public string ConvertVCFChromosomesUCSC2Ensembl(string spritzDirectory, string vcfPath, string reference, bool dryRun)
{
string convertedEnsemblVcfPath = Path.Combine(Path.GetDirectoryName(vcfPath), Path.GetFileNameWithoutExtension(vcfPath) + ".ensembl.vcf");
if (File.Exists(convertedEnsemblVcfPath) || dryRun)
{
return(convertedEnsemblVcfPath);
}
Dictionary <string, string> ucsc2EnsemblChromosomeMappings = EnsemblDownloadsWrapper.UCSC2EnsemblChromosomeMappings(spritzDirectory, reference);
using (StreamReader reader = new StreamReader(vcfPath))
using (StreamWriter writer = new StreamWriter(convertedEnsemblVcfPath))
{
while (true)
{
string line = reader.ReadLine();
if (line == null)
{
break;
}
if (line.StartsWith("#"))
{
writer.Write(line + "\n");
}
string[] splitLine = line.Split('\t');
if (splitLine.Length > 1 && ucsc2EnsemblChromosomeMappings.TryGetValue(splitLine[0], out string newChrom))
{
splitLine[0] = newChrom;
writer.Write(string.Join("\t", splitLine) + '\n');
}
}
}
return(convertedEnsemblVcfPath);
}
/// <summary>
/// Annotate predicted transcripts
/// </summary>
/// <param name="spritzDirectory"></param>
/// <param name="threads"></param>
/// <param name="predictedGeneModelUcscBedPath"></param>
/// <param name="reference"></param>
/// <param name="slnckyOutPrefix"></param>
/// <returns></returns>
public static List <string> Annotate(string spritzDirectory, string analysisDirectory, int threads, string predictedGeneModelGtfPath, string reference, string slnckyOutPrefix)
{
string sortedBed12Cuffmerge = BEDOPSWrapper.GffOrGtf2Bed12(spritzDirectory, analysisDirectory, predictedGeneModelGtfPath);
string ucscCuffmergeBedPath = EnsemblDownloadsWrapper.ConvertFirstColumnEnsembl2UCSC(spritzDirectory, reference, sortedBed12Cuffmerge);
Directory.CreateDirectory(Path.GetDirectoryName(slnckyOutPrefix));
string ucscReference = reference.Contains("38") ? "hg38" : "hg19";
return(new List <string>
{
WrapperUtility.ChangeToToolsDirectoryCommand(spritzDirectory),
"cd slncky",
"if [[ ! -f " + WrapperUtility.ConvertWindowsPath(slnckyOutPrefix + LncsBedSuffix) + " || ! -s " + WrapperUtility.ConvertWindowsPath(slnckyOutPrefix + LncsBedSuffix) + " ]]; then " +
"./slncky.v1.0" +
" --threads " + threads.ToString() +
" " + WrapperUtility.ConvertWindowsPath(ucscCuffmergeBedPath) +
" " + ucscReference +
" " + WrapperUtility.ConvertWindowsPath(slnckyOutPrefix) +
"; fi"
});
}
