public override IEnumerable<string> Process(string fileName)
{
Dictionary<string, string> genenames = File.Exists(this.affyAnnotationFile) ? AnnotationFile.GetGeneSymbolDescriptionMap(this.affyAnnotationFile) : new Dictionary<string, string>();
var items = new AnnovarGenomeSummaryItemReader().ReadFromFile(fileName);
var shFile = this.targetDir + "/" + suffix + ".sh";
using (StreamWriter sw = new StreamWriter(shFile))
{
foreach (var item in items)
{
var targetFile = string.Format("{0}/{1}_{2}-{3}_{4}_{5}",
this.targetDir,
item.Seqname,
item.Start,
item.End,
(from g in item.Genes
select g.Name).Merge("_"),
this.suffix);
sw.WriteLine("echo \"{0}.bam\"", Path.GetFileName(targetFile));
sw.WriteLine("samtools view -b {0} {1}:{2}-{3} | samtools sort - {4}",
this.bamFile,
item.Seqname,
item.Start,
item.End,
targetFile);
sw.WriteLine("samtools index {0}.bam", targetFile);
}
}
return new string[] { shFile };
}
public void TestTsv()
{
var items = new AnnovarGenomeSummaryItemReader().ReadFromFile("../../../data/annovar.snp.tsv");
Assert.AreEqual(3, items.Count);
Assert.AreEqual("ncRNA_intronic", items[0].Func);
Assert.AreEqual("WASH7P", items[0].GeneString);
Assert.AreEqual(string.Empty, items[0].ExonicFunc);
Assert.AreEqual("1", items[0].Seqname);
Assert.AreEqual(14907, items[0].Start);
Assert.AreEqual(14907, items[0].End);
Assert.AreEqual("GT:AD:DP:GQ:PL", items[0].Format);
Assert.AreEqual("0/1:1,4:5:24:84,0,24", items[0].Samples["IG-003"]);
}
public void TestCsv()
{
var items = new AnnovarGenomeSummaryItemReader().ReadFromFile("../../../data/annovar.genome_summary.csv");
Assert.AreEqual(9, items.Count);
Assert.AreEqual("intergenic", items[0].Func);
Assert.AreEqual("OR4F3(dist=196024),OR4F29(dist=56475)", items[0].GeneString);
Assert.AreEqual(string.Empty, items[0].ExonicFunc);
Assert.AreEqual("1", items[0].Seqname);
Assert.AreEqual(564621, items[0].Start);
Assert.AreEqual(564621, items[0].End);
Assert.AreEqual("exonic", items[8].Func);
Assert.AreEqual("KIAA1324", items[8].GeneString);
Assert.AreEqual("synonymous SNV", items[8].ExonicFunc);
Assert.AreEqual("1", items[8].Seqname);
Assert.AreEqual(109737132, items[8].Start);
Assert.AreEqual(109737132, items[8].End);
}
