public void deepCopyFoundIons(FusionCandidate original)
{
this.foundIons = new bool[original.foundIons.Length];
for (int index = 0; index < this.foundIons.Length; index++)
{
this.foundIons[index] = original.foundIons[index];
}
}
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));
}
}
});
}
}
