public override IEnumerable <string> Process()
{
var files = _options.GetAnnovarFiles();
var filelist = files.Keys.ToArray();
using (var sw = new StreamWriter(_options.OutputFile))
{
//deal with comments
using (var sr = new StreamReader(filelist[0]))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("##MuTect="))
{
sw.WriteLine(line);
for (var i = 1; i < filelist.Length; i++)
{
using (var sr2 = new StreamReader(filelist[i]))
{
while ((line = sr2.ReadLine()) != null)
{
if (!line.StartsWith("##MuTect="))
{
continue;
}
sw.WriteLine(line);
break;
}
}
}
}
else if (!line.StartsWith("#"))
{
break;
}
else
{
sw.WriteLine(line);
}
}
}
//deal with data
var data = new List <FileData>();
foreach (var file in filelist)
{
var lines = File.ReadAllLines(file);
var mutect = lines.FirstOrDefault(m => m.StartsWith("##MuTect="));
string normal, tumor, normalName, tumorName;
if (mutect != null)
{
normal = mutect.StringAfter("normal_sample_name=").StringBefore(" ");
tumor = mutect.StringAfter("tumor_sample_name=").StringBefore(" ");
normalName = normal;
tumorName = tumor;
}
else
{
normal = "NORMAL";
tumor = "TUMOR";
normalName = Path.GetFileName(file).StringBefore(".") + "_normal";
tumorName = Path.GetFileName(file).StringBefore(".") + "_tumor";
}
var header = lines.First(m => !m.StartsWith("#"));
var headers = header.Split('\t');
var infoIndex = Array.IndexOf(headers, "INFO");
var formatIndex = Array.IndexOf(headers, "FORMAT");
var normalIndex = Array.IndexOf(headers, normal);
var tumorIndex = Array.IndexOf(headers, tumor);
var dictionary = new Dictionary <string, FileDataValue>();
foreach (var line in lines)
{
if (string.IsNullOrWhiteSpace(line) || line.StartsWith("#") || line.StartsWith("Chr"))
{
continue;
}
var parts = line.Split('\t');
if (parts.Length != headers.Length)
{
continue;
}
var vnormal = GetAllele(parts, normalIndex);
var vtumor = GetAllele(parts, tumorIndex);
var value = new FileDataValue()
{
Key = parts[0] + "_" + parts[1],
Parts = parts,
VNormal = vnormal,
VTumor = vtumor
};
dictionary.Add(value.Key, value);
}
data.Add(new FileData()
{
File = file,
Normal = normalName,
Tumor = tumorName,
Headers = headers,
InfoIndex = infoIndex,
FormatIndex = formatIndex,
NormalIndex = normalIndex,
TumorIndex = tumorIndex,
Data = dictionary
});
}
//get all positions
var keys = (from d in data
from k in d.Data.Keys
select k).Distinct().ToList().ConvertAll(m =>
{
var p = m.Split('_');
return(new
{
Key = m,
Chr = p[0],
Position = int.Parse(p[1])
});
}
);
GenomeUtils.SortChromosome(keys, m => m.Chr, m => m.Position);
var keyMap = keys.ToDictionary(m => m.Key);
//check by original vcf file to fill the other columns
foreach (var d in data)
{
var vcf = files[d.File];
if (string.IsNullOrEmpty(vcf))
{
continue;
}
var vd = d.Data;
using (var sr = new StreamReader(vcf))
{
string line;
var normalIndex = -1;
var tumorIndex = -1;
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("#CHROM"))
{
continue;
}
var parts = line.Split('\t');
normalIndex = Array.IndexOf(parts, d.Normal);
tumorIndex = Array.IndexOf(parts, d.Tumor);
break;
}
if (normalIndex == -1)
{
throw new Exception(string.Format("Normal {0} is not included in detail vcf file {1} but in annovar result {1}", d.Normal, vcf, d.File));
}
if (tumorIndex == -1)
{
throw new Exception(string.Format("Tumor {0} is not included in detail vcf file {1} but in annovar result {1}", d.Tumor, vcf, d.File));
}
var minIndex = Math.Max(normalIndex, tumorIndex) + 1;
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split('\t');
if (parts.Length < minIndex)
{
break;
}
var key = parts[0] + "_" + parts[1];
if (!keyMap.ContainsKey(key))
{
continue;
}
FileDataValue fdv;
if (!vd.TryGetValue(key, out fdv))
{
fdv = new FileDataValue()
{
Key = key,
Parts = null
};
vd[key] = fdv;
}
fdv.VNormal = GetAllele(parts, normalIndex);
fdv.VTumor = GetAllele(parts, tumorIndex);
}
}
}
//write header
for (var i = 0; i < data[0].Headers.Length; i++)
{
if (i == data[0].NormalIndex || i == data[0].TumorIndex || i == data[0].InfoIndex || i == data[0].FormatIndex)
{
continue;
}
else
{
if (i != 0)
{
sw.Write("\t");
}
sw.Write(data[0].Headers[i]);
}
}
var normalnames = (from d in data
select d.Normal).Distinct().ToArray();
sw.Write("\t{0}", normalnames.Merge('\t'));
var tumornames = (from d in data
select d.Tumor).Distinct().ToArray();
sw.WriteLine("\t{0}", tumornames.Merge('\t'));
foreach (var key in keys)
{
var d1 = data.First(d => d.Data.ContainsKey(key.Key) && d.Data[key.Key].Parts != null);
var v1 = d1.Data[key.Key];
for (var i = 0; i < v1.Parts.Length; i++)
{
if (i == 0)
{
sw.Write("{0}", v1.Parts[0]);
}
else if (i == d1.InfoIndex || i == d1.FormatIndex || i == d1.NormalIndex || i == d1.TumorIndex)
{
continue;
}
else
{
sw.Write("\t{0}", v1.Parts[i]);
}
}
foreach (var name in normalnames)
{
var dn = (from d in data
where d.Normal.Equals(name) && d.Data.ContainsKey(key.Key)
select d).FirstOrDefault();
if (dn == null)
{
sw.Write("\t");
}
else
{
var vn = dn.Data[key.Key].VNormal;
sw.Write("\t{0}", vn);
}
}
foreach (var name in tumornames)
{
var dn = (from d in data
where d.Tumor.Equals(name) && d.Data.ContainsKey(key.Key)
select d).FirstOrDefault();
if (dn == null)
{
sw.Write("\t");
}
else
{
var vn = dn.Data[key.Key].VTumor;
sw.Write("\t{0}", vn);
}
}
sw.WriteLine();
}
}
return(new[] { _options.OutputFile });
}
public override IEnumerable<string> Process()
{
var files = _options.GetAnnovarFiles();
var filelist = files.Keys.ToArray();
using (var sw = new StreamWriter(_options.OutputFile))
{
//deal with comments
using (var sr = new StreamReader(filelist[0]))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("##MuTect="))
{
sw.WriteLine(line);
for (var i = 1; i < filelist.Length; i++)
{
using (var sr2 = new StreamReader(filelist[i]))
{
while ((line = sr2.ReadLine()) != null)
{
if (!line.StartsWith("##MuTect="))
continue;
sw.WriteLine(line);
break;
}
}
}
}
else if (!line.StartsWith("#"))
{
break;
}
else
{
sw.WriteLine(line);
}
}
}
//deal with data
var data = new List<FileData>();
foreach (var file in filelist)
{
var lines = File.ReadAllLines(file);
var mutect = lines.FirstOrDefault(m => m.StartsWith("##MuTect="));
string normal, tumor, normalName, tumorName;
if (mutect != null)
{
normal = mutect.StringAfter("normal_sample_name=").StringBefore(" ");
tumor = mutect.StringAfter("tumor_sample_name=").StringBefore(" ");
normalName = normal;
tumorName = tumor;
}
else
{
normal = "NORMAL";
tumor = "TUMOR";
normalName = Path.GetFileName(file).StringBefore(".") + "_normal";
tumorName = Path.GetFileName(file).StringBefore(".") + "_tumor";
}
var header = lines.First(m => !m.StartsWith("#"));
var headers = header.Split('\t');
var infoIndex = Array.IndexOf(headers, "INFO");
var formatIndex = Array.IndexOf(headers, "FORMAT");
var normalIndex = Array.IndexOf(headers, normal);
var tumorIndex = Array.IndexOf(headers, tumor);
var dictionary = new Dictionary<string, FileDataValue>();
foreach (var line in lines)
{
if (string.IsNullOrWhiteSpace(line) || line.StartsWith("#") || line.StartsWith("Chr"))
continue;
var parts = line.Split('\t');
if (parts.Length != headers.Length)
continue;
var vnormal = GetAllele(parts, normalIndex);
var vtumor = GetAllele(parts, tumorIndex);
var value = new FileDataValue()
{
Key = parts[0] + "_" + parts[1],
Parts = parts,
VNormal = vnormal,
VTumor = vtumor
};
dictionary.Add(value.Key, value);
}
data.Add(new FileData()
{
File = file,
Normal = normalName,
Tumor = tumorName,
Headers = headers,
InfoIndex = infoIndex,
FormatIndex = formatIndex,
NormalIndex = normalIndex,
TumorIndex = tumorIndex,
Data = dictionary
});
}
//get all positions
var keys = (from d in data
from k in d.Data.Keys
select k).Distinct().ToList().ConvertAll(m =>
{
var p = m.Split('_');
return new
{
Key = m,
Chr = p[0],
Position = int.Parse(p[1])
};
}
);
GenomeUtils.SortChromosome(keys, m => m.Chr, m => m.Position);
var keyMap = keys.ToDictionary(m => m.Key);
//check by original vcf file to fill the other columns
foreach (var d in data)
{
var vcf = files[d.File];
if (string.IsNullOrEmpty(vcf))
continue;
var vd = d.Data;
using (var sr = new StreamReader(vcf))
{
string line;
var normalIndex = -1;
var tumorIndex = -1;
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("#CHROM"))
continue;
var parts = line.Split('\t');
normalIndex = Array.IndexOf(parts, d.Normal);
tumorIndex = Array.IndexOf(parts, d.Tumor);
break;
}
if (normalIndex == -1)
{
throw new Exception(string.Format("Normal {0} is not included in detail vcf file {1} but in annovar result {1}", d.Normal, vcf, d.File));
}
if (tumorIndex == -1)
{
throw new Exception(string.Format("Tumor {0} is not included in detail vcf file {1} but in annovar result {1}", d.Tumor, vcf, d.File));
}
var minIndex = Math.Max(normalIndex, tumorIndex) + 1;
while ((line = sr.ReadLine()) != null)
{
var parts = line.Split('\t');
if (parts.Length < minIndex)
{
break;
}
var key = parts[0] + "_" + parts[1];
if (!keyMap.ContainsKey(key))
continue;
FileDataValue fdv;
if(!vd.TryGetValue(key, out fdv))
{
fdv = new FileDataValue()
{
Key = key,
Parts = null
};
vd[key] = fdv;
}
fdv.VNormal = GetAllele(parts, normalIndex);
fdv.VTumor = GetAllele(parts, tumorIndex);
}
}
}
//write header
for (var i = 0; i < data[0].Headers.Length; i++)
{
if (i == data[0].NormalIndex || i == data[0].TumorIndex || i == data[0].InfoIndex || i == data[0].FormatIndex)
{
continue;
}
else
{
if (i != 0)
{
sw.Write("\t");
}
sw.Write(data[0].Headers[i]);
}
}
var normalnames = (from d in data
select d.Normal).Distinct().ToArray();
sw.Write("\t{0}", normalnames.Merge('\t'));
var tumornames = (from d in data
select d.Tumor).Distinct().ToArray();
sw.WriteLine("\t{0}", tumornames.Merge('\t'));
foreach (var key in keys)
{
var d1 = data.First(d => d.Data.ContainsKey(key.Key) && d.Data[key.Key].Parts != null);
var v1 = d1.Data[key.Key];
for (var i = 0; i < v1.Parts.Length; i++)
{
if (i == 0)
{
sw.Write("{0}", v1.Parts[0]);
}
else if (i == d1.InfoIndex || i == d1.FormatIndex || i == d1.NormalIndex || i == d1.TumorIndex)
{
continue;
}
else
{
sw.Write("\t{0}", v1.Parts[i]);
}
}
foreach (var name in normalnames)
{
var dn = (from d in data
where d.Normal.Equals(name) && d.Data.ContainsKey(key.Key)
select d).FirstOrDefault();
if (dn == null)
{
sw.Write("\t");
}
else
{
var vn = dn.Data[key.Key].VNormal;
sw.Write("\t{0}", vn);
}
}
foreach (var name in tumornames)
{
var dn = (from d in data
where d.Tumor.Equals(name) && d.Data.ContainsKey(key.Key)
select d).FirstOrDefault();
if (dn == null)
{
sw.Write("\t");
}
else
{
var vn = dn.Data[key.Key].VTumor;
sw.Write("\t{0}", vn);
}
}
sw.WriteLine();
}
}
return new[] { _options.OutputFile };
}