/// <summary>
/// Finds a suitable parser that supports the specified file, opens the file and returns the parser.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFileName(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (Helper.IsZippedFasta(fileName))
{
parser = new FastAZippedParser(fileName);
}
else if (Helper.IsZippedFastQ(fileName))
{
parser = new FastQZippedParser(fileName);
}
else if (IsFasta(fileName))
{
parser = new FastAParser(fileName);
}
else if (IsFastQ(fileName))
{
parser = new FastQParser(fileName);
}
else if (Helper.IsBAM(fileName))
{
throw new NotImplementedException();
//parser = new BAMSequenceParser(fileName);
}
else if (IsGenBank(fileName))
{
parser = new GenBankParser(fileName);
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
string fileExtension = Path.GetExtension(fileName);
if (!string.IsNullOrEmpty(fileExtension))
{
parser = All.FirstOrDefault(p => p.SupportedFileTypes.Contains(fileExtension));
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific parser was created for
// the passed filename - the parser is opened automatically in the constructor.
if (parser != null)
{
parser.Open(fileName);
}
}
}
}
return(parser);
}
public static void RunTests()
{
Dictionary <string, Sequence> loadedGenomes = new Dictionary <string, Sequence>();
System.IO.StreamWriter sw = new System.IO.StreamWriter("FailedTests.txt");
sw.WriteLine("Haplogroup\tAccession\tReasonFailed\tInGenbankNotHaplogrep\tInHaplogrepNotGenbank");
//First to load up the accession numbers
string fileName = "PhyloTreeSequences.fasta.gz";
FastAZippedParser fap = new FastAZippedParser(fileName);
foreach (var seq in fap.Parse())
{
var accession = seq.ID.Split('|')[3];
loadedGenomes[accession] = seq as Sequence;
if (accession.Contains('.'))
{
loadedGenomes[accession.Split('.')[0]] = seq as Sequence;
}
}
//now to grab all the trees
//var tree = TreeLoader.LoadTree(CONSTANTS.TREE_XML_FILE);
var tree = TreeLoader.LoadTree();
int FailedTests = 0;
int PassedTests = 0;
int AmbiguousFail = 0;
int SharedPolys = 0;
int UnSharedPolys = 0;
HashSet <int> BadPositions = new HashSet <int>();
foreach (var node in tree.GetAllChildren())
{
//if (node.haplogroup.id != "J1c3g")
//{ continue; }
try
{
//ignore empty and thousand genomes
if (!String.IsNullOrEmpty(node.haplogroup.AccessionId) &&
!node.haplogroup.AccessionId.StartsWith("NA") &&
!node.haplogroup.AccessionId.StartsWith("HG"))
{
var id = node.haplogroup.AccessionId;
if (id == "NC_012920")
{
continue;
}
var seq = loadedGenomes[id];
if (seq.Alphabet.HasAmbiguity)
{
//sw.WriteLine(node.haplogroup.id + "\t" + node.haplogroup.AccessionId + "\tAmbiguousSequence");
AmbiguousFail++;
continue;
}
//now check for differences
var origfoundPolys = NewSearchMethods.GenomeToHaploGrepConverter.FindPolymorphisms(seq).Where(x => !CONSTANTS.EXCLUDED_POSITIONS.Contains(x.position)).ToList();
var currentPolys = node.Mutations.ToList();//copy
List <Polymorphism> removeLater = new List <Polymorphism>();
var foundPolys = origfoundPolys.ToList();
foreach (var poly in origfoundPolys)
{
if (currentPolys.Contains(poly))
{
SharedPolys++; currentPolys.Remove(poly); foundPolys.Remove(poly);
}
}
currentPolys.Sort((x, y) => x.position.CompareTo(y.position));
currentPolys = CONSTANTS.CommonPolymorphismFilter(currentPolys).ToList();
foundPolys = CONSTANTS.CommonPolymorphismFilter(foundPolys).ToList();
if (currentPolys.Count > 0)// || foundPolys.Count > 0)
{
UnSharedPolys += currentPolys.Count + foundPolys.Count;
sw.WriteLine(node.haplogroup.id
+ "\t" + node.haplogroup.AccessionId
+ "\tMismatchedPolymorphisms"
+ "\t" + String.Join("-", foundPolys.Select(x => (object)x).ToArray())
+ "\t" + String.Join("-", currentPolys.Select(x => (object)x).ToArray())
);
FailedTests++;
foreach (var v in foundPolys)
{
BadPositions.Add(v.position);
}
foreach (var v in currentPolys)
{
BadPositions.Add(v.position);
}
}
else
{
PassedTests++;
}
}
}
catch (Exception thrown)
{
sw.WriteLine(node.haplogroup.id
+ "\t" + node.haplogroup.AccessionId
+ "\t" + thrown.Message);
}
}
sw.Close();
sw = new System.IO.StreamWriter("TestReport.txt");
sw.WriteLine("Failed Tests\t" + FailedTests.ToString());
sw.WriteLine("Passed Tests\t" + PassedTests.ToString());
sw.WriteLine("Ambiguous Sequences\t" + AmbiguousFail.ToString());
sw.WriteLine("Polymorphisms overlapping between genbank and haplogrep\t" + SharedPolys.ToString());
sw.WriteLine("Not Overlapping\t" + UnSharedPolys.ToString());
sw.WriteLine("Total Discordant Positions\t" + BadPositions.Count.ToString());
sw.WriteLine("Bad Position Listing");
var bps = BadPositions.ToList();
bps.Sort();
foreach (var bp in bps)
{
sw.WriteLine(bp.ToString());
}
sw.Close();
}
