public CodingSequenceCollection FetchCodingSequenceData(CodingSequenceCollection codingSequenceCollection, string[] cdsArray) { List <string> nonMatchedCds = new List <string>(); CodingSequenceCollection updatedCodingSequenceCollection = new CodingSequenceCollection(); foreach (string givenCds in cdsArray) { bool isMatch = false; foreach (CodingSequence codingSequence in codingSequenceCollection.collection) { if (codingSequence.GeneProduct.Equals(givenCds)) { updatedCodingSequenceCollection.AddCodingSequence(codingSequence); isMatch = true; } } if (!isMatch) { nonMatchedCds.Add(givenCds); } } //If all CDS entries did not match: if (!updatedCodingSequenceCollection.collection.Any()) { Console.WriteLine("None of the provided entries could be found."); } else if (!nonMatchedCds.Any()) { //Display list of CDS entries that did not match. String message = ""; foreach (String cds in nonMatchedCds) { if (message == "") { message += "Some of the provided CDS could not be found. Here is the list of CDS; "; message += cds; } else { message += ", " + cds; } } Console.WriteLine("\n" + message); } updatedCodingSequenceCollection.Sort(); return(updatedCodingSequenceCollection); }
public CollectedGeneBankData ReadGenebankFile(string inputFile) { //Split path to get file name. GeneCollection geneCollection = new GeneCollection(); CodingSequenceCollection codingSequenceCollection = new CodingSequenceCollection(); string fileName = Path.GetFileName(inputFile); string organism = ""; string accession = ""; string length = ""; string originSequence = ""; //Booleans for if/else statements. bool isFirst = true; bool isOrigin = false; bool currentEntryIsCDS = false; bool currentEntryIsGene = false; //Both patterns check if both complement and non-complement entries are present. string genePattern = " *gene *(complement)?\\(?\\d*\\.\\.\\d*\\)?"; string cdsPattern = " *CDS *(complement)?\\(?\\d*\\.\\.\\d*\\)?"; string currentEntry = ""; StreamReader reader = new StreamReader(inputFile); string gbkLine; while ((gbkLine = reader.ReadLine()) != null) { //All comming lines contain nucleotide data which can be added to the origin sequence. if (isOrigin) { originSequence += Regex.Replace(gbkLine, "(\\d| )", ""); } //Only occurs untill first entry is false. if (isFirst) { if (gbkLine.StartsWith("LOCUS")) { length = GetSequenceLength(gbkLine); } if (gbkLine.Contains(" ORGANISM")) { organism = GetOrganism(gbkLine); } if (gbkLine.Contains("ACCESSION")) { accession = GetAccessionId(gbkLine); } } //Check if if (currentEntryIsCDS && !Regex.IsMatch(gbkLine, genePattern)) { currentEntry += gbkLine + "\n"; } else if (currentEntryIsCDS && Regex.IsMatch(gbkLine, genePattern)) { currentEntryIsGene = true; currentEntryIsCDS = false; CodingSequence codingSequence = CreateCodingSequenceEntry(currentEntry); codingSequenceCollection.AddCodingSequence(codingSequence); currentEntry = gbkLine + "\n"; } else if (currentEntryIsGene && !Regex.IsMatch(gbkLine, cdsPattern)) { currentEntry += gbkLine + "\n"; } else if (currentEntryIsGene && Regex.IsMatch(gbkLine, cdsPattern)) { currentEntryIsGene = false; currentEntryIsCDS = true; Gene gene = CreateGeneEntry(currentEntry); geneCollection.AddGene(gene); currentEntry = gbkLine + "\n"; } else if (isFirst && Regex.IsMatch(gbkLine, genePattern)) { currentEntryIsGene = true; isFirst = false; currentEntry += gbkLine + "\n"; } else if (isFirst && Regex.IsMatch(gbkLine, cdsPattern)) { currentEntryIsCDS = true; isFirst = false; currentEntry += gbkLine + "\n"; } if (gbkLine.StartsWith("ORIGIN")) { //Set isOrigin to true: first if statement will be handled. isOrigin = true; string line = gbkLine.Replace("ORIGIN", ""); originSequence += Regex.Replace(line, "(\\d| )", ""); if (currentEntryIsCDS) { currentEntryIsCDS = false; CodingSequence codingSequence = CreateCodingSequenceEntry(currentEntry); codingSequenceCollection.AddCodingSequence(codingSequence); } else if (currentEntryIsGene) { currentEntryIsGene = false; Gene gene = CreateGeneEntry(currentEntry); geneCollection.AddGene(gene); } } } int geneCount = geneCollection.collection.Count; //Size of gene collection int cdsCount = codingSequenceCollection.collection.Count; //Size of coding sequence collection double totalGeneCounter = 0.0; double forwardGeneCounter = 0.0; foreach (Gene geneEntry in geneCollection.collection) { if (!geneEntry.IsReverse) { totalGeneCounter++; forwardGeneCounter++; } else { totalGeneCounter++; } } //Forward/Reverse (FR) ratio calculation. double value = (forwardGeneCounter / totalGeneCounter); double forwardReverseBalance = Math.Round(value, 1); //For each gene: if gene isForward or !isReverse > +1 to total and foward //else +1 to total Summary summary = new Summary(fileName, organism, accession, length, geneCount, forwardReverseBalance, cdsCount, originSequence); CollectedGeneBankData geneBankeData = new CollectedGeneBankData(geneCollection, codingSequenceCollection, summary); return(geneBankeData); }