/// <summary>
/// This method converts a sequence list into a distinct PDB ID list.
/// </summary>
/// <param name="sequenceList"></param>
/// <param name="distinct"></param>
/// <returns></returns>
public static List <string> SequenceListToPdbIdList(List <ISequence> sequenceList, bool distinct = true)
{
if (sequenceList == null)// || sequenceList.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequenceList));
}
if (distinct)
{
return(sequenceList.Select(a => SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).PdbId).Distinct().ToList());
}
else
{
return(sequenceList.Select(a => SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).PdbId).ToList());
}
}
/// <summary>
/// This method loads a single sequence file. FASTA is the preferred format.
/// </summary>
/// <param name="sequenceFilename"></param>
/// <param name="molNames"></param>
/// <param name="distinct"></param>
/// <returns></returns>
public static List <ISequence> LoadSequenceFile(string sequenceFilename, string[] molNames, bool distinct = true)
{
if (string.IsNullOrWhiteSpace(sequenceFilename))
{
throw new ArgumentOutOfRangeException(nameof(sequenceFilename));
}
if (!File.Exists(sequenceFilename))
{
throw new FileNotFoundException(sequenceFilename);
}
List <ISequence> sequences = null;
ISequenceParser sequenceParser = null;
try
{
sequenceParser = SequenceParsers.FindParserByFileName(sequenceFilename);
}
catch (DirectoryNotFoundException directoryNotFoundException)
{
// just forward exception for now
throw new DirectoryNotFoundException(directoryNotFoundException.Message, directoryNotFoundException.InnerException);
}
if (sequenceParser != null)
{
sequences = sequenceParser.Parse().ToList();
sequenceParser.Close();
if (distinct)
{
sequences = sequences.Distinct().ToList();
}
}
if (sequences != null && sequences.Count > 0 && molNames != null && molNames.Length > 0)
{
sequences = sequences.Where(a => molNames.Contains(SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).Mol)).ToList();
}
return(sequences);
}
/// <summary>
/// Save to disk a list of sequences in CSV/TSV format.
/// </summary>
/// <param name="sequences"></param>
/// <param name="filename"></param>
public static string[] SaveSequencesAsSpreadsheet(List <ISequence> sequences, string filename, bool tsvFormat = false, bool xlsxFormat = true)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentOutOfRangeException(nameof(filename));
}
if (!tsvFormat && !xlsxFormat)
{
throw new ArgumentOutOfRangeException(nameof(tsvFormat), tsvFormat, "No file formats were selected");
}
var headerColumnsRow = new[]
{
new SpreadsheetCell("PDB ID"),
new SpreadsheetCell("Chain"),
new SpreadsheetCell("Sequence"),
};
var rowList = new List <SpreadsheetCell[]>();
rowList.Add(headerColumnsRow);
foreach (ISequence sequence in sequences)
{
SequenceIdSplit.SequenceIdToPdbIdAndChainIdResult id = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequence.ID);
var row = new[]
{
new SpreadsheetCell(id.PdbId),
new SpreadsheetCell(id.ChainId),
new SpreadsheetCell(sequence.ConvertToString()),
};
rowList.Add(row);
}
string[] filesSavedStrings = SpreadsheetFileHandler.SaveSpreadsheet(filename, null, rowList, null, tsvFormat, xlsxFormat);
return(filesSavedStrings);
}
public static Dictionary <string, List <string> > PdbIdChainIdList(List <ISequence> sequenceList)
{
var result = new Dictionary <string, List <string> >();
foreach (var seq in sequenceList)
{
var seqId = SequenceIdSplit.SequenceIdToPdbIdAndChainId(seq.ID);
if (!result.ContainsKey(seqId.PdbId))
{
result.Add(seqId.PdbId, new List <string>());
}
result[seqId.PdbId].Add(seqId.ChainId);
}
return(result);
}
/// <summary>
/// This method removes sequences from the list which are not proteins (e.g. DNA, RNA, Hybrid).
/// </summary>
/// <returns></returns>
public static List <ISequence> RemoveNonProteinAlphabetSequences(CancellationToken cancellationToken, List <ISequence> sequences, ProgressActionSet progressActionSet, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
WorkDivision <List <string> > workDivision = new WorkDivision <List <string> >(sequences.Count, totalThreads);
ProgressActionSet.StartAction(sequences.Count, progressActionSet);
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
Task <List <string> > task = Task.Run(() =>
{
var taskResult = new List <string>();
for (int index = workDivision.ThreadFirstIndex[localThreadIndex]; index <= workDivision.ThreadLastIndex[localThreadIndex]; index++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
string proteinId = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[index].ID).PdbId;
if (sequences[index].Alphabet != Alphabets.Protein)
{
taskResult.Add(proteinId);
}
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
}
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var result = new List <string>();
foreach (var task in workDivision.TaskList.Where(t => t != null && t.Result != null && t.IsCompleted && !t.IsCanceled && !t.IsFaulted))
{
result.AddRange(task.Result);
}
result = result.Distinct().ToList();
List <ISequence> seq = RemoveSequences(cancellationToken, sequences, result);
return(seq);
}
/// <summary>
/// This method removes specified ids from the list of sequences.
/// </summary>
/// <param name="sequences"></param>
/// <param name="sequencesToKeepOrRemove"></param>
/// <param name="options"></param>
/// <returns></returns>
public static List <ISequence> RemoveSequences(CancellationToken cancellationToken, List <ISequence> sequences, List <string> sequencesToKeepOrRemove, RemoveSequencesOptions options = RemoveSequencesOptions.RemoveSequencesInList, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (sequencesToKeepOrRemove == null)
{
throw new ArgumentOutOfRangeException(nameof(sequencesToKeepOrRemove));
}
if (sequencesToKeepOrRemove != null)// && sequencesToKeepOrRemove.Count > 0)
{
var workDivision = new WorkDivision <List <int> >(sequences.Count, totalThreads);
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
Task <List <int> > task = Task.Run(() =>
{
var taskResult = new List <int>();
for (int sequencesIndex = workDivision.ThreadFirstIndex[localThreadIndex]; sequencesIndex <= workDivision.ThreadLastIndex[localThreadIndex]; sequencesIndex++)
{
string proteinId = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[sequencesIndex].ID).PdbId;
if (((options == RemoveSequencesOptions.RemoveSequencesInList) && (sequencesToKeepOrRemove.Contains(proteinId))) ||
((options == RemoveSequencesOptions.RemoveSequencesNotInList) && (!sequencesToKeepOrRemove.Contains(proteinId))))
{
taskResult.Add(sequencesIndex);
}
workDivision.IncrementItemsCompleted(1);
}
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var sequenceIndexesToRemove = new List <int>();
foreach (var task in workDivision.TaskList.Where(t => t != null && t.Result != null && t.IsCompleted && !t.IsCanceled && !t.IsFaulted))
{
sequenceIndexesToRemove.AddRange(task.Result);
}
sequenceIndexesToRemove = sequenceIndexesToRemove.Distinct().ToList();
sequenceIndexesToRemove.Sort();
for (int sequenceIndexesToRemoveIndex = sequenceIndexesToRemove.Count - 1; sequenceIndexesToRemoveIndex >= 0; sequenceIndexesToRemoveIndex--)
{
sequences.RemoveAt(sequenceIndexesToRemove[sequenceIndexesToRemoveIndex]);
}
}
return(sequences);
}
public static List <ISequence> RemoveDuplicates(CancellationToken cancellationToken, List <ISequence> sequences, ProgressActionSet progressActionSet, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
var pdbIdList = SequenceListToPdbIdList(sequences);
var pdbIdSequences = pdbIdList.Select(a => sequences.Where(b => SequenceIdSplit.SequenceIdToPdbIdAndChainId(b.ID).PdbId == a).ToList()).ToList();
var workDivision = new WorkDivision(pdbIdList.Count, totalThreads);
ProgressActionSet.StartAction(pdbIdList.Count, progressActionSet);
var done = new List <ISequence>();
var remove = new List <ISequence>();
var removeLock = new object();
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
var task = Task.Run(() =>
{
for (int index = workDivision.ThreadFirstIndex[localThreadIndex]; index <= workDivision.ThreadLastIndex[localThreadIndex]; index++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
var iterationPdbId = pdbIdList[index];
var iterationPdbIdSeqs = pdbIdSequences[index];// sequences.Where(a => SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).PdbId == pdbId).ToList();
//var seq = sequences[index];
//var seqid = SequenceIdSplit.SequenceIdToPdbIdAndChainId(seq.ID).PdbId.ToUpperInvariant();
lock (done)
{
if (iterationPdbIdSeqs.All(done.Contains))
{
continue;
}
}
foreach (var pdbIdSeqSet in pdbIdSequences)
{
if (pdbIdSeqSet == iterationPdbIdSeqs)
{
continue;
}
foreach (var pdbIdSeq in pdbIdSeqSet)
{
foreach (var iterationPdbIdSeq in iterationPdbIdSeqs)
{
}
}
}
// find sequences equal to the current iteration item
//var equalseq = sequences.Where(a => a.SequenceEqual(seq)).ToList();
/*
* var equalseq = sequences.Where(a => AlignedSequenceSimilarityPercentage(seq,a) >= 90).ToList();
*
*
*
* // get a list of pdbids, ordered alphabetically
* var equalseqids = equalseq.Select(p => SequenceIdSplit.SequenceIdToPdbIdAndChainId(p.ID).PdbId.ToUpperInvariant()).OrderBy(p => p).ToList();
*
* // one or more of the chains might have a difference sequence and so not in the list, update by the ids in the list
* //equalseq = sequences.Where(p => equalseqids.Contains(SequenceIdSplit.SequenceIdToPdbIdAndChainId(p.ID).PdbId.ToUpperInvariant())).ToList();
*
* // add this iteration item and all others with the same sequence to a list to skip in future
* lock (done)
* {
* done.AddRange(equalseq);
* }
*
* // keep the very last item in the list and all with the same pdbid that it has
* var keepid = equalseqids.Last();
* var equalseqkeep = equalseq.Where(p => SequenceIdSplit.SequenceIdToPdbIdAndChainId(p.ID).PdbId.ToUpperInvariant() == keepid).ToList();
*
* // remove the sequences to keep from the removal list
* equalseq = equalseq.Where(a => !equalseqkeep.Contains(a)).ToList();
*
* lock (remove)
* {
* remove.AddRange(equalseq);
* }
*/
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
}
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var remove2 = remove.Distinct().ToList();
return(RemoveSequences(cancellationToken, sequences, remove2.Select(p => SequenceIdSplit.SequenceIdToPdbIdAndChainId(p.ID).PdbId.ToUpperInvariant()).ToList()));
}
/// <summary>
/// Perform sequence alignment on the chains of each protein to see if it is a homodimer or heterodimer
/// </summary>
/// <returns></returns>
public static DimerSequenceTypeCategories <string> SplitDimersHomoHetero(CancellationToken cancellationToken, List <ISequence> sequences, decimal minimumHeterodimerSimilarityRequired = 30.0m, decimal minimumHomodimerSimiliarityRequired = 90.0m, ProgressActionSet progressActionSet = null, int totalThreads = -1)
{
if (sequences == null || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (progressActionSet == null)
{
throw new ArgumentNullException(nameof(progressActionSet));
}
var workDivision = new WorkDivision <DimerSequenceTypeCategories <string> >(sequences.Count, totalThreads);
ProgressActionSet.StartAction(sequences.Count, progressActionSet);
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
Task <DimerSequenceTypeCategories <string> > task = Task.Run(() =>
{
var taskResult = new DimerSequenceTypeCategories <string>();
for (int sequencesIndexA = workDivision.ThreadFirstIndex[localThreadIndex]; sequencesIndexA <= workDivision.ThreadLastIndex[localThreadIndex]; sequencesIndexA++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
string proteinIdA = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[sequencesIndexA].ID).PdbId;
for (int sequencesIndexB = 0; sequencesIndexB < sequences.Count; sequencesIndexB++)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
// Don't align the same sequence index. Skip calculating indexes already calculated. Perform alignment operation if protein id is the same.
var proteinIdB = SequenceIdSplit.SequenceIdToPdbIdAndChainId(sequences[sequencesIndexB].ID).PdbId;
if (sequencesIndexA == sequencesIndexB || sequencesIndexB < sequencesIndexA || proteinIdA != proteinIdB)
{
continue;
}
var dimerType = FindDimerType(sequences[sequencesIndexA], sequences[sequencesIndexB], minimumHeterodimerSimilarityRequired, minimumHomodimerSimiliarityRequired);
if (dimerType == DimerType.HeteroDimer)
{
taskResult.HeteroDimerPdbIdList.Add(proteinIdA);
}
else if (dimerType == DimerType.HomoDimer)
{
taskResult.HomoDimerPdbIdList.Add(proteinIdA);
}
else if (dimerType == DimerType.HomologyDimer)
{
taskResult.HomologyDimerPdbIdList.Add(proteinIdA);
}
}
workDivision.IncrementItemsCompleted(1);
ProgressActionSet.ProgressAction(1, progressActionSet);
ProgressActionSet.EstimatedTimeRemainingAction(workDivision.StartTicks, workDivision.ItemsCompleted, workDivision.ItemsToProcess, progressActionSet);
}
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
workDivision.WaitAllTasks();
var dimerSequenceTypeCategories = new DimerSequenceTypeCategories <string>();
foreach (var task in workDivision.TaskList.Where(t => t != null && t.IsCompleted && !t.IsFaulted && !t.IsCanceled && t.Result != null))
{
dimerSequenceTypeCategories.HeteroDimerPdbIdList.AddRange(task.Result.HeteroDimerPdbIdList);
dimerSequenceTypeCategories.HomoDimerPdbIdList.AddRange(task.Result.HomoDimerPdbIdList);
dimerSequenceTypeCategories.HomologyDimerPdbIdList.AddRange(task.Result.HomologyDimerPdbIdList);
}
dimerSequenceTypeCategories.HeteroDimerPdbIdList = dimerSequenceTypeCategories.HeteroDimerPdbIdList.Distinct().ToList();
dimerSequenceTypeCategories.HomoDimerPdbIdList = dimerSequenceTypeCategories.HomoDimerPdbIdList.Distinct().ToList();
dimerSequenceTypeCategories.HomologyDimerPdbIdList = dimerSequenceTypeCategories.HomologyDimerPdbIdList.Distinct().ToList();
return(dimerSequenceTypeCategories);
}
/// <summary>
/// This method loads multiple sequence files. FASTA is the preferred format.
/// </summary>
/// <param name="sequenceFilenames"></param>
/// <param name="numberSequencesLoaded"></param>
/// <param name="distinct"></param>
/// <returns></returns>
public static List <ISequence> LoadSequenceFileList(string[] sequenceFilenames, string[] molNames, out int[] numberSequencesLoaded, bool distinct = true)
{
if (sequenceFilenames == null || sequenceFilenames.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequenceFilenames));
}
var sequences = new List <ISequence>();
numberSequencesLoaded = new int[sequenceFilenames.Length];
for (int sequenceFilenameIndex = sequenceFilenames.GetLowerBound(0); sequenceFilenameIndex <= sequenceFilenames.GetUpperBound(0); sequenceFilenameIndex++)
{
List <ISequence> nextSequences = LoadSequenceFile(sequenceFilenames[sequenceFilenameIndex], molNames, distinct);
if ((nextSequences != null) && (nextSequences.Count > 0))
{
nextSequences = nextSequences.Where(a => !ProteinDataBankFileOperations.PdbIdBadList.Contains(SequenceIdSplit.SequenceIdToPdbIdAndChainId(a.ID).PdbId.ToUpperInvariant())).ToList();
numberSequencesLoaded[sequenceFilenameIndex] = nextSequences.Count;
sequences.AddRange(nextSequences);
}
else
{
numberSequencesLoaded[sequenceFilenameIndex] = 0;
}
}
if (distinct)
{
sequences = sequences.Distinct().ToList();
}
return(sequences);
}
