public override IEnumerable <string> Process()
{
using (var file = new PlinkBedRandomFile(_options.InputFile)
{
Progress = this.Progress
})
{
var locusList = file.Data.Locus;
var individualList = file.Data.Individual;
Progress.SetRange(0, locusList.Count);
for (int i = 0; i < locusList.Count; i++)
{
Progress.SetPosition(i);
var locus = locusList[i];
var data = file.Read(locus.MarkerId);
int count1 = 0;
int count2 = 0;
int validSample = 0;
for (int j = 0; j < individualList.Count; j++)
{
if (PlinkData.IsMissing(data[0, j], data[1, j]))
{
continue;
}
validSample++;
if (data[0, j])
{
count2++;
}
else
{
count1++;
}
if (data[1, j])
{
count2++;
}
else
{
count1++;
}
}
locus.Allele1Frequency = ((double)(count1)) / (count1 + count2);
locus.TotalSample = individualList.Count;
locus.ValidSample = validSample;
}
PlinkLocus.WriteToFile(_options.OutputFile, locusList, false, true, true);
}
return(new string[] { _options.OutputFile });
}
public override IEnumerable<string> Process()
{
using (var file = new PlinkBedRandomFile(_options.InputFile) { Progress = this.Progress })
{
var locusList = file.Data.Locus;
var individualList = file.Data.Individual;
Progress.SetRange(0, locusList.Count);
for (int i = 0; i < locusList.Count; i++)
{
Progress.SetPosition(i);
var locus = locusList[i];
var data = file.Read(locus.MarkerId);
int count1 = 0;
int count2 = 0;
int validSample = 0;
for (int j = 0; j < individualList.Count; j++)
{
if (PlinkData.IsMissing(data[0, j], data[1, j]))
{
continue;
}
validSample++;
if (data[0, j])
{
count2++;
}
else
{
count1++;
}
if (data[1, j])
{
count2++;
}
else
{
count1++;
}
}
locus.Allele1Frequency = ((double)(count1)) / (count1 + count2);
locus.TotalSample = individualList.Count;
locus.ValidSample = validSample;
}
PlinkLocus.WriteToFile(_options.OutputFile, locusList, false, true, true);
}
return new string[] { _options.OutputFile };
}
public void TestMethod()
{
var file = new PlinkBedRandomFile();
file.OpenBinaryFile("../../../data/plink/plink.bed");
try
{
var data = file.Read("RS168753");
Assert.IsTrue(data[0, 0]);
Assert.IsFalse(data[0, 1]);
Assert.IsFalse(data[0, 2]);
Assert.IsFalse(data[0, 3]);
Assert.IsTrue(data[0, 4]);
Assert.IsTrue(data[1, 0]);
Assert.IsFalse(data[1, 1]);
Assert.IsTrue(data[1, 2]);
Assert.IsTrue(data[1, 3]);
Assert.IsTrue(data[1, 4]);
data = file.Read("RS11267092");
Assert.IsTrue(data[0, 0]);
Assert.IsFalse(data[0, 1]);
Assert.IsFalse(data[0, 2]);
Assert.IsFalse(data[0, 3]);
Assert.IsTrue(data[0, 4]);
Assert.IsTrue(data[1, 0]);
Assert.IsTrue(data[1, 1]);
Assert.IsTrue(data[1, 2]);
Assert.IsFalse(data[1, 3]);
Assert.IsTrue(data[1, 4]);
}
finally
{
file.Close();
}
}
public override IEnumerable<string> Process()
{
var result = new List<string>();
var bimfile = Path.ChangeExtension(options.InputFile, ".bim");
var snps = PlinkLocus.ReadFromBimFile(bimfile, false, false);
snps.RemoveAll(m => IsIndel(m) || IsMissing(m));
var snpItems = (from snp in snps
select new SNPItem()
{
Chrom = snp.Chromosome,
Name = snp.MarkerId,
Position = snp.PhysicalPosition,
Allele1 = snp.Allele1[0],
Allele2 = snp.Allele2
}).ToList();
var nameMap = snpItems.FillDbsnpIdByPosition(options.DbsnpFile, this.Progress);
using (var sw = new StreamWriter(options.OutputPrefix + ".namemap"))
{
sw.WriteLine("NewName\tOldName");
foreach (var n in nameMap)
{
sw.WriteLine("{0}\t{1}", n.Key, n.Value);
}
}
//remove all snps without corresponding dbsnp entry
snpItems.RemoveAll(m => m.DbsnpRefAllele == ' ');
var nameDic = snpItems.ToGroupDictionary(m => m.Name);
foreach (var n in nameDic)
{
if (n.Value.Count > 1)
{
Console.Error.WriteLine("Duplicated SNP:" + n.Key);
foreach (var v in n.Value)
{
Console.Error.WriteLine("{0}:{1}-{2}:{3},{4}:{5},{6}", n.Key, v.Chrom, v.Position, v.Allele1, v.Allele2, v.DbsnpRefAllele, v.DbsnpAltAllele);
}
}
}
if (File.Exists(options.G1000File))
{
snpItems.FindAllele2FrequencyFrom1000GomeByName(options.G1000File, this.Progress);
}
if (File.Exists(options.FastaFile))
{
snpItems.FillReferenceAlleleFromFasta(options.FastaFile, this.Progress);
}
Dictionary<string, StrandAction> actionMap = new Dictionary<string, StrandAction>();
var statFile = options.OutputPrefix + ".stat";
result.Add(statFile);
using (var sw = new StreamWriter(statFile))
{
sw.WriteLine("Name\tChromosome\tPosition\tSource_Allele1\tSource_Allele2\tReference_Allele\tDbsnp_RefAllele\tDbsnp_AltAllele\tDbsnp_IsReversed\tG1000_RefAllele\tG1000_AltAllele\tG1000_MAF\tAction");
foreach (var v in snpItems)
{
StrandAction action = v.SuggestAction();
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11:0.####}\t{12}", v.Name, v.Chrom, v.Position, v.Allele1, v.Allele2, v.RefChar, v.DbsnpRefAllele, v.DbsnpAltAllele, v.DbsnpIsReversed, v.G1000Allele1, v.G1000Allele2, v.G1000Allele2Frequency, action);
actionMap[v.Name] = action;
}
}
using (var reader = new PlinkBedRandomFile(options.InputFile) { Progress = this.Progress })
{
var data = reader.Data;
var chrs = (from v in snpItems select v.Chrom).Distinct().OrderBy(m => m).ToArray();
foreach (var chr in chrs)
{
var genfile = string.Format("{0}.{1}.gen", options.OutputPrefix, chr.ToString().PadLeft(2, '0'));
result.Add(genfile);
var map = FileUtils.ChangeExtension(genfile, ".sample");
new GwasSampleFormat().WriteToFile(map, data.Individual);
//save gen file
using (var sw = new StreamWriter(genfile))
{
sw.NewLine = Environment.NewLine;
var chrItems = snpItems.Where(m => m.Chrom == chr).ToList();
GenomeUtils.SortChromosome(chrItems, m => chr.ToString(), m => m.Position);
foreach (var snp in chrItems)
{
var ldata = reader.Read(nameMap[snp.Name]);
var action = actionMap[snp.Name];
sw.Write("{0} {1} {2} {3} {4}", snp.Chrom, snp.Name, snp.Position, snp.DbsnpRefAllele, snp.DbsnpAltAllele);
for (int individualIndex = 0; individualIndex < data.Individual.Count; individualIndex++)
{
if (PlinkData.IsMissing(ldata[0, individualIndex], ldata[1, individualIndex]))
{
sw.Write(" 0 0 0");
}
else
{
char alle1, alle2;
if (StrandAction.Switch == action || StrandAction.FlipSwitch == action)
{
alle1 = ldata[0, individualIndex] ? snp.DbsnpAltAllele : snp.DbsnpRefAllele;
alle2 = ldata[1, individualIndex] ? snp.DbsnpAltAllele : snp.DbsnpRefAllele;
}
else
{
alle1 = ldata[0, individualIndex] ? snp.DbsnpRefAllele : snp.DbsnpAltAllele;
alle2 = ldata[1, individualIndex] ? snp.DbsnpRefAllele : snp.DbsnpAltAllele;
}
if (alle1 != alle2)
{
sw.Write(" 0 1 0");
}
else if (alle1 == snp.DbsnpRefAllele)
{
sw.Write(" 1 0 0");
}
else
{
sw.Write(" 0 0 1");
}
}
}
sw.WriteLine();
}
}
}
}
return result;
}
public override IEnumerable <string> Process()
{
var result = new List <string>();
var bimfile = Path.ChangeExtension(options.InputFile, ".bim");
var snps = PlinkLocus.ReadFromBimFile(bimfile, false, false);
snps.RemoveAll(m => IsIndel(m) || IsMissing(m));
var snpItems = (from snp in snps
select new SNPItem()
{
Chrom = snp.Chromosome,
Name = snp.MarkerId,
Position = snp.PhysicalPosition,
Allele1 = snp.Allele1[0],
Allele2 = snp.Allele2
}).ToList();
var nameMap = snpItems.FillDbsnpIdByPosition(options.DbsnpFile, this.Progress);
using (var sw = new StreamWriter(options.OutputPrefix + ".namemap"))
{
sw.WriteLine("NewName\tOldName");
foreach (var n in nameMap)
{
sw.WriteLine("{0}\t{1}", n.Key, n.Value);
}
}
//remove all snps without corresponding dbsnp entry
snpItems.RemoveAll(m => m.DbsnpRefAllele == ' ');
var nameDic = snpItems.ToGroupDictionary(m => m.Name);
foreach (var n in nameDic)
{
if (n.Value.Count > 1)
{
Console.Error.WriteLine("Duplicated SNP:" + n.Key);
foreach (var v in n.Value)
{
Console.Error.WriteLine("{0}:{1}-{2}:{3},{4}:{5},{6}", n.Key, v.Chrom, v.Position, v.Allele1, v.Allele2, v.DbsnpRefAllele, v.DbsnpAltAllele);
}
}
}
if (File.Exists(options.G1000File))
{
snpItems.FindAllele2FrequencyFrom1000GomeByName(options.G1000File, this.Progress);
}
if (File.Exists(options.FastaFile))
{
snpItems.FillReferenceAlleleFromFasta(options.FastaFile, this.Progress);
}
Dictionary <string, StrandAction> actionMap = new Dictionary <string, StrandAction>();
var statFile = options.OutputPrefix + ".stat";
result.Add(statFile);
using (var sw = new StreamWriter(statFile))
{
sw.WriteLine("Name\tChromosome\tPosition\tSource_Allele1\tSource_Allele2\tReference_Allele\tDbsnp_RefAllele\tDbsnp_AltAllele\tDbsnp_IsReversed\tG1000_RefAllele\tG1000_AltAllele\tG1000_MAF\tAction");
foreach (var v in snpItems)
{
StrandAction action = v.SuggestAction();
sw.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11:0.####}\t{12}", v.Name, v.Chrom, v.Position, v.Allele1, v.Allele2, v.RefChar, v.DbsnpRefAllele, v.DbsnpAltAllele, v.DbsnpIsReversed, v.G1000Allele1, v.G1000Allele2, v.G1000Allele2Frequency, action);
actionMap[v.Name] = action;
}
}
using (var reader = new PlinkBedRandomFile(options.InputFile)
{
Progress = this.Progress
})
{
var data = reader.Data;
var chrs = (from v in snpItems select v.Chrom).Distinct().OrderBy(m => m).ToArray();
foreach (var chr in chrs)
{
var genfile = string.Format("{0}.{1}.gen", options.OutputPrefix, chr.ToString().PadLeft(2, '0'));
result.Add(genfile);
var map = FileUtils.ChangeExtension(genfile, ".sample");
new GwasSampleFormat().WriteToFile(map, data.Individual);
//save gen file
using (var sw = new StreamWriter(genfile))
{
sw.NewLine = Environment.NewLine;
var chrItems = snpItems.Where(m => m.Chrom == chr).ToList();
GenomeUtils.SortChromosome(chrItems, m => chr.ToString(), m => m.Position);
foreach (var snp in chrItems)
{
var ldata = reader.Read(nameMap[snp.Name]);
var action = actionMap[snp.Name];
sw.Write("{0} {1} {2} {3} {4}", snp.Chrom, snp.Name, snp.Position, snp.DbsnpRefAllele, snp.DbsnpAltAllele);
for (int individualIndex = 0; individualIndex < data.Individual.Count; individualIndex++)
{
if (PlinkData.IsMissing(ldata[0, individualIndex], ldata[1, individualIndex]))
{
sw.Write(" 0 0 0");
}
else
{
char alle1, alle2;
if (StrandAction.Switch == action || StrandAction.FlipSwitch == action)
{
alle1 = ldata[0, individualIndex] ? snp.DbsnpAltAllele : snp.DbsnpRefAllele;
alle2 = ldata[1, individualIndex] ? snp.DbsnpAltAllele : snp.DbsnpRefAllele;
}
else
{
alle1 = ldata[0, individualIndex] ? snp.DbsnpRefAllele : snp.DbsnpAltAllele;
alle2 = ldata[1, individualIndex] ? snp.DbsnpRefAllele : snp.DbsnpAltAllele;
}
if (alle1 != alle2)
{
sw.Write(" 0 1 0");
}
else if (alle1 == snp.DbsnpRefAllele)
{
sw.Write(" 1 0 0");
}
else
{
sw.Write(" 0 0 1");
}
}
}
sw.WriteLine();
}
}
}
}
return(result);
}