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update to gptmd engine (smith-chem-wisc#2447)
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* update to gptmd engine

* increment mods added

* scores a property

* eliminate unneccesary else

* eliminate spaces

* thread safe increment
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@trishorts
trishorts authored Dec 6, 2024
1 parent fee5a0c commit 5842b49
Showing 1 changed file with 35 additions and 41 deletions.
76 changes: 35 additions & 41 deletions MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@
using System.Linq;
using Omics;
using Omics.Modifications;
using System.Threading.Tasks;
using System.Collections.Concurrent;
using MassSpectrometry;
using Omics.Fragmentation;
using System.Collections.Concurrent;
using System.Threading.Tasks;

namespace EngineLayer.Gptmd
{
Expand All @@ -18,7 +18,9 @@ public class GptmdEngine : MetaMorpheusEngine
private readonly IEnumerable<Tuple<double, double>> Combos;
private readonly List<Modification> GptmdModifications;
private readonly Dictionary<string, Tolerance> FilePathToPrecursorMassTolerance; // this exists because of file-specific tolerances

//The ScoreTolerance property is used to differentiatie when a PTM candidate is added to a peptide. We check the score at each position and then add that mod where the score is highest.
private readonly double ScoreTolerance = 0.1;

public GptmdEngine(List<SpectralMatch> allIdentifications, List<Modification> gptmdModifications, IEnumerable<Tuple<double, double>> combos, Dictionary<string, Tolerance> filePathToPrecursorMassTolerance, CommonParameters commonParameters, List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, List<string> nestedIds) : base(commonParameters, fileSpecificParameters, nestedIds)
{
AllIdentifications = allIdentifications;
Expand All @@ -34,6 +36,7 @@ public static bool ModFits(Modification attemptToLocalize, IBioPolymer protein,
var proteinToMotifOffset = proteinOneBasedIndex - hehe - 1;
var indexUp = 0;
// Look up starting at and including the capital letter

while (indexUp < motif.ToString().Length)
{
if (indexUp + proteinToMotifOffset < 0 || indexUp + proteinToMotifOffset >= protein.Length || (!char.ToUpper(motif.ToString()[indexUp]).Equals('X') && !char.ToUpper(motif.ToString()[indexUp]).Equals(protein.BaseSequence[indexUp + proteinToMotifOffset])))
Expand Down Expand Up @@ -66,17 +69,14 @@ protected override MetaMorpheusEngineResults RunSpecific()
int modsAdded = 0;

int maxThreadsPerFile = CommonParameters.MaxThreadsToUsePerFile;
int[] threads = Enumerable.Range(0, maxThreadsPerFile).ToArray();
var psms = AllIdentifications.Where(b => b.FdrInfo.QValueNotch <= 0.05 && !b.IsDecoy).ToList();
Parallel.ForEach(threads, (i) =>
if (psms.Any() == false)
{
var localModDict = new ConcurrentDictionary<string, ConcurrentBag<Tuple<int, Modification>>>();
int localModsAdded = 0;

//foreach peptide in each psm and for each modification that matches the notch,
//add that modification to every allowed residue
//return those matches that give the highest score
for (; i < psms.Count(); i += maxThreadsPerFile)
return new GptmdResults(this, new Dictionary<string, HashSet<Tuple<int, Modification>>>(), 0);
}
Parallel.ForEach(Partitioner.Create(0, psms.Count), new ParallelOptions() { MaxDegreeOfParallelism = maxThreadsPerFile }, (range) =>
{
for (int i = range.Item1; i < range.Item2; i++)
{
foreach (var pepWithSetMods in psms[i].BestMatchingBioPolymersWithSetMods.Select(v => v.Peptide as PeptideWithSetModifications))
{
Expand Down Expand Up @@ -109,16 +109,16 @@ protected override MetaMorpheusEngineResults RunSpecific()

// If the score is within tolerance of the highest score, add the mod to the peptide
// If the tolerance is too tight, then the number of identifications in subsequent searches will be reduced
double scoreTolerance = 0.1;
var highScoreIndices = scores.Select((item, index) => new { item, index })
.Where(x => x.item > (scores.Max() - scoreTolerance))
.Where(x => x.item > (scores.Max() - ScoreTolerance))
.Select(x => x.index)
.ToList();

foreach (var index in highScoreIndices)
{
AddIndexedMod(localModDict, pepWithSetMods.Protein.Accession, new Tuple<int, Modification>(pepWithSetMods.OneBasedStartResidue + possibleIndices[index], mod));
System.Threading.Interlocked.Increment(ref localModsAdded);
AddIndexedMod(modDict, pepWithSetMods.Protein.Accession, new Tuple<int, Modification>(pepWithSetMods.OneBasedStartResidue + possibleIndices[index], mod));
System.Threading.Interlocked.Increment(ref modsAdded); ;
}
}
}
Expand All @@ -145,49 +145,42 @@ protected override MetaMorpheusEngineResults RunSpecific()
// if a variant protein and the mod is on the variant, index to the variant protein sequence
if (modIsOnVariant)
{
AddIndexedMod(localModDict, pepWithSetMods.Protein.Accession, new Tuple<int, Modification>(indexInProtein, mod));
System.Threading.Interlocked.Increment(ref localModsAdded);
AddIndexedMod(modDict, pepWithSetMods.Protein.Accession, new Tuple<int, Modification>(indexInProtein, mod));
foundSite = true;
System.Threading.Interlocked.Increment(ref modsAdded); ;
break;
}

// otherwise back calculate the index to the original protein sequence
if (modIsBeforeVariant)
{
AddIndexedMod(localModDict, pepWithSetMods.Protein.NonVariantProtein.Accession, new Tuple<int, Modification>(indexInProtein - offset, mod));
System.Threading.Interlocked.Increment(ref localModsAdded);
AddIndexedMod(modDict, pepWithSetMods.Protein.NonVariantProtein.Accession, new Tuple<int, Modification>(indexInProtein - offset, mod));
foundSite = true;
System.Threading.Interlocked.Increment(ref modsAdded); ;
break;
}

offset += variant.VariantSequence.Length - variant.OriginalSequence.Length;
}
if (!foundSite)
{
AddIndexedMod(localModDict, pepWithSetMods.Protein.NonVariantProtein.Accession, new Tuple<int, Modification>(indexInProtein - offset, mod));
System.Threading.Interlocked.Increment(ref localModsAdded);
AddIndexedMod(modDict, pepWithSetMods.Protein.NonVariantProtein.Accession, new Tuple<int, Modification>(indexInProtein - offset, mod));
System.Threading.Interlocked.Increment(ref modsAdded); ;
}
}
}
}
}
}
}
foreach (var kvp in localModDict)
{
modDict.AddOrUpdate(kvp.Key, kvp.Value, (key, existingBag) =>
{
foreach (var item in kvp.Value)
{
existingBag.Add(item);
}
return existingBag;
});
}
System.Threading.Interlocked.Add(ref modsAdded, localModsAdded);
});

return new GptmdResults(this, modDict.ToDictionary(kvp => kvp.Key, kvp => new HashSet<Tuple<int, Modification>>(kvp.Value)), modsAdded);
// Convert ConcurrentDictionary to Dictionary with HashSet
var finalModDictionary = modDict.ToDictionary(
kvp => kvp.Key,
kvp => new HashSet<Tuple<int, Modification>>(kvp.Value)
);
return new GptmdResults(this, finalModDictionary, modsAdded);
}
private List<double> CalculatePeptideScores(List<PeptideWithSetModifications> newPeptides, DissociationType dissociationType, SpectralMatch psm)
{
Expand All @@ -211,13 +204,14 @@ private List<double> CalculatePeptideScores(List<PeptideWithSetModifications> ne
}
private static void AddIndexedMod(ConcurrentDictionary<string, ConcurrentBag<Tuple<int, Modification>>> modDict, string proteinAccession, Tuple<int, Modification> indexedMod)
{
modDict.AddOrUpdate(proteinAccession, new ConcurrentBag<Tuple<int, Modification>> { indexedMod }, (key, existingBag) =>
{
existingBag.Add(indexedMod);
return existingBag;
});
modDict.AddOrUpdate(proteinAccession,
new ConcurrentBag<Tuple<int, Modification>> { indexedMod },
(key, existingBag) =>
{
existingBag.Add(indexedMod);
return existingBag;
});
}

private static IEnumerable<Modification> GetPossibleMods(double totalMassToGetTo, IEnumerable<Modification> allMods, IEnumerable<Tuple<double, double>> combos, Tolerance precursorTolerance, PeptideWithSetModifications peptideWithSetModifications)
{
foreach (var Mod in allMods.Where(b => b.ValidModification == true))
Expand Down

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