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Only quantify peptides that clear the q-value threshold #2375
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e25660a
Only quantify peptides that clear the q-value threshold
Alexander-Sol 5dd1ce9
Fixed failing test
Alexander-Sol 716cd40
Added OnlyQuantifyConfidentPeptides toggle
Alexander-Sol e2437c9
Reimplemented FdrInfo field, which now points to PsmFdrInfo
Alexander-Sol 3109c19
Fewer files changed
Alexander-Sol bb224d9
Fixed merge conflicts
Alexander-Sol 454d20c
Merge branch 'master' into PeptideFdrAndQuant
nbollis f4845b8
Hopefully fixed merge conflicts
Alexander-Sol 30b1bf5
pretty broken
Alexander-Sol eb5b703
Fixed broken things
Alexander-Sol 40f3f23
Merge branch 'master' into PeptideFdrAndQuant
trishorts a7e0680
Merge branch 'master' into PeptideFdrAndQuant
trishorts 02697cc
Merge branch 'master' into PeptideFdrAndQuant
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Original file line number | Diff line number | Diff line change |
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@@ -101,6 +101,16 @@ public static void AllResultsAndResultsTxtContainsCorrectValues_PepQValue_Bottom | |
Assert.AreEqual("TaGe_SA_A549_3_snip_2 - Target protein groups within 1 % FDR: 140", results[15]); | ||
} | ||
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[Test] | ||
public static void TestPeptideQuantificationResults() | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. This test seems subject to break in the future due to the hard coded number. Could you instead read in the peptides file, count the results at threshold, then use that in your assert? |
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{ | ||
EverythingRunnerEngineTestCase.TryGetTestCase(EverythingRunnerEngineTestCases.BottomUpQValue, out var testCase); | ||
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string peptideQuantFile = Path.Combine(testCase.OutputDirectory, @"postSearchAnalysisTaskTestOutput\AllQuantifiedPeptides.tsv"); | ||
string[] peptideQuant = File.ReadAllLines(peptideQuantFile); | ||
Assert.AreEqual(175, peptideQuant.Length); // 174 peptides + header. Make sure that we're quantifying only those peptides with q-value <= 0.01 | ||
} | ||
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/// <summary> | ||
/// Ensures that there is the proper ratio of summary and individual lines in the result.txt file and that peptides and proteoforms are distinct | ||
/// </summary> | ||
|
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should we instead default the value to -1 or 1 to make it more clear from instantiation instead of within this method?