Example #1
0
 public IEnumerable <Polymorphism> FilterPolys(IEnumerable <Polymorphism> polys)
 {
     if (additionalFilter == null)
     {
         return(CONSTANTS.CommonPolymorphismFilter(polys));
     }
     else
     {
         return(CONSTANTS.CommonPolymorphismFilter(polys.Where(z => additionalFilter(z))));
     }
 }
        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();
        }