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trishortstrishorts
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Merge branch 'master' into customOxoniumIons
2 parents 51fd64f + 3c8e0b8 commit d6c347e

16 files changed

Lines changed: 1275 additions & 81 deletions

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‎.github/workflows/Test.yml‎

Lines changed: 27 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,11 +27,36 @@ jobs:
2727
run: dotnet add ./MetaMorpheus/Test/Test.csproj package coverlet.collector -v 6.0.2
2828

2929
- name: Run unit tests with coverage
30-
run: dotnet test .\MetaMorpheus\Test\Test.csproj --configuration Release --verbosity normal --collect:"XPlat Code Coverage"
31-
30+
# Exclude live external-service tests (UniProt, etc.) from the required run; they run in the
31+
# separate, non-blocking external-service-tests job below.
32+
run: dotnet test .\MetaMorpheus\Test\Test.csproj --configuration Release --verbosity normal --filter "Category!=ExternalService" --collect:"XPlat Code Coverage"
33+
3234
- name: Upload coverage to Codecov
3335
uses: codecov/codecov-action@v4
3436
with:
3537
token: ${{ secrets.CODECOV_TOKEN }}
3638
verbose: true
3739
flags: unittests
40+
41+
# Runs tests that depend on live external web services (UniProt, ...). Kept separate and
42+
# intentionally NOT a required status check, so a third-party outage never blocks a PR. The tests
43+
# self-classify: an outage is reported as Skipped (Assert.Ignore) and only a genuine contract
44+
# break fails this job. Do NOT add this job to branch-protection required checks.
45+
external-service-tests:
46+
name: External-service tests (non-blocking)
47+
runs-on: windows-latest
48+
49+
steps:
50+
- uses: actions/checkout@v4
51+
- name: Setup .NET
52+
uses: actions/setup-dotnet@v4
53+
with:
54+
dotnet-version: 8.0.204
55+
- name: Restore dependencies
56+
run: dotnet restore ./MetaMorpheus/MetaMorpheus.sln
57+
58+
- name: Build
59+
run: dotnet build --no-restore ./MetaMorpheus/MetaMorpheus.sln --configuration Release
60+
61+
- name: Run external-service tests
62+
run: dotnet test .\MetaMorpheus\Test\Test.csproj --configuration Release --no-build --verbosity normal --filter "Category=ExternalService"

‎MetaMorpheus/EngineLayer/CommonParameters.cs‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -62,7 +62,8 @@ public CommonParameters(
6262
DeconvolutionParameters productDeconParams = null,
6363
bool useMostAbundantPrecursorIntensity = true,
6464
DIAparameters diaParameters = null,
65-
IFragmentationParams fragmentationParams = null)
65+
IFragmentationParams fragmentationParams = null,
66+
string rtPredictorName = "Chronologer")
6667

6768
{
6869
TaskDescriptor = taskDescriptor;
@@ -131,6 +132,8 @@ public CommonParameters(
131132
FragmentationParameters = fragmentationParams ?? new FragmentationParams();
132133
}
133134

135+
RTPredictorName = rtPredictorName;
136+
134137
CustomIons = digestionParams.ProductsFromDissociationType()[DissociationType.Custom];
135138

136139
// reset custom fragmentation product types to default empty list
@@ -206,6 +209,7 @@ public int DeconvolutionMaxAssumedChargeState
206209
public bool UseMostAbundantPrecursorIntensity { get; set; }
207210
public DIAparameters? DIAparameters { get; set; } //only for DIA analysis involving pseudo ms2 scan generation
208211
public IFragmentationParams FragmentationParameters { get; set; }
212+
public string RTPredictorName { get; private set; }
209213

210214
public CommonParameters Clone()
211215
{

‎MetaMorpheus/EngineLayer/DIA/DIAEngine.cs‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,6 @@
1212
using EngineLayer.Util;
1313
using Omics;
1414
using FlashLFQ;
15-
using ThermoFisher.CommonCore.Data.Business;
1615
using Readers;
1716

1817
namespace EngineLayer.DIA

‎MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs‎

Lines changed: 28 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,8 @@
1-
using EngineLayer.CrosslinkSearch;
1+
using Chromatography.RetentionTimePrediction;
2+
using Chromatography.RetentionTimePrediction.Chronologer;
3+
using EngineLayer.CrosslinkSearch;
24
using EngineLayer.SpectrumMatch;
5+
using PredictionClients.Koina.SupportedModels.RetentionTimeModels;
36
using Proteomics.ProteolyticDigestion;
47
using System;
58
using System.Collections.Generic;
@@ -9,6 +12,11 @@ namespace EngineLayer.FdrAnalysis
912
{
1013
public class FdrAnalysisEngine : MetaMorpheusEngine
1114
{
15+
private static readonly Lazy<ChronologerRetentionTimePredictor> _chronologerInstance =
16+
new Lazy<ChronologerRetentionTimePredictor>(
17+
() => new ChronologerRetentionTimePredictor(),
18+
System.Threading.LazyThreadSafetyMode.ExecutionAndPublication);
19+
1220
private List<SpectralMatch> AllPsms;
1321
private readonly int MassDiffAcceptorNumNotches;
1422
private readonly string AnalysisType;
@@ -401,7 +409,25 @@ public static void Compute_PEPValue(FdrAnalysisResults myAnalysisResults, List<S
401409
_ => "standard"
402410
};
403411

404-
myAnalysisResults.BinarySearchTreeMetrics = new PepAnalysisEngine(psms, searchType, fileSpecificParameters, outputFolder).ComputePEPValuesForAllPSMs();
412+
var rtPredictor = GetRTPredictor(searchType, fileSpecificParameters);
413+
myAnalysisResults.BinarySearchTreeMetrics = new PepAnalysisEngine(psms, searchType, fileSpecificParameters, outputFolder, rtPredictor).ComputePEPValuesForAllPSMs();
414+
}
415+
416+
private static IRetentionTimePredictor GetRTPredictor(string searchType, List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters)
417+
{
418+
if (searchType != "standard")
419+
return null;
420+
421+
// Get predictor name from the first file's parameters
422+
var predictorName = fileSpecificParameters.FirstOrDefault().fileSpecificParameters?.RTPredictorName;
423+
424+
return predictorName switch
425+
{
426+
"Chronologer" => _chronologerInstance.Value,
427+
"Prosit2019iRT" => new Prosit2019iRT(),
428+
"Prosit2020iRTTMT" => new Prosit2020iRTTMT(),
429+
_ => null
430+
};
405431
}
406432

407433
/// <summary>

‎MetaMorpheus/EngineLayer/FdrAnalysis/PsmData.cs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -195,4 +195,4 @@ public string ToString(string searchType)
195195
[LoadColumn(29)]
196196
public float PrecursorDeconvolutionScore { get; set; }
197197
}
198-
}
198+
}

‎MetaMorpheus/GuiFunctions/MetaDraw/PlotModelStat.cs‎

Lines changed: 77 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,9 @@ public class PlotModelStat
4343
"Histogram of Missed Cleavages",
4444
"Histogram of Fragment Ion Types by Count",
4545
"Histogram of Fragment Ion Types by Intensity",
46-
"Histogram of Ids by Retention Time"
46+
"Histogram of Ids by Retention Time",
47+
"Histogram of Spectral Match Ambiguity Levels",
48+
"Histogram of Notch (Ambiguous PSMs Split Across Notches)"
4749
};
4850

4951
public PlotModel Model => privateModel;
@@ -124,6 +126,12 @@ private void createPlot(string plotType)
124126
case "Histogram of Ids by Retention Time":
125127
histogramPlot(12);
126128
break;
129+
case "Histogram of Spectral Match Ambiguity Levels":
130+
histogramPlot(13);
131+
break;
132+
case "Histogram of Notch (Ambiguous PSMs Split Across Notches)":
133+
histogramPlot(14);
134+
break;
127135
}
128136
}
129137

@@ -153,7 +161,7 @@ private void histogramPlot(int plotType)
153161
int[] totalCounts;
154162
int categoriesPerGroup = 0;
155163
List<string> allGroupKeys = null;
156-
bool isCategoryHistogram = plotType == 5 || plotType == 10 || plotType == 11;
164+
bool isCategoryHistogram = plotType == 5 || plotType == 10 || plotType == 11 || plotType == 13;
157165

158166
if (isCategoryHistogram)
159167
{
@@ -336,6 +344,34 @@ private HistogramRawData GetHistogramData(int plotType)
336344
dictsBySourceFile.Add(fileName, result);
337345
}
338346
break;
347+
case 13: // Histogram of Spectral Match Ambiguity Levels
348+
xAxisTitle = "Ambiguity Level";
349+
labelAngle = 0;
350+
foreach (var fileName in psmsBySourceFile.Keys)
351+
{
352+
var result = psmsBySourceFile[fileName]
353+
.GroupBy(p => NormalizeAmbiguityLevel(p.AmbiguityLevel))
354+
.ToDictionary(p => p.Key, p => p.Count());
355+
dictsBySourceFile.Add(fileName, result);
356+
}
357+
break;
358+
case 14: // Histogram of Notch (ambiguous PSMs contribute to each of their pipe-delimited notches)
359+
xAxisTitle = "Notch";
360+
binSize = 1;
361+
labelAngle = 0;
362+
foreach (var fileName in psmsBySourceFile.Keys)
363+
{
364+
var values = new List<double>();
365+
foreach (var psm in psmsBySourceFile[fileName])
366+
{
367+
foreach (double notch in ParseAmbiguousNotchValues(psm.Notch))
368+
values.Add(notch);
369+
}
370+
numbersBySourceFile.Add(fileName, values);
371+
var results = values.GroupBy(p => roundToBin(p, binSize)).OrderBy(p => p.Key).Select(p => p);
372+
dictsBySourceFile.Add(fileName, results.ToDictionary(p => p.Key.ToString(CultureInfo.InvariantCulture), v => v.Count()));
373+
}
374+
break;
339375
}
340376

341377
return new HistogramRawData(xAxisTitle, yAxisTitle, binSize, labelAngle, numbersBySourceFile, dictsBySourceFile);
@@ -515,6 +551,13 @@ private Dictionary<string, int> GetCategoryDictForGroup(int plotType, Observable
515551
return mods.GroupBy(p => p.IdWithMotif).ToDictionary(p => p.Key, v => v.Count());
516552
}
517553

554+
if (plotType == 13)
555+
{
556+
return groupPsms
557+
.GroupBy(p => NormalizeAmbiguityLevel(p.AmbiguityLevel))
558+
.ToDictionary(p => p.Key, p => p.Count());
559+
}
560+
518561
var allMatchedIons = groupPsms.SelectMany(p => p.MatchedIons).ToList();
519562
if (plotType == 10)
520563
{
@@ -1013,6 +1056,7 @@ private IEnumerable<double> GetNumbersFromPsms(ObservableCollection<SpectrumMatc
10131056
8 => GetHydrophobicityScores(psms),
10141057
9 => psms.Where(p => !p.MissedCleavage.Contains("|")).Select(p => double.Parse(p.MissedCleavage)),
10151058
12 => psms.Select(p => (double)(int)Math.Round(p.RetentionTime, 0)),
1059+
14 => psms.SelectMany(p => ParseAmbiguousNotchValues(p.Notch)),
10161060
_ => Enumerable.Empty<double>()
10171061
};
10181062
}
@@ -1042,6 +1086,37 @@ public HistItem(double value, int categoryIndex, string bin, int total, string g
10421086
}
10431087
}
10441088

1089+
private static IEnumerable<string> SplitAmbiguousNotch(string notch)
1090+
{
1091+
if (string.IsNullOrWhiteSpace(notch))
1092+
return new[] { "0" };
1093+
1094+
return notch.Split('|')
1095+
.Select(p => p.Trim())
1096+
.Where(p => p.Length > 0)
1097+
.DefaultIfEmpty("0");
1098+
}
1099+
1100+
private static IEnumerable<double> ParseAmbiguousNotchValues(string notch)
1101+
{
1102+
foreach (var part in SplitAmbiguousNotch(notch))
1103+
{
1104+
if (double.TryParse(part, NumberStyles.Float, CultureInfo.InvariantCulture, out double value))
1105+
yield return value;
1106+
else
1107+
yield return 0.0;
1108+
}
1109+
}
1110+
1111+
private static string NormalizeAmbiguityLevel(string ambiguityLevel)
1112+
{
1113+
if (string.IsNullOrWhiteSpace(ambiguityLevel))
1114+
return "1";
1115+
1116+
var first = ambiguityLevel.Split('|')[0].Trim();
1117+
return string.IsNullOrEmpty(first) ? "1" : first;
1118+
}
1119+
10451120
/// <summary>
10461121
/// Orders strings numerically if all values are numeric, otherwise alphabetically.
10471122
/// </summary>

‎MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -154,7 +154,6 @@ private void CalculatePsmAndPeptideFdr(List<SpectralMatch> psms, string analysis
154154

155155
Status($"Done estimating {GlobalVariables.AnalyteType.GetSpectralMatchLabel()} FDR!", Parameters.SearchTaskId);
156156
}
157-
158157
private void DisambiguateSpectralMatches()
159158
{
160159
try

‎MetaMorpheus/Test/AddCompIonsTest.cs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ public static void TestAddCompIonsClassic()
3939

4040
List<DigestionMotif> motifs = new List<DigestionMotif> { new DigestionMotif("K", null, 1, null) };
4141
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
42-
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
42+
ProteaseDictionary.Dictionary[protease.Name] = protease;
4343

4444
CommonParameters CommonParameters = new CommonParameters(
4545
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
@@ -458,4 +458,4 @@ public static void AddCompIonsMzOutput()
458458

459459
}
460460
}
461-
}
461+
}

‎MetaMorpheus/Test/DatabaseTests/UniProtMock/phi29_mock_reviewed.fasta‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
>sp|P03680|MCP_BPPH2 Major capsid protein OS=Bacillus phage phi29 OX=10756 GN=8 PE=1 SV=1
2+
MAGKKQNIVLESAWRELVGK
3+
>sp|P03681|PORT_BPPH2 Head-tail connector protein OS=Bacillus phage phi29 OX=10756 GN=10 PE=1 SV=1
4+
MSKTLNEVLGQVADSFRTKGWK
5+
>sp|P03682|DPOL_BPPH2 DNA polymerase OS=Bacillus phage phi29 OX=10756 GN=2 PE=1 SV=1
6+
MPRKMYSCDFETTTKLDDCRVWAY

‎MetaMorpheus/Test/DatabaseTests/UniProtMock/phi29_mock_reviewed.xml‎

Lines changed: 61 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,61 @@
1+
<?xml version='1.0' encoding='UTF-8'?>
2+
<uniprot xmlns="http://uniprot.org/uniprot" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://uniprot.org/uniprot http://www.uniprot.org/support/docs/uniprot.xsd">
3+
<!--
4+
Local, offline mock of a UniProtKB XML "stream" response.
5+
Stands in for a live download of Bacillus phage phi29 (proteome UP000001207)
6+
so GuiFunctionsTest can exercise the ProteinDbLoader.LoadProteinXML path without
7+
reaching rest.uniprot.org. Sequences are truncated/synthetic; only the file
8+
structure and the number of entries (3) matter for the test.
9+
-->
10+
<entry dataset="Swiss-Prot" created="1986-07-21" modified="2021-09-29" version="1">
11+
<accession>P03680</accession>
12+
<name>MCP_BPPH2</name>
13+
<protein>
14+
<recommendedName>
15+
<fullName>Major capsid protein</fullName>
16+
</recommendedName>
17+
</protein>
18+
<gene>
19+
<name type="primary">8</name>
20+
</gene>
21+
<organism>
22+
<name type="scientific">Bacillus phage phi29</name>
23+
<dbReference type="NCBI Taxonomy" id="10756"/>
24+
</organism>
25+
<sequence length="20" mass="2100" checksum="0000000000000000" modified="1986-07-21" version="1">MAGKKQNIVLESAWRELVGK</sequence>
26+
</entry>
27+
<entry dataset="Swiss-Prot" created="1986-07-21" modified="2021-09-29" version="1">
28+
<accession>P03681</accession>
29+
<name>PORT_BPPH2</name>
30+
<protein>
31+
<recommendedName>
32+
<fullName>Head-tail connector protein</fullName>
33+
</recommendedName>
34+
</protein>
35+
<gene>
36+
<name type="primary">10</name>
37+
</gene>
38+
<organism>
39+
<name type="scientific">Bacillus phage phi29</name>
40+
<dbReference type="NCBI Taxonomy" id="10756"/>
41+
</organism>
42+
<sequence length="22" mass="2300" checksum="1111111111111111" modified="1986-07-21" version="1">MSKTLNEVLGQVADSFRTKGWK</sequence>
43+
</entry>
44+
<entry dataset="Swiss-Prot" created="1986-07-21" modified="2021-09-29" version="1">
45+
<accession>P03682</accession>
46+
<name>DPOL_BPPH2</name>
47+
<protein>
48+
<recommendedName>
49+
<fullName>DNA polymerase</fullName>
50+
</recommendedName>
51+
</protein>
52+
<gene>
53+
<name type="primary">2</name>
54+
</gene>
55+
<organism>
56+
<name type="scientific">Bacillus phage phi29</name>
57+
<dbReference type="NCBI Taxonomy" id="10756"/>
58+
</organism>
59+
<sequence length="24" mass="2600" checksum="2222222222222222" modified="1986-07-21" version="1">MPRKMYSCDFETTTKLDDCRVWAY</sequence>
60+
</entry>
61+
</uniprot>

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