public ParsedFile CreateDbEntry(ParsedFile parsedFile) { var finishedFile = parsedFile; finishedFile.Run.AccessionSections = parsedFile.AccessionSections; finishedFile.Run.FamilySections = parsedFile.FamilySections; finishedFile.Run.FastaSections = parsedFile.FastaSections; return(finishedFile); }
public ParsedFile ParseAccessionSection(ParsedFile partiallyParsedFileCF, UnparsedFile unparsedFile) { int i = 1; string[] temp; foreach (string line in unparsedFile.AccessionLinesFromFile) { temp = line.Split(new char[] { ';' }); var accessionSection = ParseAccessionSectionLine(temp, i, unparsedFile.Sra); partiallyParsedFileCF.AccessionSections.Add(accessionSection); i++; } var partiallyParsedFileCFA = partiallyParsedFileCF; return(partiallyParsedFileCFA); }
public ParsedFile ParseFamilySection(ParsedFile partiallyParsedFileC, UnparsedFile unparsedFile) { int i = 1; string[] temp; foreach (string line in unparsedFile.FamilyLinesFromFile) { temp = line.Split(new char[] { ';' }); var familySection = ParseFamilySectionLine(temp, i, unparsedFile.Sra); partiallyParsedFileC.FamilySections.Add(familySection); i++; } var partiallyParsedFileCF = partiallyParsedFileC; return(partiallyParsedFileCF); }
public ParsedFile ParseCommentLine(string fileName, UnparsedFile unparsedFile) { string[] split = unparsedFile.CommentLineFromFile.Split(new char[] { ',' }); string[] sra = split[0].Split(new char[] { '=' }); string[] gen = split[1].Split(new char[] { '=' }); string[] date = split[2].Split(new char[] { '=' }); unparsedFile.Sra = sra[2]; var run = new Run(); run.FileName = fileName; run.Sra = sra[2]; run.Genome = gen[1]; run.Date = date[1]; var partiallyParsedFile = new ParsedFile(); partiallyParsedFile.Run = run; return(partiallyParsedFile); }
public ParsedFile ParseFastaSection(ParsedFile partiallyParsedFileCFA, UnparsedFile unparsedFile) { bool first = true; bool second = false; int i = 1; int j = 0; List <string> firstLine = new List <string>(); List <string> secondLine = new List <string>(); List <int> lineNumber = new List <int>(); foreach (string line in unparsedFile.FastaLinesFromFile) { if (first) { firstLine.Add(line); first = !first; } if (second) { secondLine.Add(line); lineNumber.Add(i); i++; first = !first; partiallyParsedFileCFA.FastaSections.Add(new FastaSection { FastaSectionLineId = lineNumber[j], Sra = unparsedFile.Sra, SequenceId = firstLine[j], Sequence = secondLine[j] }); j++; } second = !second; } var parsedFile = partiallyParsedFileCFA; return(parsedFile); }