/// <summary>
/// Filters the given FASTA files and PDB files with the given options and saves the results to disk. Data needs to be
/// cleaned for two reasons, firstly to not pollute or distort the results, and secondly to save unnecessary processing
/// operations.
/// </summary>
/// <param name="cancellationToken"></param>
/// <param name="pdbFilesFolders"></param>
/// <param name="fastaFiles"></param>
/// <param name="proteinOperationOptionFlags"></param>
/// <param name="saveFastaFilenameTemplate"></param>
/// <param name="consoleTextBox"></param>
/// <param name="progressBar"></param>
/// <param name="estimatedTimeRemaining"></param>
public static void CleanProteins(CancellationToken cancellationToken, decimal maxAtomInterationDistance, string[] pdbFilesFolders, string[] fastaFiles, ProteinOperation proteinOperationOptionFlags, string saveFastaFilenameTemplate, ProgressActionSet progressActionSet, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
if (pdbFilesFolders == null || pdbFilesFolders.Length == 0)
{
if (proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveMultipleModelsInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonInteractingProteinsInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonSymmetricalInStructure) || proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInStructure))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilesFolders));
}
}
if (fastaFiles == null || fastaFiles.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(fastaFiles));
}
if (string.IsNullOrWhiteSpace(saveFastaFilenameTemplate))
{
throw new ArgumentOutOfRangeException(nameof(saveFastaFilenameTemplate));
}
string[] pdbFilesArray = ProteinDataBankFileOperations.GetPdbFilesArray(pdbFilesFolders);
//List<string> pdbIdList = null;
int beforeCount = 0;
int afterCount = 0;
string saveFilename = saveFastaFilenameTemplate;
var currentProteinOperation = ProteinOperation.LoadFile;
int[] numberSequencesLoaded;
var sequences = new List <ISequence> [3];
//UserProteinInterfaceOperations.TextBoxClear(consoleTextBox);
ProgressActionSet.Report("Filtering proteins.", progressActionSet);
// Load fasta/sequence files.
sequences[0] = SequenceFileHandler.LoadSequenceFileList(fastaFiles, StaticValues.MolNameProteinAcceptedValues, out numberSequencesLoaded, true);
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences[0]);
for (int numberSequencesLoadedIndex = 0; numberSequencesLoadedIndex < numberSequencesLoaded.Length; numberSequencesLoadedIndex++)
{
if (numberSequencesLoaded[numberSequencesLoadedIndex] > 0)
{
ProgressActionSet.Report("Loaded " + numberSequencesLoaded[numberSequencesLoadedIndex] / 2 + " proteins from file: " + fastaFiles[numberSequencesLoadedIndex], progressActionSet);
}
else
{
ProgressActionSet.Report("Error could not load file: " + fastaFiles[numberSequencesLoadedIndex], progressActionSet);
}
}
if (numberSequencesLoaded.Count(a => a > 0) == 0)
{
return;
}
// Replace placeholder variable names.
saveFilename = saveFilename.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
saveFilename = saveFilename.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
// Save initial loaded sequences.
if (File.Exists(saveFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
saveFilename = FileExistsHandler.FindNextFreeOutputFilename(saveFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
return;
}
}
// Removes any entries not having a protein alphabet.
while (currentProteinOperation != ProteinOperation.Finished)
{
if (cancellationToken.IsCancellationRequested)
{
break;
}
currentProteinOperation = (ProteinOperation)((int)currentProteinOperation * 2);
sequences[1] = null;
sequences[2] = null;
var sequencesDescriptions = new string[3];
if (currentProteinOperation == ProteinOperation.Finished)
{
break;
}
if (currentProteinOperation == ProteinOperation.RemoveNonProteinAlphabetInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonProteinAlphabetInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveWrongNumberOfChainsInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveExactDuplicatesInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveExactDuplicatesInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonHomodimersInSequence && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonHomodimersInSequence))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveWrongNumberOfChainsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveWrongNumberOfChainsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveMultipleModelsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveMultipleModelsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonInteractingProteinsInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonInteractingProteinsInStructure))
{
continue;
}
if (currentProteinOperation == ProteinOperation.RemoveNonSymmetricalInStructure && !proteinOperationOptionFlags.HasFlag(ProteinOperation.RemoveNonSymmetricalInStructure))
{
continue;
}
// Count sequences before operation.
beforeCount = sequences[0].Count / 2;
// Update user about what is happening.
ProgressActionSet.Report("", progressActionSet);
ProgressActionSet.Report("Removing " + ProteinOperationString(currentProteinOperation) + " entries [from " + beforeCount + " proteins]", progressActionSet);
// Start stopwatch to count duration of operation.
Stopwatch stopwatch = Stopwatch.StartNew();
// Perform specified operation.
switch (currentProteinOperation)
{
case ProteinOperation.RemoveNonProteinAlphabetInSequence:
{
sequencesDescriptions[0] = "01 - Removed non-protein sequences (sequence filter)";
sequences[0] = FilterProteins.RemoveNonProteinAlphabetSequences(cancellationToken, sequences[0], progressActionSet);
break;
}
case ProteinOperation.RemoveWrongNumberOfChainsInSequence:
{
sequencesDescriptions[0] = "02 - Removed non-dimers (sequence filter)";
sequences[0] = FilterProteins.RemoveSequencesWithIncorrectNumberOfChains(cancellationToken, sequences[0], 2, progressActionSet);
break;
}
case ProteinOperation.RemoveExactDuplicatesInSequence:
{
sequencesDescriptions[0] = "03 - Removed exact duplicates (sequence filter)";
sequences[0] = FilterProteins.RemoveDuplicates(cancellationToken, sequences[0], progressActionSet);
break;
}
case ProteinOperation.RemoveNonHomodimersInSequence:
{
// homodimers - all types - unfiltered for interactions or symmetry
var result = FilterProteins.SplitDimerTypes(cancellationToken, sequences[0], 30, 90, progressActionSet);
sequencesDescriptions[0] = "04 - Homodimers only (sequence filter)";
sequences[0] = result.HomoDimerPdbIdList;
sequencesDescriptions[1] = "04 - Heterodimers only (sequence filter)";
sequences[1] = result.HeteroDimerPdbIdList;
sequencesDescriptions[2] = "04 - Homology dimers only (sequence filter)";
sequences[2] = result.HomologyDimerPdbIdList;
break;
}
case ProteinOperation.RemoveMultipleModelsInStructure:
{
sequencesDescriptions[0] = "05 - Removed multiple models (structure filter)";
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
pdbIdList = FilterProteins.RemoveMultipleStructureModels(cancellationToken, pdbFilesFolders, pdbIdList, progressActionSet);
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveWrongNumberOfChainsInStructure:
{
sequencesDescriptions[0] = "06 - Removed non-dimers (structure filter)";
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
//var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences[0]);
pdbIdList = FilterProteins.RemoveStructuresWithIncorrectNumberOfChains(cancellationToken, pdbFilesFolders, pdbIdList, pdbIdChainIdList, 2, progressActionSet);
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveNonInteractingProteinsInStructure:
{
// Make copy of sequences as we will split the list into two parts - with and without interactions.
sequences[1] = new List <ISequence>(sequences[0]);
// Get pdb id list from sequences, to check for pdb file, load, perform processing.
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
// Makes a list of sequences with interactions.
pdbIdList = FilterProteins.RemoveSequencesWithoutInteractions(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
// Remove any protein not in the list, keep the ones in the list.
sequencesDescriptions[0] = "08 - dimers - with interactions - unfiltered for symmetry";
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[1] = "07 - dimers - no observed interactions";
sequences[1] = FilterProteins.RemoveSequences(cancellationToken, sequences[1], pdbIdList, FilterProteins.RemoveSequencesOptions.RemoveSequencesInList);
break;
}
case ProteinOperation.RemoveNonSymmetricalInStructure:
{
// Make copy of sequences as we will split the list into two parts - with and without symmetry.
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences[0]);
sequences[1] = new List <ISequence>(sequences[0]);
sequences[2] = new List <ISequence>(sequences[0]);
Dictionary <string, decimal> symmetryPercentage = FilterProteins.CalculateStructureSymmetry(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
var pdbSymmetrical = new List <string>();
var pdbPartSymmetrical = new List <string>();
var pdbNonSymmetrical = new List <string>();
foreach (var symmetryPercentageKeyValuePair in symmetryPercentage)
{
if (symmetryPercentageKeyValuePair.Value == 0.0m)
{
pdbNonSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else if (symmetryPercentageKeyValuePair.Value == 100.0m)
{
pdbSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else if (symmetryPercentageKeyValuePair.Value > 0.0m && symmetryPercentageKeyValuePair.Value < 100.0m)
{
pdbPartSymmetrical.Add(symmetryPercentageKeyValuePair.Key);
}
else
{
ProgressActionSet.Report("Error: Out of bounds symmetry value of " + symmetryPercentageKeyValuePair.Value + " was found in " + symmetryPercentageKeyValuePair.Key + ".", progressActionSet);
}
}
sequencesDescriptions[0] = "11 - dimers - with interactions - 100% symmetrical";
sequences[0] = FilterProteins.RemoveSequences(cancellationToken, sequences[0], pdbSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[1] = "10 - dimers - with interactions - 1% to 99% symmetrical";
sequences[1] = FilterProteins.RemoveSequences(cancellationToken, sequences[1], pdbPartSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
sequencesDescriptions[2] = "09 - dimers - with interactions - 0% symmetrical";
sequences[2] = FilterProteins.RemoveSequences(cancellationToken, sequences[2], pdbNonSymmetrical, FilterProteins.RemoveSequencesOptions.RemoveSequencesNotInList);
break;
}
}
// Stop stopwatch immediately after operation.
stopwatch.Stop();
// Count sequences after operation.
afterCount = sequences[0].Count / 2;
if (!cancellationToken.IsCancellationRequested)
{
for (int sequencesIndex = sequences.GetLowerBound(0); sequencesIndex <= sequences.GetUpperBound(0); sequencesIndex++)
{
if (sequences[sequencesIndex] != null)
{
// Find free filename to save the latest sequence results of operations.
string localSaveFilename = saveFilename;
localSaveFilename = localSaveFilename.Replace("%fasta_filename%", sequencesDescriptions[sequencesIndex]);
bool skipFile = false;
if (File.Exists(localSaveFilename))
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
localSaveFilename = FileExistsHandler.FindNextFreeOutputFilename(localSaveFilename);
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
skipFile = true;
}
}
if (!skipFile)
{
// Save the sequence results to previous set filename.
string savedFile /*s*/ = SequenceFileHandler.SaveSequencesAsFasta(sequences[sequencesIndex], localSaveFilename);
// Inform user that file has been saved.
//foreach (char savedFile in savedFiles)
//{
ProgressActionSet.Report("Saved file: " + savedFile, progressActionSet);
//}
}
}
}
// Update the user about the results.
ProgressActionSet.Report("Removed " + (beforeCount - afterCount) + " proteins. [" + afterCount + " proteins remaining]. Elapsed: " + stopwatch.Elapsed.ToString(@"dd\:hh\:mm\:ss"), progressActionSet);
}
}
if (!cancellationToken.IsCancellationRequested)
{
ProgressActionSet.Report("Finished all selected filtering operations.", progressActionSet);
}
else
{
ProgressActionSet.Report("Cancelled.", progressActionSet);
//UserProteinInterfaceOperations.ProgressBarReset(progressBar, 0, 100, 0);
////UserProteinInterfaceOperations.LabelEstimatedTimeRemainingUpdate(estimatedTimeRemaining, 0, 1, 1);
ProgressActionSet.StartAction(100, progressActionSet);
ProgressActionSet.ProgressAction(100, progressActionSet);
ProgressActionSet.FinishAction(false, progressActionSet);
}
}
/// <summary>
/// Save to disk a list of sequences in FASTA format.
/// </summary>
/// <param name="sequences"></param>
/// <param name="saveFilename"></param>
public static string SaveSequencesAsFasta(List <ISequence> sequences, string saveFilename, bool appendSequenceCountToFilename = true, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename, ProgressActionSet progressActionSet = null)
{
if (sequences == null) // || sequences.Count == 0)
{
throw new ArgumentOutOfRangeException(nameof(sequences));
}
if (string.IsNullOrWhiteSpace(saveFilename))
{
throw new ArgumentOutOfRangeException(nameof(saveFilename));
}
string result = null; // new List<string>();
if (appendSequenceCountToFilename)
{
saveFilename = AddSequenceAndProteinCountToFilename(sequences, saveFilename);
}
// make sure directory exists
var fileInfo = new FileInfo(saveFilename);
if (fileInfo.Exists)
{
if (fileExistsOptions == FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
fileInfo = new FileInfo(FileExistsHandler.FindNextFreeOutputFilename(fileInfo.FullName));
if (progressActionSet != null)
{
ProgressActionSet.Report("Save sequence: already exists, appended number: " + fileInfo.FullName, progressActionSet);
}
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.OverwriteFile)
{
if (progressActionSet != null)
{
ProgressActionSet.Report("Save sequence: overwriting file: " + fileInfo.FullName, progressActionSet);
}
}
else if (fileExistsOptions == FileExistsHandler.FileExistsOptions.SkipFile)
{
if (progressActionSet != null)
{
ProgressActionSet.Report("Save sequence: skipped file, already exists: " + fileInfo.FullName, progressActionSet);
}
return(result);
}
}
else
{
if (progressActionSet != null)
{
ProgressActionSet.Report("Save sequence: new file: " + fileInfo.FullName, progressActionSet);
}
}
if (fileInfo.Directory != null)
{
fileInfo.Directory.Create();
}
var formatter = new FastAFormatter(fileInfo.FullName);
formatter.Write(sequences);
formatter.Close();
result = fileInfo.FullName;
return(result);
}