public void CosmicOutputTest()
{
var sa = new SupplementaryAnnotationPosition(115256529);
var saCreator = new SupplementaryPositionCreator(sa);
var altAllele = "C";
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var saReader = new MockSupplementaryAnnotationReader(sa);
VcfUtilities.FieldContains(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", "cosmic=1|COSM1000", VcfCommon.InfoIndex);
}
public void AllSuppAnnotOutputTest()
{
const string altAllele = "C";
var sa = new SupplementaryAnnotationPosition(115256529);
var oneKg = new OneKGenAnnotation
{
OneKgAllAn = 5008,
OneKgAllAc = 2130,
OneKgAmrAn = 694,
OneKgAmrAc = 250
};
var dbSnp = new DbSnpAnnotation
{
DbSnp = new List <long> {
11554290
}
};
var saCreator = new SupplementaryPositionCreator(sa);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, "C", oneKg);
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, "C", dbSnp);
var cosmicItem1 = new CosmicItem("chr1", 115256529, "COSM1000", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, 1,
altAllele);
var cosmicItem2 = new CosmicItem("chr1", 115256529, "COSM1001", "T", altAllele, "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, 1,
altAllele);
cosmicItem1.AddCosmicToSa(saCreator);
cosmicItem2.AddCosmicToSa(saCreator);
var clinvarItem1 = new ClinVarItem(null, 0, null, altAllele, null, "RCV001",
null, null, new List <string> {
"ORPHA2462"
}, null, null, "other");
sa.ClinVarItems.Add(clinvarItem1);
var saReader = new MockSupplementaryAnnotationReader(sa);
var infoColumn = VcfUtilities.GetVcfColumn(saReader,
"chr1\t115256529\t.\tT\tC\t1000\tPASS\t.\tGT\t0/1", VcfCommon.InfoIndex);
Assert.Contains("AF1000G=0.425319", infoColumn);
Assert.Contains("cosmic=1|COSM1000,1|COSM1001", infoColumn);
Assert.Contains("clinvar=1|other", infoColumn);
}
public void GetJsonString()
{
var cosmicItem = new CosmicItem(ChromosomeUtilities.Chr1, 100, "rs101", "A", "C", "GENE0", new HashSet <CosmicItem.CosmicStudy>
{
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" }),
new CosmicItem.CosmicStudy("101", new [] { "primary histology 0", "histology subtype 2" }, new [] { "primarySite 0", "site subtype 1" })
}, 1);
Assert.Equal("\"id\":\"rs101\",\"refAllele\":\"A\",\"altAllele\":\"C\",\"gene\":\"GENE0\",\"sampleCount\":1,\"cancerTypesAndCounts\":[{\"cancerType\":\"primary histology 0\",\"count\":2},{\"cancerType\":\"histology subtype 1\",\"count\":1},{\"cancerType\":\"histology subtype 2\",\"count\":1}],\"cancerSitesAndCounts\":[{\"cancerSite\":\"primarySite 0\",\"count\":2},{\"cancerSite\":\"site subtype 1\",\"count\":2}]", cosmicItem.GetJsonString());
}
public void MergeDbSnpCosmic1Kg()
{
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
const string vcfLine2 = "1 10228 . TA T 100 PASS AC=2130;AF=0.425319;AN=5008;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE)";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(10229));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(sa)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy(null, "carcinoma", "oesophagus")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(sa));
var oneKGenItem = _oneKGenReader.ExtractItems(vcfLine2)[0];
additionalItems.Add(oneKGenItem.SetSupplementaryAnnotations(sa));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa);
}
var asa = sa.SaPosition.AlleleSpecificAnnotations["1"];
var dbSnp = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as DbSnpAnnotation;
var oneKg = asa.Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.OneKg)] as OneKGenAnnotation;
Assert.NotNull(oneKg);
var oneKgAc = oneKg.OneKgAllAc;
var oneKgAn = oneKg.OneKgAllAn;
Assert.NotNull(oneKgAc);
Assert.NotNull(oneKgAn);
Assert.NotNull(dbSnp);
Assert.NotNull(oneKg);
Assert.Equal(dbSnp.DbSnp, new List <long> {
143255646
});
Assert.Equal("0.425319", (oneKgAc.Value / (double)oneKgAn.Value).ToString(JsonCommon.FrequencyRoundingFormat));
Assert.True(sa.SaPosition.ContainsCosmicId("COSM1000"));
}
public void EqualityAndHash()
{
var cosmicItem = new CosmicItem("chr1", 100, "rs101", "A", "C", "GENE0", new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("100", "histology", "primarySite")
}, 1);
var customHash = new HashSet <CosmicItem> {
cosmicItem
};
Assert.Equal(1, customHash.Count);
Assert.True(customHash.Contains(cosmicItem));
}
public void GetCancerTypeCount_same_study()
{
var cosmicItem = new CosmicItem(ChromosomeUtilities.Chr1, 100, "rs101", "A", "C", "GENE0", new HashSet <CosmicItem.CosmicStudy>
{
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" }),
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" })
}, 1);
var cancerTypeCounts = cosmicItem.GetCancerTypeCounts();
Assert.Equal(2, cancerTypeCounts.Count);
Assert.Equal(1, cancerTypeCounts["primary histology 0"]);
Assert.Equal(1, cancerTypeCounts["histology subtype 1"]);
}
public void GetTissueCount_same_study()
{
var cosmicItem = new CosmicItem(new Chromosome("chr1", "1", 0), 100, "rs101", "A", "C", "GENE0", new HashSet <CosmicItem.CosmicStudy>
{
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" }),
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" })
}, 1);
var tissueCounts = cosmicItem.GetTissueCounts();
Assert.Equal(2, tissueCounts.Count());
Assert.Equal(1, tissueCounts["primarySite 0"]);
Assert.Equal(1, tissueCounts["site subtype 1"]);
}
public void GetCancerTypeCount_different_studies()
{
var cosmicItem = new CosmicItem(new Chromosome("chr1", "1", 0), 100, "rs101", "A", "C", "GENE0", new HashSet <CosmicItem.CosmicStudy>
{
new CosmicItem.CosmicStudy("100", new [] { "primary histology 0", "histology subtype 1" }, new [] { "primarySite 0", "site subtype 1" }),
new CosmicItem.CosmicStudy("101", new [] { "primary histology 0", "histology subtype 2" }, new [] { "primarySite 0", "site subtype 1" })
}, 1);
var cancerTypeCounts = cosmicItem.GetCancerTypeCounts();
Assert.Equal(3, cancerTypeCounts.Count());
Assert.Equal(2, cancerTypeCounts["primary histology 0"]);
Assert.Equal(1, cancerTypeCounts["histology subtype 1"]);
Assert.Equal(1, cancerTypeCounts["histology subtype 2"]);
}
public void MergeDbSnpCosmic()
{
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryPositionCreator(new SupplementaryAnnotationPosition(10229));
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(sa)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy(null, "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(sa));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(sa));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(sa);
}
var dbSnpAnnotation =
sa.SaPosition.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(dbSnpAnnotation);
Assert.Equal(dbSnpAnnotation.DbSnp, new List <long> {
143255646
});
Assert.True(sa.SaPosition.ContainsCosmicId("COSM1000"));
}
private void FillChunk(ChunkCoords c)
{
ChunkCoords signedCoords = c;
signedCoords.ConvertToSignedCoords();
float amount = Mathf.PerlinNoise(c.x * perlinStretchModifier + perlinOffset.x,
c.y * perlinStretchModifier + perlinOffset.y);
float min = Mathf.Min(cosmicDensity.x, cosmicDensity.y);
float max = Mathf.Max(cosmicDensity.x, cosmicDensity.y);
amount = amount * (max - min) + min;
for (int i = 0; i < (int)amount; i++)
{
Vector3 spawnPos = new Vector3(UnityEngine.Random.Range(0f, EntityNetwork.CHUNK_SIZE),
UnityEngine.Random.Range(0f, EntityNetwork.CHUNK_SIZE),
(1f - Mathf.Pow(UnityEngine.Random.value, 7f * (max / amount))) * starDistanceRange + starMinDistance);
bool common = lessFrequentTypes.Count == 0 || UnityEngine.Random.value <= commonTypeFrequency;
List <Sprite> listToChooseFrom = common ? types : lessFrequentTypes;
CosmicItem newItem = new CosmicItem((byte)UnityEngine.Random.Range(0, listToChooseFrom.Count), spawnPos,
UnityEngine.Random.Range(scaleRange.x, scaleRange.y), (byte)UnityEngine.Random.Range(0, 8), common);
Chunk(c).Add(newItem);
}
}
public void ReadWriteDbSnpCosmic()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var cosmicVersion = new DataSourceVersion("COSMIC", "GRCh37_v71", DateTime.Parse("2014-10-21").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, cosmicVersion
};
// create our expected supplementary annotations
const string vcfLine1 = "1 10228 rs143255646 TA T . . RS=143255646;RSPOS=10229;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;WGT=1;VC=DIV;R5;ASP";
var sa = new SupplementaryAnnotationPosition(10229);
var saCreator = new SupplementaryPositionCreator(sa);
var dbsnpReader = new DbSnpReader(_renamer);
var dbSnpItem1 = dbsnpReader.ExtractItem(vcfLine1)[0];
var additionalItems = new List <SupplementaryDataItem>
{
dbSnpItem1.SetSupplementaryAnnotations(saCreator)
};
var cosmicItem1 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("", "carcinoma", "oesophagus")
}, null);
var cosmicItem2 = new CosmicItem("1", 10229, "COSM1000", "TA", "T", "TP53",
new HashSet <CosmicItem.CosmicStudy> {
new CosmicItem.CosmicStudy("01", "carcinoma", "large_intestine")
}, null);
additionalItems.Add(cosmicItem1.SetSupplementaryAnnotations(saCreator));
additionalItems.Add(cosmicItem2.SetSupplementaryAnnotations(saCreator));
//sa.Clear();
foreach (var item in additionalItems)
{
item.SetSupplementaryAnnotations(saCreator);
}
Assert.Equal(1, sa.CosmicItems.Count);
// the preceeding code has been unit tested in MergeDbSnpCosmic()
// write the supplementary annotation file
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(10229) as SupplementaryAnnotationPosition;
Assert.NotNull(observedAnnotation1);
var expDbSnp =
sa.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(expDbSnp);
var obsDbSnp =
observedAnnotation1.AlleleSpecificAnnotations["1"].Annotations[DataSourceCommon.GetIndex(DataSourceCommon.DataSource.DbSnp)] as
DbSnpAnnotation;
Assert.NotNull(obsDbSnp);
Assert.Equal(expDbSnp.DbSnp, obsDbSnp.DbSnp);
Assert.True(observedAnnotation1.ContainsCosmicId(sa.CosmicItems[0].ID));
Assert.Equal(1, observedAnnotation1.CosmicItems.Count);
}
File.Delete(randomPath);
File.Delete(randomPath + ".idx");
}
private void SetUpScenery(ChunkCoords cc, ChunkCoords loopedCoords)
{
ChunkCoords c = ChunkCoords.ConvertToUpRight(cc);
Vector2 chunkPos = new Vector2(c.x * EntityNetwork.CHUNK_SIZE,
c.y * EntityNetwork.CHUNK_SIZE);
for (int i = 0; i < Chunk(loopedCoords).Count; i++)
{
CosmicItem item = Chunk(loopedCoords)[i];
StarFieldMaterialPropertyManager sfmpm;
SpriteRenderer rend;
Transform tr;
GameObject obj;
if (transitionActive.Count > 0)
{
int last = transitionActive.Count - 1;
sfmpm = transitionActive[last];
transitionActive.RemoveAt(last);
rend = sfmpm.rend;
tr = sfmpm.transform;
obj = sfmpm.obj;
}
else
{
sfmpm = GetFromPool();
rend = sfmpm.rend;
tr = sfmpm.transform;
obj = sfmpm.obj;
}
Vector3 itemPos = item.pos + (Vector3)chunkPos;
tr.position = itemPos;
List <Sprite> listToUse = item.common ? types : lessFrequentTypes;
if (item.type >= listToUse.Count)
{
Debug.Log($"Is common? {item.common}. List size: {listToUse.Count}. Item value: {item.type}.", obj);
}
else
{
rend.sprite = item.common ? types[item.type] : lessFrequentTypes[item.type];
}
//Color col = transparent ? nebulaFadeBackground : Color.white;
Color col = Color.white;
if (fadeBasedOnDistance)
{
float delta = (1f - (item.pos.z - starMinDistance) / starDistanceRange) * 0.9f + 0.1f;
if (item.common)
{
col.a *= delta;
}
else
{
col = Color.Lerp(Color.black, Color.white,
Mathf.Clamp(delta, imageBrightnessRange.x, imageBrightnessRange.y));
}
}
sfmpm.SetColor(col);
active.Add(sfmpm);
tr.localScale.Set(item.size, item.size, 1f);
tr.eulerAngles.Set(0f, 0f, item.rotation * 45f);
sfmpm.coord = cc;
}
transitionActive.ForEach(t => t.rend.enabled = false);
pool.AddRange(transitionActive);
transitionActive.Clear();
}