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);
}