private void AnnotateQuantEntries(string annotationString, List <AnnotationType> annotationsToAdd, Dictionary <string, AnnotationEntry> annotationEntryDict, Dictionary <string, Dictionary <AnnotationType, List <string> > > uniprotToAnnotationList)
{
foreach (QuantEntry quantEntry in CombinedQuantEntryDict.Values)
{
quantEntry.PopulateUniprotList(UniprotHeader);
foreach (string uniprotID in quantEntry.UniprotIDList)
{
Dictionary <AnnotationType, List <string> > annotationTypeToAnnotationEntry = null;
if (uniprotToAnnotationList.TryGetValue(uniprotID, out annotationTypeToAnnotationEntry))
{
foreach (AnnotationType annotationType in annotationsToAdd)
{
List <string> goTermsToadd = null;
if (annotationTypeToAnnotationEntry.TryGetValue(annotationType, out goTermsToadd))
{
foreach (string goID in goTermsToadd)
{
if (annotationType.Equals(AnnotationType.ProteinInteraction))
{
AnnotationEntry addEntry = new AnnotationEntry(goID, goID, AnnotationType.ProteinInteraction);
quantEntry.AddAnnotation(annotationType, addEntry);
}
else
{
quantEntry.AddAnnotation(annotationType, annotationEntryDict[goID]);
}
}
}
}
}
}
}
}
public void AddAnnotation(AnnotationType annotationType, AnnotationEntry annotationEntry)
{
List <AnnotationEntry> outEntries = null;
if (AnnotationEntries.TryGetValue(annotationType, out outEntries))
{
if (!outEntries.Contains(annotationEntry))
{
outEntries.Add(annotationEntry);
}
}
else
{
List <AnnotationEntry> addList = new List <AnnotationEntry>();
addList.Add(annotationEntry);
AnnotationEntries.Add(annotationType, addList);
}
}
public void AddAnnotation(AnnotationType annotationType, AnnotationEntry annotationEntry)
{
List<AnnotationEntry> outEntries = null;
if (AnnotationEntries.TryGetValue(annotationType, out outEntries))
{
if(!outEntries.Contains(annotationEntry))
{
outEntries.Add(annotationEntry);
}
}
else
{
List<AnnotationEntry> addList = new List<AnnotationEntry>();
addList.Add(annotationEntry);
AnnotationEntries.Add(annotationType, addList);
}
}
private void AnnotateQuantEntries(string annotationString, List<AnnotationType> annotationsToAdd, Dictionary<string, AnnotationEntry> annotationEntryDict, Dictionary<string, Dictionary<AnnotationType, List<string>>> uniprotToAnnotationList)
{
foreach (QuantEntry quantEntry in CombinedQuantEntryDict.Values)
{
quantEntry.PopulateUniprotList(UniprotHeader);
foreach(string uniprotID in quantEntry.UniprotIDList)
{
Dictionary<AnnotationType, List<string>> annotationTypeToAnnotationEntry = null;
if (uniprotToAnnotationList.TryGetValue(uniprotID, out annotationTypeToAnnotationEntry))
{
foreach (AnnotationType annotationType in annotationsToAdd)
{
List<string> goTermsToadd = null;
if (annotationTypeToAnnotationEntry.TryGetValue(annotationType, out goTermsToadd))
{
foreach (string goID in goTermsToadd)
{
if (annotationType.Equals(AnnotationType.ProteinInteraction))
{
AnnotationEntry addEntry = new AnnotationEntry(goID, goID, AnnotationType.ProteinInteraction);
quantEntry.AddAnnotation(annotationType, addEntry);
}
else
{
quantEntry.AddAnnotation(annotationType, annotationEntryDict[goID]);
}
}
}
}
}
}
}
}
private void BuildAnnotationDictionary(string databaseString, List<AnnotationType> annotationsToAdd)
{
//Fill the AnnotationEntryDict and UniprotIDtoAnnotationList
CurrentOrganism = databaseString;
string databaseFile = GetDatabasePath(databaseString);
UniProtXml uniprotXml = new UniProtXml(databaseFile);
Dictionary<string, List<string>> ensemblToUniprotDict = new Dictionary<string, List<string>>();
foreach (entry uniprotEntry in uniprotXml.Entries)
{
List<string> uniprotIDs = new List<string>();
List<AnnotationEntry> annotationEntries = new List<AnnotationEntry>();
foreach (string acession in uniprotEntry.accession)
{
uniprotIDs.Add(acession);
}
if (uniprotEntry.keyword != null)
{
if (annotationsToAdd.Contains(AnnotationType.Keywords))
{
foreach (keywordType keyword in uniprotEntry.keyword)
{
string keywordID = keyword.id;
AnnotationEntry outEntry = null;
if (AnnotationEntryDict.TryGetValue(keywordID, out outEntry))
{
annotationEntries.Add(outEntry);
}
else
{
AnnotationEntry addEntry = new AnnotationEntry(keywordID, keyword.Value, AnnotationType.Keywords);
annotationEntries.Add(addEntry);
AnnotationEntryDict.Add(addEntry.UniqueID, addEntry);
}
}
}
}
if (uniprotEntry.dbReference != null)
{
foreach (dbReferenceType goTerm in uniprotEntry.dbReference)
{
if (goTerm.type.Equals("GO"))
{
string goID = goTerm.id;
AnnotationEntry outEntry = null;
if (AnnotationEntryDict.TryGetValue(goID, out outEntry))
{
annotationEntries.Add(outEntry);
}
else
{
string goName = null;
AnnotationType goType = AnnotationType.GOCellularComponent;
foreach (propertyType property in goTerm.property)
{
if (property.type.Equals("term"))
{
string goString = property.value;
string[] goArray = goString.Split(':');
if (goArray[0].Equals("C"))
{
goType = AnnotationType.GOCellularComponent;
}
else if (goArray[0].Equals("F"))
{
goType = AnnotationType.GOMolecularFunction;
}
else if (goArray[0].Equals("P"))
{
goType = AnnotationType.GOBiologicalProcesses;
}
goName = goArray[1];
}
}
if (annotationsToAdd.Contains(goType))
{
AnnotationEntry addEntry = new AnnotationEntry(goID, goName, goType);
annotationEntries.Add(addEntry);
AnnotationEntryDict.Add(addEntry.UniqueID, addEntry);
}
}
}
if (goTerm.type.Equals("Ensembl"))
{
foreach (propertyType property in goTerm.property)
{
if (property.type.Equals("protein sequence ID"))
{
string ensemblID = property.value;
AnnotationEntry addEntry = new AnnotationEntry(ensemblID, "Ensembl ID", AnnotationType.EnsemblID);
List<string> outList1 = null;
if (ensemblToUniprotDict.TryGetValue(ensemblID, out outList1))
{
foreach (string id in uniprotIDs)
{
if(!outList1.Contains(id))
{
outList1.Add(id);
}
}
}
else
{
List<string> addList = new List<string>();
foreach (string id in uniprotIDs)
{
addList.Add(id);
}
ensemblToUniprotDict.Add(ensemblID, addList);
}
}
}
}
}
}
//Build the connections to the UniprotIDs
foreach (AnnotationEntry annotationEntry in annotationEntries)
{
foreach (string uniprotID in uniprotIDs)
{
Dictionary<AnnotationType, List<string>> outDict = null;
if (UniprotIDtoAnnotationList.TryGetValue(uniprotID, out outDict))
{
List<string> outList = null;
if (outDict.TryGetValue(annotationEntry.Type, out outList))
{
if(!outList.Contains(annotationEntry.UniqueID))
{
outList.Add(annotationEntry.UniqueID);
}
}
else
{
List<string> addList = new List<string>();
addList.Add(annotationEntry.UniqueID);
outDict.Add(annotationEntry.Type, addList);
}
}
else
{
Dictionary<AnnotationType, List<string>> addDict = new Dictionary<AnnotationType, List<string>>();
List<string> addList = new List<string>();
addList.Add(annotationEntry.UniqueID);
addDict.Add(annotationEntry.Type, addList);
UniprotIDtoAnnotationList.Add(uniprotID, addDict);
}
}
}
}
//Import the Protein Interactions
string interactionFile = "C:\\Users\\Chris\\Desktop\\Programs\\Mouse_Protein_Interactions.csv";
Dictionary<string, Dictionary<string, int>> ProteinInteractionDict = ImportProteinInteractionDictionary(interactionFile);
foreach (KeyValuePair<string, Dictionary<string, int>> kvp in ProteinInteractionDict)
{
List<string> outList = null;
if (ensemblToUniprotDict.TryGetValue(kvp.Key, out outList))
{
foreach (string primaryUniprotID in outList)
{
//Grab the annotation list for the uniprot ID
Dictionary<AnnotationType, List<string>> outDict = null;
if (UniprotIDtoAnnotationList.TryGetValue(primaryUniprotID, out outDict))
{
List<string> outList2 = null;
if (outDict.TryGetValue(AnnotationType.ProteinInteraction, out outList2))
{
foreach (string secondaryProtein in kvp.Value.Keys)
{
List<string> outList3 = null;
if (ensemblToUniprotDict.TryGetValue(secondaryProtein, out outList3))
{
foreach (string secondaryUniprotID in outList3)
{
outList2.Add(secondaryUniprotID);
}
}
}
}
else
{
List<string> addList = new List<string>();
foreach (string secondaryProtein in kvp.Value.Keys)
{
List<string> outList3 = null;
if (ensemblToUniprotDict.TryGetValue(secondaryProtein, out outList3))
{
foreach (string secondaryUniprotID in outList3)
{
addList.Add(secondaryUniprotID);
}
}
}
outDict.Add(AnnotationType.ProteinInteraction, addList);
}
}
}
}
}
uniprotXml.Dispose();
}
private void LoadEmbededDatabase(string databaseString)
{
string databaseLocation = null;
if (databaseString.Equals("Mouse"))
{
databaseLocation = "Coon.Compass.Procyon.Procyon_Mouse_GODatabase.csv";
}
else if (databaseString.Equals("Human"))
{
databaseLocation = "Coon.Compass.Procyon.Procyon_Human_GODatabase.csv";
}
else if (databaseString.Equals("Yeast"))
{
databaseLocation = "Coon.Compass.Procyon.Procyon_Yeast_GODatabase.csv";
}
if (databaseLocation != null)
{
using (var stream = Assembly.GetExecutingAssembly().GetManifestResourceStream(databaseLocation))
using (CsvReader reader = new CsvReader(new StreamReader(stream), true))
{
while (reader.ReadNextRecord())
{
if (reader["Linkage"].Equals("Connection") || reader["Linkage"].Equals("Interaction"))
{
string uniprotID = reader["ID"];
string goIDList = reader["Contents"];
string type = reader["Type"];
AnnotationType addType = GetAnnotationType(type);
Dictionary<AnnotationType, List<string>> outDict = new Dictionary<AnnotationType, List<string>>();
if (UniprotIDtoAnnotationList.TryGetValue(uniprotID, out outDict))
{
List<string> outStringList = null;
if (outDict.TryGetValue(addType, out outStringList))
{
foreach (string goID in goIDList.Split('|').ToList())
{
outStringList.Add(goID);
}
}
else
{
List<String> addList = new List<string>();
foreach (string goID in goIDList.Split('|').ToList())
{
addList.Add(goID);
}
outDict.Add(addType, addList);
}
}
else
{
List<string> addList = new List<string>();
foreach (string goID in goIDList.Split('|').ToList())
{
addList.Add(goID);
}
Dictionary<AnnotationType, List<string>> addDict = new Dictionary<AnnotationType, List<string>>();
addDict.Add(addType, addList);
UniprotIDtoAnnotationList.Add(uniprotID, addDict);
}
}
else if (reader["Linkage"].Equals("Annotation"))
{
string annotationID = reader["ID"];
string annotationName = reader["Contents"];
string type = reader["Type"];
AnnotationType addType = GetAnnotationType(type);
AnnotationEntry addEntry = new AnnotationEntry(annotationID, annotationName, addType);
AnnotationEntryDict.Add(addEntry.UniqueID, addEntry);
}
}
}
}
}
private void ImportSavedProcyonDatabase(string databaseFile)
{
using (CsvReader reader = new CsvReader(new StreamReader(databaseFile), true))
{
while (reader.ReadNextRecord())
{
if (reader["Linkage"].Equals("Connection") || reader["Linkage"].Equals("Interaction"))
{
string uniprotID = reader["ID"];
string goIDList = reader["Contents"];
string type = reader["Type"];
AnnotationType addType = GetAnnotationType(type);
Dictionary<AnnotationType, List<string>> outDict = new Dictionary<AnnotationType, List<string>>();
if (UniprotIDtoAnnotationList.TryGetValue(uniprotID, out outDict))
{
List<string> outStringList = null;
if (outDict.TryGetValue(addType, out outStringList))
{
foreach (string goID in goIDList.Split('|').ToList())
{
outStringList.Add(goID);
}
}
else
{
List<String> addList = new List<string>();
foreach (string goID in goIDList.Split('|').ToList())
{
addList.Add(goID);
}
outDict.Add(addType, addList);
}
}
else
{
List<string> addList = new List<string>();
foreach (string goID in goIDList.Split('|').ToList())
{
addList.Add(goID);
}
Dictionary<AnnotationType, List<string>> addDict = new Dictionary<AnnotationType, List<string>>();
addDict.Add(addType, addList);
UniprotIDtoAnnotationList.Add(uniprotID, addDict);
}
}
else if (reader["Linkage"].Equals("Annotation"))
{
string annotationID = reader["ID"];
string annotationName = reader["Contents"];
string type = reader["Type"];
AnnotationType addType = GetAnnotationType(type);
AnnotationEntry addEntry = new AnnotationEntry(annotationID, annotationName, addType);
AnnotationEntryDict.Add(addEntry.UniqueID, addEntry);
}
}
}
}