/**
* Method for load tree
* Status: OK
* Note: if you add a new treeLoader, update the switch...
*/
public void LoadTree(string path, TreeType treeType = TreeType.StockTechTree)
{
ResetTree();
if (_treeData == null)
{
return;
}
var parser = new Parser();
_config = parser.ParseConfig(path);
switch (treeType)
{
case TreeType.StockTechTree:
_treeLoader = new StockTechTreeLoader();
break;
case TreeType.YongeTech:
_treeLoader = new YongeTechTreeLoader();
break;
default:
throw new Exception("The techtree's file format is not reconized !");
}
_treeLoader.LoadTree(_config, _treeData);
_treeData.LinkNodes();
_treeData.WorkspaceViewModel.StatusBarText = "Tree Loaded";
}
public void LoadTree(int index)
{
DisableWorldError();
TreeLoader.LoadTree(index);
if (TreeLoader.CurrentTree != null)
{
TreeBuilder.Instance.BuildTree(TreeLoader.CurrentTree);
}
else //it's all gone horribly wrong - the newick parser has failed to parse the tree
{
GameManager.DebugLog("Tree loading failed");
TreeBuilder.Instance.ResetTreeContainer();
ShowWorldError(NewickParser.ErrorMessage);
}
}
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();
}
public HaplotypeSearcher()
{
treeRoot = TreeLoader.LoadTree(); //CONSTANTS.TREE_XML_FILE);
var skipped = HaploSearchManager.SetPhylogeneticWeights(); //CONSTANTS.WEIGHT_FILE);
}