Ejemplo n.º 1
0
 public static string[] ExpectedPdbFilenames(string folder, string pdbId)
 {
     return(new[]
     {
         FileAndPathMethods.MergePathAndFilename(folder, pdbId + ".pdb"),
         FileAndPathMethods.MergePathAndFilename(folder, "pdb" + pdbId + ".ent")
     });
 }
        /// <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);
        }