Skip to content

Commit 7f3739d

Browse files
author
stefanks
authored
Output ObservedCharges
* uhuh * Make shared reading * fix * fixup * uuuh * fixup * packages * packages * rename * Update README.md * gloff * gaahf * gahh * gaaah * sdafdsfasdf * cool * gahh * gahh * What * Whatwhat * glahaha * ah * hmhm * aha! * glaahj * gloof * aha
1 parent 1ac95f5 commit 7f3739d

File tree

5 files changed

+133
-121
lines changed

5 files changed

+133
-121
lines changed

‎ConsoleApp1/Program.cs

Lines changed: 119 additions & 112 deletions
Original file line numberDiff line numberDiff line change
@@ -54,136 +54,143 @@ private static void DeconTest()
5454
ThermoStaticData a = ThermoStaticData.LoadAllStaticData(file);
5555
//ThermoDynamicData a = ThermoDynamicData.InitiateDynamicConnection(@"C:\Users\stepa\Desktop\Decon\09-01-17_iodo_1-4th_rep1_human.raw");
5656

57-
//using (StreamWriter output = new StreamWriter(@"output.tsv"))
58-
//{
59-
//Console.WriteLine("intensityRatio, deconvolutionTolerancePpm, maxAssumedChargeState: " + (intensityRatio, deconvolutionTolerancePpm, maxAssumedChargeState));
60-
61-
//int goodScans = 0;
62-
63-
int numMatchToOnlyOld = 0;
64-
int numMatchToOnlyNew = 0;
65-
int numMatchToBoth = 0;
66-
int numScansWithThermoMasses = 0;
67-
68-
int numMatchToOld = 0;
69-
int numMatchToOldPlusMM = 0;
70-
int numMatchToOldMinusMM = 0;
71-
int numMatchToNew = 0;
72-
int numMatchToNewPlusMM = 0;
73-
int numMatchToNewMinusMM = 0;
74-
75-
//output.WriteLine("Scan\tType");
76-
//foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().Where(b => b.OneBasedScanNumber >= 8356))
77-
//foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().Skip(2000))
78-
foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>())
57+
using (StreamWriter output = new StreamWriter(@"unmatched.tsv"))
7958
{
80-
double thermoMz = double.NaN;
81-
if (ok.SelectedIonChargeStateGuess.HasValue)
82-
{
83-
thermoMz = ok.SelectedIonMZ;
84-
if (ok.SelectedIonMonoisotopicGuessMz.HasValue)
85-
thermoMz = ok.SelectedIonMonoisotopicGuessMz.Value;
86-
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + thermoMz.ToString("G6"));
87-
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value).ToString("G6"));
88-
}
89-
else
90-
{
91-
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + " ");
92-
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + " ");
93-
}
94-
95-
var precursorSpectrum = a.GetOneBasedScan(ok.OneBasedPrecursorScanNumber.Value).MassSpectrum;
59+
output.WriteLine("Scan\tmatchToNewMinusMM\tmatchToNewPlusMM\tThermoMass");
9660

97-
var oldResults = ok.GetIsolatedMassesAndChargesOld(precursorSpectrum, maxAssumedChargeState, deconvolutionTolerance, intensityRatio).OrderBy(b => b.Item1.First().Mz.ToMass(b.Item2)).ToList();
61+
//Console.WriteLine("intensityRatio, deconvolutionTolerancePpm, maxAssumedChargeState: " + (intensityRatio, deconvolutionTolerancePpm, maxAssumedChargeState));
9862

99-
//output.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMzs\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToString("G6"))));
100-
//output.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMasses\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToMass(b.Item2).ToString("G6"))));
63+
//int goodScans = 0;
10164

102-
var newResults = ok.GetIsolatedMassesAndCharges(precursorSpectrum, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatio).OrderBy(b => b.monoisotopicMass).ToList();
65+
int numMatchToOnlyOld = 0;
66+
int numMatchToOnlyNew = 0;
67+
int numMatchToBoth = 0;
68+
int numScansWithThermoMasses = 0;
10369

104-
//output.WriteLine(ok.OneBasedScanNumber + "\tNewLowestObservedMzs\t" + string.Join("\t", newResults.Select(b => b.peaks.OrderBy(c => c.Item1).First().Item1.ToString("G6"))));
105-
//output.WriteLine(ok.OneBasedScanNumber + "\tNewMonoisotopicMasses\t" + string.Join("\t", newResults.Select(b => b.monoisotopicMass.ToString("G6"))));
70+
int numMatchToOld = 0;
71+
int numMatchToOldPlusMM = 0;
72+
int numMatchToOldMinusMM = 0;
73+
int numMatchToNew = 0;
74+
int numMatchToNewPlusMM = 0;
75+
int numMatchToNewMinusMM = 0;
10676

107-
if (ok.SelectedIonChargeStateGuess.HasValue)
77+
//output.WriteLine("Scan\tType");
78+
foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().Where(b => b.OneBasedScanNumber == 447))
79+
//foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>().Skip(2000))
80+
//foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>())
10881
{
109-
numScansWithThermoMasses++;
110-
var thermoMass = thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value);
111-
bool matchToOld = false;
112-
bool matchToNew = false;
113-
bool matchToOldPlusMM = false;
114-
bool matchToNewPlusMM = false;
115-
bool matchToOldMinusMM = false;
116-
bool matchToNewMinusMM = false;
117-
foreach (var hm in oldResults)
82+
double thermoMz = double.NaN;
83+
if (ok.SelectedIonChargeStateGuess.HasValue)
11884
{
119-
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2), thermoMass))
120-
{
121-
matchToOld = true;
122-
}
123-
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2) + 1.0029, thermoMass))
124-
{
125-
matchToOldPlusMM = true;
126-
}
127-
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2) - 1.0029, thermoMass))
128-
{
129-
matchToOldMinusMM = true;
130-
}
85+
thermoMz = ok.SelectedIonMZ;
86+
if (ok.SelectedIonMonoisotopicGuessMz.HasValue)
87+
thermoMz = ok.SelectedIonMonoisotopicGuessMz.Value;
88+
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + thermoMz.ToString("G6"));
89+
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value).ToString("G6"));
13190
}
132-
foreach (var hm in newResults)
91+
else
13392
{
134-
if (sameMassTolerancePpm.Within(hm.monoisotopicMass, thermoMass))
93+
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + " ");
94+
//output.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + " ");
95+
}
96+
97+
var precursorSpectrum = a.GetOneBasedScan(ok.OneBasedPrecursorScanNumber.Value).MassSpectrum;
98+
99+
var oldResults = ok.GetIsolatedMassesAndChargesOld(precursorSpectrum, maxAssumedChargeState, deconvolutionTolerance, intensityRatio).OrderBy(b => b.Item1.First().Mz.ToMass(b.Item2)).ToList();
100+
101+
//output.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMzs\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToString("G6"))));
102+
//output.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMasses\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToMass(b.Item2).ToString("G6"))));
103+
104+
var newResults = ok.GetIsolatedMassesAndCharges(precursorSpectrum, maxAssumedChargeState, deconvolutionTolerancePpm, intensityRatio).OrderBy(b => b.monoisotopicMass).ToList();
105+
106+
//output.WriteLine(ok.OneBasedScanNumber + "\tNewLowestObservedMzs\t" + string.Join("\t", newResults.Select(b => b.peaks.OrderBy(c => c.Item1).First().Item1.ToString("G6"))));
107+
//output.WriteLine(ok.OneBasedScanNumber + "\tNewMonoisotopicMasses\t" + string.Join("\t", newResults.Select(b => b.monoisotopicMass.ToString("G6"))));
108+
109+
if (ok.SelectedIonChargeStateGuess.HasValue)
110+
{
111+
numScansWithThermoMasses++;
112+
var thermoMass = thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value);
113+
bool matchToOld = false;
114+
bool matchToNew = false;
115+
bool matchToOldPlusMM = false;
116+
bool matchToNewPlusMM = false;
117+
bool matchToOldMinusMM = false;
118+
bool matchToNewMinusMM = false;
119+
foreach (var hm in oldResults)
135120
{
136-
matchToNew = true;
121+
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2), thermoMass))
122+
{
123+
matchToOld = true;
124+
}
125+
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2) + 1.0029, thermoMass))
126+
{
127+
matchToOldPlusMM = true;
128+
}
129+
if (sameMassTolerancePpm.Within(hm.Item1.First().Mz.ToMass(hm.Item2) - 1.0029, thermoMass))
130+
{
131+
matchToOldMinusMM = true;
132+
}
137133
}
138-
if (sameMassTolerancePpm.Within(hm.monoisotopicMass + 1.0029, thermoMass))
134+
foreach (var hm in newResults)
139135
{
140-
matchToNewPlusMM = true;
136+
if (sameMassTolerancePpm.Within(hm.monoisotopicMass, thermoMass))
137+
{
138+
matchToNew = true;
139+
}
140+
if (sameMassTolerancePpm.Within(hm.monoisotopicMass + 1.0029, thermoMass))
141+
{
142+
matchToNewPlusMM = true;
143+
}
144+
if (sameMassTolerancePpm.Within(hm.monoisotopicMass - 1.0029, thermoMass))
145+
{
146+
matchToNewMinusMM = true;
147+
}
141148
}
142-
if (sameMassTolerancePpm.Within(hm.monoisotopicMass - 1.0029, thermoMass))
149+
numMatchToOld += matchToOld ? 1 : 0;
150+
numMatchToOldPlusMM += matchToOldPlusMM ? 1 : 0;
151+
numMatchToOldMinusMM += matchToOldMinusMM ? 1 : 0;
152+
numMatchToNew += matchToNew ? 1 : 0;
153+
numMatchToNewPlusMM += matchToNewPlusMM ? 1 : 0;
154+
numMatchToNewMinusMM += matchToNewMinusMM ? 1 : 0;
155+
if (matchToOld && !matchToNew)
156+
numMatchToOnlyOld++;
157+
if (matchToNew && !matchToOld)
158+
numMatchToOnlyNew++;
159+
if (matchToOld && matchToNew)
160+
numMatchToBoth++;
161+
162+
if (!matchToNew)
143163
{
144-
matchToNewMinusMM = true;
164+
output.WriteLine(ok.OneBasedScanNumber + "\t" + matchToNewMinusMM + "\t" + matchToNewPlusMM + "\t" + thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value).ToString("G6") + "\t" + string.Join("\t", newResults.Select(b => b.monoisotopicMass)));
145165
}
166+
//if (matchToOld && !matchToNew && thermoMz > 500)
167+
//{
168+
// Console.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + thermoMz.ToString("G6"));
169+
// Console.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value).ToString("G6"));
170+
// Console.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMzs\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToString("G6"))));
171+
// Console.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMasses\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToMass(b.Item2).ToString("G6"))));
172+
// Console.WriteLine(ok.OneBasedScanNumber + "\tNewLowestObservedMzs\t" + string.Join("\t", newResults.Select(b => b.peaks.OrderBy(c => c.Item1).First().Item1.ToString("G6"))));
173+
// Console.WriteLine(ok.OneBasedScanNumber + "\tNewMonoisotopicMasses\t" + string.Join("\t", newResults.Select(b => b.monoisotopicMass.ToString("G6"))));
174+
175+
//}
176+
//else
177+
//{
178+
// Console.WriteLine(ok.OneBasedScanNumber + " good ");
146179
}
147-
numMatchToOld += matchToOld ? 1 : 0;
148-
numMatchToOldPlusMM += matchToOldPlusMM ? 1 : 0;
149-
numMatchToOldMinusMM += matchToOldMinusMM ? 1 : 0;
150-
numMatchToNew += matchToNew ? 1 : 0;
151-
numMatchToNewPlusMM += matchToNewPlusMM ? 1 : 0;
152-
numMatchToNewMinusMM += matchToNewMinusMM ? 1 : 0;
153-
if (matchToOld && !matchToNew)
154-
numMatchToOnlyOld++;
155-
if (matchToNew && !matchToOld)
156-
numMatchToOnlyNew++;
157-
if (matchToOld && matchToNew)
158-
numMatchToBoth++;
159-
//if (matchToOld && !matchToNew && thermoMz > 500)
160-
//{
161-
// Console.WriteLine(ok.OneBasedScanNumber + "\tThermoMz\t" + thermoMz.ToString("G6"));
162-
// Console.WriteLine(ok.OneBasedScanNumber + "\tThermoMass\t" + thermoMz.ToMass(ok.SelectedIonChargeStateGuess.Value).ToString("G6"));
163-
// Console.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMzs\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToString("G6"))));
164-
// Console.WriteLine(ok.OneBasedScanNumber + "\tOldMonoisotopicMasses\t" + string.Join("\t", oldResults.Select(b => b.Item1.First().Mz.ToMass(b.Item2).ToString("G6"))));
165-
// Console.WriteLine(ok.OneBasedScanNumber + "\tNewLowestObservedMzs\t" + string.Join("\t", newResults.Select(b => b.peaks.OrderBy(c => c.Item1).First().Item1.ToString("G6"))));
166-
// Console.WriteLine(ok.OneBasedScanNumber + "\tNewMonoisotopicMasses\t" + string.Join("\t", newResults.Select(b => b.monoisotopicMass.ToString("G6"))));
167-
168-
//}
169-
//else
170-
//{
171-
// Console.WriteLine(ok.OneBasedScanNumber + " good ");
172-
//}
173180
}
174-
}
175181

176-
Console.WriteLine("numMatchToOld: " + numMatchToOld);
177-
Console.WriteLine("numMatchToOldPlusMM: " + numMatchToOldPlusMM);
178-
Console.WriteLine("numMatchToOldMinusMM: " + numMatchToOldMinusMM);
179-
Console.WriteLine("numMatchToNew: " + numMatchToNew);
180-
Console.WriteLine("numMatchToNewPlusMM: " + numMatchToNewPlusMM);
181-
Console.WriteLine("numMatchToNewMinusMM: " + numMatchToNewMinusMM);
182-
183-
Console.WriteLine("numMatchToOnlyOld: " + numMatchToOnlyOld);
184-
Console.WriteLine("numMatchToOnlyNew: " + numMatchToOnlyNew);
185-
Console.WriteLine("numMatchToBoth: " + numMatchToBoth);
186-
Console.WriteLine("numScansWithThermoMasses: " + numScansWithThermoMasses);
182+
Console.WriteLine("numMatchToOld: " + numMatchToOld);
183+
Console.WriteLine("numMatchToOldPlusMM: " + numMatchToOldPlusMM);
184+
Console.WriteLine("numMatchToOldMinusMM: " + numMatchToOldMinusMM);
185+
Console.WriteLine("numMatchToNew: " + numMatchToNew);
186+
Console.WriteLine("numMatchToNewPlusMM: " + numMatchToNewPlusMM);
187+
Console.WriteLine("numMatchToNewMinusMM: " + numMatchToNewMinusMM);
188+
189+
Console.WriteLine("numMatchToOnlyOld: " + numMatchToOnlyOld);
190+
Console.WriteLine("numMatchToOnlyNew: " + numMatchToOnlyNew);
191+
Console.WriteLine("numMatchToBoth: " + numMatchToBoth);
192+
Console.WriteLine("numScansWithThermoMasses: " + numScansWithThermoMasses);
193+
}
187194
}
188195
}
189196

@@ -224,7 +231,7 @@ private static void DoFileDecon(string[] args)
224231

225232
using (StreamWriter output = new StreamWriter(@"DeconvolutionOutput-" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss", CultureInfo.InvariantCulture) + ".tsv"))
226233
{
227-
output.WriteLine("Mass\tNumPeaks\tNumScans\tMinScan\tMaxScan\tAverageElutionTime\tIntensity\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope");
234+
output.WriteLine("Mass\tNumPeaks\tNumScans\tMinScan\tMaxScan\tAverageElutionTime\tIntensity\tObservedCharges\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope");
228235
foreach (var nice in a.Deconvolute(p.Object.MinScan, p.Object.MaxScan, p.Object.MaxAssumedChargeState, p.Object.DeconvolutionTolerancePpm, p.Object.IntensityRatioLimit, p.Object.AggregationTolerancePpm, b => b.MsnOrder == 1).OrderByDescending(b => b.TotalIntensity))
229236
{
230237
output.WriteLine(nice.OneLineString());

‎MS2decon/Program.cs

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -51,7 +51,7 @@ private static void Main(string[] args)
5151

5252
using (StreamWriter output = new StreamWriter(@"MS2DeconvolutionOutput-" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss", CultureInfo.InvariantCulture) + ".tsv"))
5353
{
54-
output.WriteLine("Mass\tNumPeaks\tNumScans\tMinScan\tMaxScan\tAverageElutionTime\tIntensity\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope");
54+
output.WriteLine("Mass\tNumPeaks\tNumScans\tMinScan\tMaxScan\tAverageElutionTime\tIntensity\tObservedCharges\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope");
5555

5656
foreach (var ok in a.OfType<IMsDataScanWithPrecursor<IMzSpectrum<IMzPeak>>>())
5757
{

‎MassSpectrometry/DeconvolutionFeature.cs

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,8 @@ internal class DeconvolutionFeature
2020

2121
public IsotopicEnvelope MostIntenseEnvelope { get { return isotopicEnvelopes.OrderByDescending(b => b.totalIntensity).First(); } }
2222

23+
public IEnumerable<int> AllCharges { get { return isotopicEnvelopes.Select(b => b.charge).ToList(); } }
24+
2325
#endregion Public Properties
2426

2527
#region Public Methods

0 commit comments

Comments
 (0)