraFileIndex];
CommonParameters combinedParams = SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[spectraFileIndex]);
var thisId = new List <string> {
taskId, "Individual Spectra Files", origDataFile
};
NewCollection(Path.GetFileName(origDataFile), thisId);
Status("Loading spectra file...", thisId);
MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams.TopNpeaks, combinedParams.MinRatio, combinedParams.TrimMs1Peaks, combinedParams.TrimMsMsPeaks, combinedParams);
Status("Getting ms2 scans...", thisId);
Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams.DoPrecursorDeconvolution, combinedParams.UseProvidedPrecursorInfo, combinedParams.DeconvolutionIntensityRatio, combinedParams.DeconvolutionMaxAssumedChargeState, combinedParams.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Import Database
Status("Loading modifications...", taskId);
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
List <string> localizeableModificationTypes = GlobalVariables.AllModTypesKnown.ToList();
// load proteins
List <Protein> proteinList = LoadProteins(taskId, dbFilenameList, true, DecoyType.None, localizeableModificationTypes, combinedParams);
//Read N and C files
string nPath = NeoParameters.NFilePath;
string cPath = NeoParameters.CFilePath;
//if termini input
if (nPath == null || cPath == null)
{
//if no termini input
string taskHeader = "Task";
string[] pathArray = OutputFolder.Split('\\');
string basePath = "";
for (int i = 0; i < pathArray.Length - 1; i++)
{
basePath += pathArray[i] + '\\';
}
string currentTaskNumber = pathArray[pathArray.Length - 1].Split('-')[0];
currentTaskNumber = currentTaskNumber.Substring(taskHeader.Length, currentTaskNumber.Length - taskHeader.Length);
string NHeader = "";
string CHeader = "";
if (cPath == null)
{
CHeader = taskHeader + (Convert.ToInt16(currentTaskNumber) - 1);
if (nPath == null)
{
NHeader = taskHeader + (Convert.ToInt16(currentTaskNumber) - 2);
}
}
else
{
NHeader = taskHeader + (Convert.ToInt16(currentTaskNumber) - 1);
}
foreach (string s in Directory.GetDirectories(basePath))
{
if (s.Contains(NHeader))
{
nPath = s;
}
else if (s.Contains(CHeader))
{
cPath = s;
}
}
string fileName = Path.GetFileNameWithoutExtension(currentRawFileList[0]) + "_PSMs.psmtsv";
nPath += "\\" + fileName;
cPath += "\\" + fileName;
}
Status("Importing Search Results...", taskId);
List <NeoPsm> psms = ImportPsmtsv.ImportNeoPsms(nPath, cPath);
//Splice
Status("Splicing Fragments...", taskId);
List <NeoPsm> candidates = NeoSplicePeptides.SplicePeptides(psms);
//Find Ambiguity
Status("Identifying Ambiguity...", taskId);
NeoFindAmbiguity.FindAmbiguity(candidates, proteinList, arrayOfMs2ScansSortedByMass, dbFilenameList[0].FilePath);
//Export Results
Status("Exporting Results...", taskId);
NeoExport.ExportAll(candidates, arrayOfMs2ScansSortedByMass, OutputFolder);
//Switch databases
string outputFolder = NeoExport.path + NeoExport.folder + @"\" + NeoExport.folder + "FusionDatabaseAppendixNC.fasta";
dbFilenameList = new List <DbForTask>()
{
new DbForTask(outputFolder, false)
};
}
}
else //if SearchTransDb
{
string outputFolder = NeoExport.path + NeoExport.folder + @"\" + NeoExport.folder + "FusionDatabaseAppendixTS.fasta";
dbFilenameList = new List <DbForTask>()
{
new DbForTask(outputFolder, false)
};
}
return(MyTaskResults);
}
