public void ExtractDgvComplex()
{
const string dgvLine = "esv2421662 1 12841928 12971833 OTHER complex Altshuler_et_al_2010 20811451 SNP array essv5038349,essv5012238 M 1184 20 70 HNRNPCL1,LOC649330,PRAMEF1,PRAMEF10,PRAMEF11,PRAMEF2,PRAMEF4 NA10838,NA10847";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":12841928,\"end\":12971833,\"variantType\":\"complex_structural_alteration\",\"id\":\"esv2421662\",\"sampleSize\":1184,\"observedGains\":20,\"observedLosses\":70,\"variantFreqAll\":0.07601", jsonString);
}
public void ExtractDgvCnv()
{
const string dgvLine = "nsv482937 1 1 2300000 CNV loss Iafrate_et_al_2004 15286789 BAC aCGH,FISH nssv2995976 M 39 0 1 ACAP3,AGRN,WASH7P ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":1,\"end\":2300000,\"variantType\":\"copy_number_loss\",\"id\":\"nsv482937\",\"sampleSize\":39,\"observedLosses\":1,\"variantFreqAll\":0.02564", jsonString);
}
public void EmptyObservedLossesAndGains()
{
const string dgvLine = "nsv161172 1 88190 89153 CNV deletion Mills_et_al_2006 16902084 Sequencing nssv179750 M 24 ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":88190,\"end\":89153,\"variantType\":\"copy_number_loss\",\"id\":\"nsv161172\",\"sampleSize\":24", jsonString);
//Assert.Equal("1", dgvInterval.Chromosome.EnsemblName);
//Assert.Equal(88190, dgvInterval.Start);
//Assert.Equal(89153, dgvInterval.End);
//Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
//Assert.Equal("dgv", dgvInterval.Source);
//Assert.Equal("nsv161172", dgvInterval.StringValues["id"]);
//Assert.Equal(24, dgvInterval.IntValues["sampleSize"]);
//Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
//Assert.False(dgvInterval.IntValues.ContainsKey("observedLosses"));
//Assert.False(dgvInterval.PopulationFrequencies.ContainsKey("variantFreqAll"));
}
public void ExtractDgvComplex()
{
const string dgvLine = "esv2421662 1 12841928 12971833 OTHER complex Altshuler_et_al_2010 20811451 SNP array essv5038349,essv5012238 M 1184 20 70 HNRNPCL1,LOC649330,PRAMEF1,PRAMEF10,PRAMEF11,PRAMEF2,PRAMEF4 NA10838,NA10847";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal(12841928, dgvInterval.Start);
Assert.Equal(12971833, dgvInterval.End);
Assert.Equal("complex_structural_alteration", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("esv2421662", dgvInterval.StringValues["id"]);
Assert.Equal("0.07601", dgvInterval.PopulationFrequencies["variantFreqAll"].ToString("0.#####"));
Assert.Equal(1184, dgvInterval.IntValues["sampleSize"]);
Assert.Equal(70, dgvInterval.IntValues["observedLosses"]);
Assert.Equal(20, dgvInterval.IntValues["observedGains"]);
}
public void ExtractDgvCnv()
{
const string dgvLine = "nsv482937 1 1 2300000 CNV loss Iafrate_et_al_2004 15286789 BAC aCGH,FISH nssv2995976 M 39 0 1 ACAP3,AGRN,WASH7P ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal(1, dgvInterval.Start);
Assert.Equal(2300000, dgvInterval.End);
Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("nsv482937", dgvInterval.StringValues["id"]);
Assert.Equal("0.02564", dgvInterval.PopulationFrequencies["variantFreqAll"].ToString("0.#####"));
Assert.Equal(39, dgvInterval.IntValues["sampleSize"]);
Assert.Equal(1, dgvInterval.IntValues["observedLosses"]);
Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
}
public void EmptyObservedLossesAndGains()
{
const string dgvLine = "nsv161172 1 88190 89153 CNV deletion Mills_et_al_2006 16902084 Sequencing nssv179750 M 24 ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal("1", dgvInterval.ReferenceName);
Assert.Equal(88190, dgvInterval.Start);
Assert.Equal(89153, dgvInterval.End);
Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("nsv161172", dgvInterval.StringValues["id"]);
Assert.Equal(24, dgvInterval.IntValues["sampleSize"]);
Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
Assert.False(dgvInterval.IntValues.ContainsKey("observedLosses"));
Assert.False(dgvInterval.PopulationFrequencies.ContainsKey("variantFreqAll"));
}