Kdn adding and diagnostic filtering #2383

RayMSMS · 2024-07-03T17:01:35Z

Add Kdn sugar type in the dictionary
Add a new function "DiagnosticIon filter", which uses the diagnostic ion to distinguish the isobaric peak.
If we find 274/292 peak in Scan, we remove the glycan without A(NeuAc) in the candidate list.
Add the corresponding test for the filter function. Isobaric case: H1N1A1 & N2K1.

…Psms, Level1-glycoPsms) into the "AllResult.txt" file for glycoSearch (1) adding text function in PostGlycoSearchAnalysisTask class (2) adding tester in TestOGlyco class (make sure we parse the certain value) (3) revise the "readCsv", enable to read the allPSMs file smoothly.

…aMorpheus into glyco-search-comment

We also allow to get the same PSMs in duplicated files.

(1) Rewrite the Summary writing function (2)Add the <summary> comment in the fuction header

…aMorpheus into glyco-search-comment

codecov · 2024-07-03T17:38:22Z

Codecov Report

Attention: Patch coverage is 89.90536% with 32 lines in your changes missing coverage. Please review.

Project coverage is 93.69%. Comparing base (7dab370) to head (48267d9).

Files	Patch %	Lines
...yer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs	73.58%	3 Missing and 11 partials ⚠️
...pheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs	86.79%	2 Missing and 5 partials ⚠️
...Morpheus/EngineLayer/GlycoSearch/GlycanDatabase.cs	89.28%	1 Missing and 5 partials ⚠️
...heus/EngineLayer/GlycoSearch/GlycoSpectralMatch.cs	92.30%	0 Missing and 2 partials ⚠️
MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs	97.56%	0 Missing and 1 partial ⚠️
...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs	96.66%	1 Missing ⚠️
...eus/EngineLayer/ModernSearch/ModernSearchEngine.cs	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2383      +/-   ##
==========================================
+ Coverage   92.97%   93.69%   +0.72%     
==========================================
  Files         139      139              
  Lines       21668    21720      +52     
  Branches     2983     3004      +21     
==========================================
+ Hits        20146    20351     +205     
+ Misses       1043      910     -133     
+ Partials      479      459      -20

Files	Coverage Δ
MetaMorpheus/EngineLayer/GlycoSearch/AdjNode.cs	`80.00% <ø> (ø)`
MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs	`96.59% <100.00%> (+14.77%)`	⬆️
...pheus/EngineLayer/GlycoSearch/LocalizationGraph.cs	`100.00% <100.00%> (ø)`
MetaMorpheus/EngineLayer/GlycoSearch/ModBox.cs	`90.90% <ø> (ø)`
MetaMorpheus/EngineLayer/GlycoSearch/Node.cs	`88.00% <ø> (+21.33%)`	⬆️
MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs	`97.74% <100.00%> (+0.04%)`	⬆️
...pheus/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs	`97.59% <100.00%> (ø)`
...rpheus/TaskLayer/GlycoSearchTask/WriteGlycoFile.cs	`95.18% <ø> (ø)`
MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs	`97.04% <97.56%> (+0.25%)`	⬆️
...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs	`88.39% <96.66%> (+0.35%)`	⬆️
... and 5 more

... and 3 files with indirect coverage changes

…ycan fragment"

1. add new tester model for "OGlycanCompositionFragments"

1. add the tester for writing function, in different search type 2. glycoBox tester for decoy glycanBox

improve the converage

1. new function "DiagonsticFilter" was built and corresponding test "IsobaricCase" was built 2. "SpectralRecoveryTest" fixing, the set up function will automatically clean the folder when we find the extra file in that.

…com/RayMSMS/MetaMorpheus into Kdn-Adding-and-diagnostic-filtering

1. delete the bin and set the file "copy always" 2. revise the "MetaDrawSettingAndViewsTest", detailed informed on comment

nbollis

Looks good overall. I had a few questions and concerns that I left as comments throughout the PR. I also checked the code coverage and did not find an area where it would be easy to test the additions that you made.

nbollis · 2024-07-18T16:42:01Z

MetaMorpheus/EngineLayer/Glycan_Mods/OGlycan/Bullfrog 64 O-glycan wKdn corrected_convert.txt

Does this need to be a separate file or should it be added to one of the existing glyco files?

I just added to the existing glyco files. The Glycan_Mods is a default glycan database collection for the user.

nbollis · 2024-07-18T16:42:36Z

MetaMorpheus/EngineLayer/Glycan_Mods/OGlycan/OGlycan_withIsobaric.gdb

Does this need to be a separate file or should it be added to one of the existing .gdb files?

nbollis · 2024-07-18T16:43:17Z

MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs


        //TO DO: Decoy O-glycan can be created, but the results need to be reasoned.
        //public static int[] SugarShift = new int[]{ -16205282, -20307937, -29109542, -14605791, -30709033, -15005282, -36513219, -40615874, 16205282, 20307937, 29109542, 14605791, 30709033, 15005282, 36513219, 40615874 };
-        private readonly static int[] SugarShift = new int[] 
+        private readonly static int[] SugarShift = new int[] //still unclear about the shift...


are we still unclear about this shift? Can you add a comment about what these numbers are and how they are used?

nbollis · 2024-07-18T16:45:28Z

MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs

+        /// Constructor of GlycanBox.
+        /// </summary>
+        /// <param name="ids"> The glycanBox composition, each number represent one glycan index in the database</param>
+        /// <param name="targetDecoy"></param>
        public GlycanBox(int[] ids, bool targetDecoy = true):base(ids)


bool targetDecoy should be changed to isTarget to make it more clear if true is a target or true is a decoy

Corrected it. Thanks

nbollis · 2024-07-18T16:48:16Z

MetaMorpheus/EngineLayer/GlycoSearch/GlycanDatabase.cs

@@ -207,7 +240,7 @@ public static List<GlycanIon> NGlycanCompositionFragments(byte[] kind)

                            for (int add_fuc_count = 2; add_fuc_count <= fuc_count; add_fuc_count++)
                            {
-                                GlycanIon add_fuc_glycanIon = ExtendGlycanIon(hexose_glycanIon, 0, 0, (byte)add_fuc_count, 0, glycan_mass);
+                                GlycanIon add_fuc_glycanIon = ExtendGlycanIon(hexose_glycanIon, 0, 0, 1, 0, glycan_mass);


Calculated values are changed to heuristics and vice versa. Is this okay? Do we have tests for glycan database reading?

The fragment is for N-glycan fragmentation, we don't use that in O-pair search right now. But, I still do a small revision to correct the fragment issue. A tester is also built.

nbollis · 2024-07-18T16:55:06Z

MetaMorpheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs

-        private readonly int OxoniumIon204Index = 9; //Check Glycan.AllOxoniumIons
-        protected readonly List<GlycoSpectralMatch>[] GlobalCsms;
+        private readonly int OxoniumIon204Index = 9;               // Check Glycan.AllOxoniumIons
+        protected readonly List<GlycoSpectralMatch>[] GlobalCsms;  // Why don't we call it GlobalGsms?


You should make this change to Gsms. They likely did it because they copied the structure from cross link search

Got it. I already changed it.

nbollis · 2024-07-18T16:56:59Z

MetaMorpheus/EngineLayer/GlycoSearch/GlycoSpectralMatch.cs

        public static List<Tuple<int, int, bool>> GetLocalizedGlycan(List<Route> OGlycanBoxLocalization, out LocalizationLevel localizationLevel)
        {
            List<Tuple<int, int, bool>> localizedGlycan = new List<Tuple<int, int, bool>>();

-            //Dictionary<string, int>: modsite-id, count
-            Dictionary<string, int> seenModSite = new Dictionary<string, int>();
+            Dictionary<string, int> ModSiteSeenCount = new Dictionary<string, int>(); // all possible glycan-sites pair, Dictionary<string, int>: site-glycan pair, count


ModSiteSeenCount should be lowercase as it is accessible only inside this function

Got it. Corrected it.

Slove the Nic's comment

1. Delete the Bullfrog glycan database (data from collaborator) 2. add the summary comment on the "WriteProteinGlycoLocalization" function

…com/RayMSMS/MetaMorpheus into Kdn-Adding-and-diagnostic-filtering

RayMSMS and others added 14 commits May 28, 2024 10:43

The lie's comment about the glyco-searching

62013c0

Merge branch 'master' into glyco-search-comment

d1da509

Merge branch 'master' into glyco-search-comment

640c503

add the contaminant tester

a0d2377

Merge branch 'glyco-search-comment' of https://github.com/RayMSMS/Met…

88ce7b5

…aMorpheus into glyco-search-comment

Delet the unused constructor of Node class to cheat the coverage check

9ff4c2f

Fix the Fdr filter (initial: < 0.1, now <= 0.1)

02bcfce

Try to pass the coverage test, add the docoy filtering tester

206fd27

We also allow to get the same PSMs in duplicated files.

Merge branch 'master' into glyco-search-comment

fdd58a3

Merge branch 'master' into glyco-search-comment

8b2898a

update 7/2/2024

8a7f48d

(1) Rewrite the Summary writing function (2)Add the <summary> comment in the fuction header

Merge branch 'glyco-search-comment' of https://github.com/RayMSMS/Met…

aebf0ec

…aMorpheus into glyco-search-comment

Search the new sugar "Kdn"

2d7467c

RayMSMS added the WIP Work in progress, not ready for review label Jul 3, 2024

RayMSMS and others added 11 commits July 3, 2024 18:15

In order to pass the converage, add the new model in the tester "N-gl…

359154d

…ycan fragment"

Update 7/4/2024

09965d8

1. add new tester model for "OGlycanCompositionFragments"

update 7/5/2024

e5f3f49

1. add the tester for writing function, in different search type 2. glycoBox tester for decoy glycanBox

Merge branch 'master' into glyco-search-comment

3952bf1

wrting fuction update and tester

3b80d8b

Merge in my comment branch

7c2c7ef

improve the converage

update 7/10

9a038a1

1. new function "DiagonsticFilter" was built and corresponding test "IsobaricCase" was built 2. "SpectralRecoveryTest" fixing, the set up function will automatically clean the folder when we find the extra file in that.

Merge branch 'master' into Kdn-Adding-and-diagnostic-filtering

9d1c68a

fix the issue: The glycan database need to reload by the tester

ea690b9

Merge branch 'Kdn-Adding-and-diagnostic-filtering' of https://github.…

f3d2831

…com/RayMSMS/MetaMorpheus into Kdn-Adding-and-diagnostic-filtering

update 7/11/2024 try to fix the failed test issue

ef33bb5

1. delete the bin and set the file "copy always" 2. revise the "MetaDrawSettingAndViewsTest", detailed informed on comment

nbollis requested changes Jul 18, 2024

View reviewed changes

update 7/24

2d5db1b

Slove the Nic's comment

RayMSMS changed the title ~~[WIP] Kdn adding and diagnostic filtering~~ Kdn adding and diagnostic filtering Jul 30, 2024

Merge branch 'master' into Kdn-Adding-and-diagnostic-filtering

7019df1

RayMSMS added ready for review and removed WIP Work in progress, not ready for review labels Jul 30, 2024

trishorts approved these changes Jul 30, 2024

View reviewed changes

Alexander-Sol approved these changes Jul 30, 2024

View reviewed changes

RayMSMS added 2 commits July 30, 2024 14:46

update 7/30

72521e8

1. Delete the Bullfrog glycan database (data from collaborator) 2. add the summary comment on the "WriteProteinGlycoLocalization" function

Merge branch 'Kdn-Adding-and-diagnostic-filtering' of https://github.…

48267d9

…com/RayMSMS/MetaMorpheus into Kdn-Adding-and-diagnostic-filtering

nbollis approved these changes Aug 2, 2024

View reviewed changes

nbollis merged commit f48d118 into smith-chem-wisc:master Aug 2, 2024
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Kdn adding and diagnostic filtering #2383

Kdn adding and diagnostic filtering #2383

RayMSMS commented Jul 3, 2024 •

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Kdn adding and diagnostic filtering #2383

Kdn adding and diagnostic filtering #2383

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RayMSMS commented Jul 3, 2024 • edited Loading

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RayMSMS commented Jul 3, 2024 •

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codecov bot commented Jul 3, 2024 •

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