public void SaveToFile(string saveFilename, int numberProteinInterfacesRequired = -1)
{
var rowList = new List <SpreadsheetCell[]> {
SpreadsheetColumnHeadersRow()
};
rowList.AddRange(SpreadsheetDataRowList(numberProteinInterfacesRequired));
SpreadsheetFileHandler.SaveSpreadsheet(saveFilename, null, rowList);
}
public static void SaveUniProtSpreadsheet(string saveFilename, ProgressActionSet progressActionSet)
{
if (saveFilename == null)
{
throw new ArgumentNullException(nameof(saveFilename));
}
List <SpreadsheetCell[]> spreadsheet = UniProtHeatMapSpreadsheet();
string[] savedFiles = SpreadsheetFileHandler.SaveSpreadsheet(saveFilename, null, spreadsheet);
foreach (string savedFile in savedFiles)
{
ProgressActionSet.Report("Saved: " + savedFile, progressActionSet);
}
}
/// <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 string[] SaveVectorDistanceMatrixSpreadsheet(string saveFilename, List <VectorProteinInterfaceWhole> vectorProteinInterfaceWholeList, double[,] vectorDistanceMatrix)
{
if (saveFilename == null)
{
throw new ArgumentNullException(nameof(saveFilename));
}
if (vectorProteinInterfaceWholeList == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfaceWholeList));
}
if (vectorDistanceMatrix == null)
{
throw new ArgumentNullException(nameof(vectorDistanceMatrix));
}
var spreadsheet = new SpreadsheetCell[vectorDistanceMatrix.GetLength(0) + 1, vectorDistanceMatrix.GetLength(1) + 1];
for (var indexX = 0; indexX < vectorDistanceMatrix.GetLength(0); indexX++)
{
spreadsheet[0, indexX + 1] = new SpreadsheetCell(vectorProteinInterfaceWholeList[indexX].FullProteinInterfaceId.ToString());
}
spreadsheet[0, 0] = new SpreadsheetCell("");
for (var indexY = 0; indexY < vectorDistanceMatrix.GetLength(1); indexY++)
{
spreadsheet[indexY + 1, 0] = new SpreadsheetCell(vectorProteinInterfaceWholeList[indexY].FullProteinInterfaceId.ToString());
}
for (var indexX = 0; indexX < vectorDistanceMatrix.GetLength(0); indexX++)
{
for (var indexY = 0; indexY < vectorDistanceMatrix.GetLength(1); indexY++)
{
spreadsheet[indexX + 1, indexY + 1] = new SpreadsheetCell(vectorDistanceMatrix[indexX, indexY]);
}
}
var savedFiles = SpreadsheetFileHandler.SaveSpreadsheet(saveFilename, null, spreadsheet);
return(savedFiles);
}
/// <summary>
/// This method iterates through the provided FASTA files creating separate calculated outputs for each of them.
/// </summary>
/// <param name="fastaFiles">The FASTA files to process.</param>
/// <param name="pdbFilesFolders">The locations where PDB files may be found.</param>
/// <param name="spreadsheetSaveFilenameTemplate">A template filename to save the outputs.</param>
/// <param name="saveTsv"></param>
/// <param name="saveXl"></param>
/// <param name="cancellationToken"></param>
/// <param name="progressActionSet"></param>
/// <param name="fileExistsOptions"></param>
public static void MakeHomodimerStatisticsSpreadsheetsAndOutputFiles(decimal maxAtomInterationDistance, string[] fastaFiles, string[] pdbFilesFolders, string spreadsheetSaveFilenameTemplate, bool saveTsv, bool saveXl, CancellationToken cancellationToken, ProgressActionSet progressActionSet = null, FileExistsHandler.FileExistsOptions fileExistsOptions = FileExistsHandler.FileExistsOptions.AppendNumberToFilename)
{
if (fastaFiles == null || fastaFiles.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(fastaFiles));
}
if (pdbFilesFolders == null || pdbFilesFolders.Length == 0)
{
throw new ArgumentOutOfRangeException(nameof(pdbFilesFolders));
}
if (!saveTsv && !saveXl)
{
throw new ArgumentOutOfRangeException(nameof(saveTsv));
}
for (int fastaFileNumber = 0; fastaFileNumber < fastaFiles.Length; fastaFileNumber++)
{
string fastaFilename = fastaFiles[fastaFileNumber];
if (string.IsNullOrWhiteSpace(fastaFilename))
{
continue;
}
ProgressActionSet.Report("Attempting to open file: " + fastaFilename, progressActionSet);
List <ISequence> sequences = SequenceFileHandler.LoadSequenceFile(fastaFilename, StaticValues.MolNameProteinAcceptedValues);
var pdbIdChainIdList = ProteinDataBankFileOperations.PdbIdChainIdList(sequences);
if ((sequences == null) || (sequences.Count == 0))
{
ProgressActionSet.Report("Error could not load file: " + fastaFilename, progressActionSet);
continue;
}
ProgressActionSet.Report("Loaded " + sequences.Count + " sequences from file: " + fastaFilename, progressActionSet);
List <string> pdbIdList = FilterProteins.SequenceListToPdbIdList(sequences);
string appendFilename = FileAndPathMethods.FullPathToFilename(fastaFilename);
ProgressActionSet.Report("Creating spreadsheets...", progressActionSet);
Stopwatch stopwatch = Stopwatch.StartNew();
var spreadsheetList = MakeHomodimerStatisticsSpreadsheetsList(cancellationToken, maxAtomInterationDistance, pdbFilesFolders, pdbIdList, pdbIdChainIdList, progressActionSet);
stopwatch.Stop();
ProgressActionSet.Report("Finished calculating spreadsheet data [Elapsed: " + stopwatch.Elapsed.ToString(@"dd\:hh\:mm\:ss") + "]", progressActionSet);
if (cancellationToken.IsCancellationRequested)
{
//UserProteinInterfaceOperations.ProgressBarReset(progressBar, 0, 100, 0);
////UserProteinInterfaceOperations.LabelEstimatedTimeRemainingUpdate(estimatedTimeRemaining, 0, 1, 1);
ProgressActionSet.StartAction(100, progressActionSet);
ProgressActionSet.ProgressAction(100, progressActionSet);
ProgressActionSet.FinishAction(false, progressActionSet);
ProgressActionSet.Report("Cancelled.", progressActionSet);
break;
}
for (int spreadsheetIndex = 0; spreadsheetIndex < spreadsheetList.Count; spreadsheetIndex++)
{
var spreadsheet = spreadsheetList[spreadsheetIndex];
if (cancellationToken.IsCancellationRequested)
{
break;
}
// Remove the first row (which has the name for use in a worksheet title, not currently used)
var sheetName = spreadsheet[0][0].CellData;
var spreadsheetName = spreadsheet[1][0].CellData;
spreadsheet.RemoveAt(0);
// "c:/dResults/Results - %date% %time% - %fasta_filename% - %spreadsheet_name%.tsv"
string saveFilename = spreadsheetSaveFilenameTemplate;
saveFilename = saveFilename.Replace("%spreadsheet_name%", spreadsheetName);
saveFilename = saveFilename.Replace("%fasta_filename%", appendFilename);
saveFilename = saveFilename.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
saveFilename = saveFilename.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
saveFilename = saveFilename.Replace("%batch_number%", ""); //string.Empty + (fastaFileNumber + 1));
saveFilename = saveFilename.Replace("%batch_letter%", ""); //SpreadsheetFileHandler.AlphabetLetterRollOver(spreadsheetIndex));
sheetName = sheetName.Replace("%spreadsheet_name%", spreadsheetName);
sheetName = sheetName.Replace("%fasta_filename%", appendFilename);
sheetName = sheetName.Replace("%date%", DateTime.Now.ToString("yyyy-MM-dd"));
sheetName = sheetName.Replace("%time%", DateTime.Now.ToString("HH.mm.ss"));
sheetName = sheetName.Replace("%batch_number%", ""); //string.Empty + (fastaFileNumber + 1));
sheetName = sheetName.Replace("%batch_letter%", ""); //SpreadsheetFileHandler.AlphabetLetterRollOver(spreadsheetIndex));
//var tsvFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".tsv");
var xlFilename = new FileInfo(FileAndPathMethods.RemoveFileExtension(saveFilename) + ".xlsx");
var savedFiles = SpreadsheetFileHandler.SaveSpreadsheet(xlFilename.FullName, new[] { sheetName }, spreadsheet, null, saveTsv, saveXl, fileExistsOptions);
ProgressActionSet.ReportFilesSaved(savedFiles, progressActionSet);
}
}
ProgressActionSet.Report("Finished processing files.", progressActionSet);
}
