static void Main(string[] args)
{
/*
* ExACAnnotator.GetVarAnnotation("1", 931393, "G", "T");
* ExACAnnotator.GetVarAnnotation("1-935222-C-A");
* ExACAnnotator.GetVarAnnotation("14-21853913-T-C");
* ExACAnnotator.GetVarAnnotation("22-46615746-A-G");
* ExACAnnotator.GetVarAnnotation("1-6475586-TC-GA");
* List<string> list = new List<string>();
* list.Add("1-931393-G-T");
* list.Add("14-21853913-T-C");
* list.Add("22-46615746-A-G");
* list.Add("1-6475586-TC-GA");
* ExACAnnotator.GetBulkVarAnnotations(list);*/
if (args.Length != 2)
{
Console.WriteLine("Please use:\ndotnet run yourfile.vcf output.txt");
return;
}
string vcfFile = args[0];
if (!File.Exists(vcfFile))
{
Console.WriteLine("Error! Can not find vcf file to annotate: " + vcfFile);
return;
}
string outputFile = args[1];
IVcfAnnotator annot = new ExACAnnotator();
VCFFile vf = new VCFFile(vcfFile);
annot.AnnotateVcfFile(vf, outputFile);
vf.Close();
}
public void AnnotateVcfFile(VCFFile file, string outputFile)
{
string headerLine = "#CHROM\tPOS\tID\tREF\tALT\tTYPE\tDP\tRO\tAO\tARO\t" +
"ExAC_Consequence\tExAC_Transcripts\tExAC_rsID\tExAC_AlleleCount\tExAC_AlleleNumber\tExAC_HomozygousNumber\tExAC_AlleleFrequence\tExACBrowser_Link";
using (StreamWriter writer = new StreamWriter(outputFile))
{
writer.WriteLine(headerLine);
if (useBulkMode)
{
file.Traverse(BulkLineLimit, delegate(string[] lines)
{
try
{
List <string> queries = new List <string>();
Dictionary <string, string> outputinfo1 = new Dictionary <string, string>();
foreach (string line in lines)
{
string[] vcfvalues = line.Split('\t');
string chrom = vcfvalues[0].Trim();
string pos = vcfvalues[1].Trim();
string id = vcfvalues[2].Trim();
string refAllele = vcfvalues[3].Trim();
string altAllele = vcfvalues[4].Trim();
string info = vcfvalues[7].Trim();
Dictionary <string, string> dict = VCFFile.ParseInfoLine(info);
string type = dict.ContainsKey("TYPE") ? dict["TYPE"] : ".";
string dp = dict.ContainsKey("DP") ? dict["DP"] : ".";
string ro = dict.ContainsKey("RO") ? dict["RO"] : ".";
string ao = dict.ContainsKey("AO") ? dict["AO"] : ".";
string[] alts = altAllele.Split(',');
string[] aos = ao.Split(',');
string[] altTypes = type.Split(',');
float[] aros = new float[alts.Length];
for (int i = 0; i < alts.Length; i++)
{
string altAl = alts[i];
float aro = float.Parse(aos[i]) / float.Parse(ro);
bool modifyAllele = false;
string newRefAl = refAllele;
string newAltAl = altAl;
int movepos = 0;
if (refAllele.Length > 1 && altAl.Length > 1)
{
modifyAllele = ModifyAlleleForQuery(refAllele, altAl, out newRefAl, out newAltAl, out movepos);
}
int origpos = int.Parse(pos);
int newpos = (movepos > 0)? origpos + movepos : origpos;
string query = (modifyAllele) ? chrom + "-" + newpos + "-" + newRefAl + "-" + newAltAl : chrom + "-" + pos + "-" + refAllele + "-" + altAl;
queries.Add(query);
string info1 = chrom + "\t" + pos + "\t" + id + "\t" + refAllele + "\t" + altAl
+ "\t" + altTypes[i] + "\t" + dp + "\t" + ro + "\t" + aos[i] + "\t" + aro;
outputinfo1[query] = info1;
}
}
Dictionary <string, IVarAnnotation> annots = this.BulkAnnotateVars(queries.ToArray());
foreach (KeyValuePair <string, string> pair in outputinfo1)
{
if (annots.ContainsKey(pair.Key))
{
IVarAnnotation annot = annots[pair.Key];
if (annot == null)
{
Console.WriteLine("annotation is empty for: " + pair.Key);
continue;
}
else
{
string httpLink = HttpVarUrl + pair.Key;
writer.WriteLine(pair.Value + "\t" + annot.ToString() + "\t" + httpLink);
}
}
else
{
Console.WriteLine("annotation is empty for: " + pair.Key);
continue;
}
}
return(false);
}
catch (Exception e)
{
Console.WriteLine(e);
}
return(true);
});
}
else
{
file.Traverse(delegate(string line, long index)
{
try
{
string[] vcfvalues = line.Split('\t');
string chrom = vcfvalues[0].Trim();
string pos = vcfvalues[1].Trim();
string id = vcfvalues[2].Trim();
string refAllele = vcfvalues[3].Trim();
string altAllele = vcfvalues[4].Trim();
string info = vcfvalues[7].Trim();
Dictionary <string, string> dict = VCFFile.ParseInfoLine(info);
string type = dict.ContainsKey("TYPE") ? dict["TYPE"] : ".";
string dp = dict.ContainsKey("DP") ? dict["DP"] : ".";
string ro = dict.ContainsKey("RO") ? dict["RO"] : ".";
string ao = dict.ContainsKey("AO") ? dict["AO"] : ".";
if (altAllele.Contains(','))
{
string[] alts = altAllele.Split(',');
string[] aos = ao.Split(',');
string[] altTypes = type.Split(',');
for (int i = 0; i < alts.Length; i++)
{
string altAl = alts[i];
bool modifyAllele = false;
string newRefAl = refAllele;
string newAltAl = altAl;
int movepos = 0;
if (refAllele.Length > 1 && altAl.Length > 1)
{
modifyAllele = ModifyAlleleForQuery(refAllele, altAl, out newRefAl, out newAltAl, out movepos);
}
int origpos = int.Parse(pos);
int newpos = (movepos > 0)? origpos + movepos : origpos;
string query = (modifyAllele) ? chrom + "-" + newpos + "-" + newRefAl + "-" + newAltAl : chrom + "-" + pos + "-" + refAllele + "-" + altAl;
IVarAnnotation annot = this.AnnotateVar(query);
if (annot == null)
{
continue;
}
else
{
float aro = float.Parse(aos[i]) / float.Parse(ro);
string info1 = chrom + "\t" + pos + "\t" + id + "\t" + refAllele + "\t" + altAl
+ "\t" + altTypes[i] + "\t" + dp + "\t" + ro + "\t" + aos[i] + "\t" + aro;
string httpLink = HttpVarUrl + query;
writer.WriteLine(info1 + "\t" + annot.ToString() + "\t" + httpLink);
}
}
}
else
{
float aro = float.Parse(ao) / float.Parse(ro);
bool modifyAllele = false;
string newRefAl = refAllele;
string newAltAl = altAllele;
int movepos = 0;
if (refAllele.Length > 1 && altAllele.Length > 1)
{
modifyAllele = ModifyAlleleForQuery(refAllele, altAllele, out newRefAl, out newAltAl, out movepos);
}
int origpos = int.Parse(pos);
int newpos = (movepos > 0)? origpos + movepos : origpos;
string query = (modifyAllele) ? chrom + "-" + newpos + "-" + newRefAl + "-" + newAltAl : chrom + "-" + pos + "-" + refAllele + "-" + altAllele;
IVarAnnotation annot = this.AnnotateVar(query);
string info1 = chrom + "\t" + pos + "\t" + id + "\t" + refAllele + "\t" + altAllele
+ "\t" + type + "\t" + dp + "\t" + ro + "\t" + ao + "\t" + aro;
string httpLink = HttpVarUrl + query;
writer.WriteLine(info1 + "\t" + annot.ToString() + "\t" + httpLink);
}
return(false);
}
catch (Exception e)
{
Console.WriteLine(e);
}
return(true);
});
}
}
}
