public List <string> PrimaryVariantAnnotation(string spritzDirectory, string reference, string inputVcfPath, bool fromReference = false)
{
string outPrefix = Path.Combine(Path.GetDirectoryName(inputVcfPath), Path.GetFileNameWithoutExtension(inputVcfPath));
AnnotatedVcfPath = outPrefix + ".snpEffAnnotated.vcf";
HtmlReportPath = outPrefix + ".snpEffAnnotated.html";
AnnotatedGenesSummaryPath = outPrefix + ".snpEffAnnotated.genes.txt";
VariantProteinFastaPath = outPrefix + ".snpEffAnnotated.protein.fasta";
VariantProteinXmlPath = outPrefix + ".snpEffAnnotated.protein.xml";
Directory.CreateDirectory(Path.Combine(spritzDirectory, "Tools", "SnpEff", "data"));
string[] existingDatabases = Directory.GetDirectories(Path.Combine(spritzDirectory, "Tools", "SnpEff", "data"));
if (File.Exists(AnnotatedVcfPath) && new FileInfo(AnnotatedVcfPath).Length > 0)
{
return(new List <string>());
}
return(new List <string>
{
WrapperUtility.ChangeToToolsDirectoryCommand(spritzDirectory),
SnpEff(Workers) + " -v -stats " + WrapperUtility.ConvertWindowsPath(HtmlReportPath) +
" -fastaProt " + WrapperUtility.ConvertWindowsPath(VariantProteinFastaPath) +
" -xmlProt " + WrapperUtility.ConvertWindowsPath(VariantProteinXmlPath) +
" " + Path.GetFileName(existingDatabases.FirstOrDefault(x => Path.GetFileName(x).StartsWith(reference, true, null))) +
(fromReference ? "" : $" {WrapperUtility.ConvertWindowsPath(inputVcfPath)} > {WrapperUtility.ConvertWindowsPath(AnnotatedVcfPath)}"),
// ensure that the files get closed before continuing
WrapperUtility.EnsureClosedFileCommands(WrapperUtility.ConvertWindowsPath(AnnotatedVcfPath)),
WrapperUtility.EnsureClosedFileCommands(WrapperUtility.ConvertWindowsPath(VariantProteinFastaPath)),
WrapperUtility.EnsureClosedFileCommands(WrapperUtility.ConvertWindowsPath(VariantProteinXmlPath)),
// remove the annotated VCF file if snpEff didn't work, e.g. if there was no VCF file to annotate
"if [[ ( -f " + WrapperUtility.ConvertWindowsPath(AnnotatedVcfPath) + " && ! -s " + WrapperUtility.ConvertWindowsPath(AnnotatedVcfPath) + " ) ]]; then",
" rm " + WrapperUtility.ConvertWindowsPath(AnnotatedVcfPath),
"fi",
});
}
// see here for how to generate them from scratch: http://lab.loman.net/2012/11/16/how-to-get-snpeff-working-with-bacterial-genomes-from-ncbi/
public void DownloadSnpEffDatabase(string spritzDirectory, string analysisDirectory, string reference)
{
DatabaseListPath = Path.Combine(spritzDirectory, "snpEffDatabases.txt");
// check for existing list and database
bool databaseListExists = File.Exists(DatabaseListPath);
string databaseDirectory = Path.Combine(spritzDirectory, "Tools", "SnpEff", "data");
string[] existingDatabases = Directory.Exists(databaseDirectory) ? Directory.GetDirectories(databaseDirectory) : new string[0];
bool databaseExists = existingDatabases.Any(d => Path.GetFileName(d).StartsWith(reference, true, null));
if (databaseListExists && databaseExists)
{
return;
}
// download database list
string scriptPath = WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "SnpEffDatabaseDownloadList.bash");
WrapperUtility.GenerateAndRunScript(scriptPath, new List <string>
{
WrapperUtility.ChangeToToolsDirectoryCommand(spritzDirectory),
"echo \"Downloading list of SnpEff references\"",
SnpEff(Workers) + " databases > " + WrapperUtility.ConvertWindowsPath(DatabaseListPath),
WrapperUtility.EnsureClosedFileCommands(DatabaseListPath)
}).WaitForExit();
List <string> databases = new List <string>();
using (StreamReader reader = new StreamReader(DatabaseListPath))
{
while (true)
{
string line = reader.ReadLine();
if (line == null)
{
break;
}
databases.Add(line.Split('\t')[0].TrimEnd());
}
}
string snpeffReference = databases.FirstOrDefault(d => d.StartsWith(reference, true, CultureInfo.InvariantCulture));
// download database (it downloads automatically now, with more feedback), but still need the mitochondrial references
scriptPath = WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "SnpEffDatabaseDownload.bash");
WrapperUtility.GenerateAndRunScript(scriptPath, new List <string>
{
WrapperUtility.ChangeToToolsDirectoryCommand(spritzDirectory),
"echo \"\n# " + snpeffReference + "\" >> " + WrapperUtility.ConvertWindowsPath(Path.Combine(spritzDirectory, "Tools", "SnpEff", "snpEff.config")),
"echo \"" + snpeffReference + ".genome : Human genome " + snpeffReference.Split('.')[0] + " using RefSeq transcripts\" >> " + WrapperUtility.ConvertWindowsPath(Path.Combine(spritzDirectory, "Tools", "SnpEff", "snpEff.config")),
"echo \"" + snpeffReference + ".reference : ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/\" >> " + WrapperUtility.ConvertWindowsPath(Path.Combine(spritzDirectory, "Tools", "SnpEff", "snpEff.config")),
"echo \"\t" + snpeffReference + ".M.codonTable : Vertebrate_Mitochondrial\" >> " + WrapperUtility.ConvertWindowsPath(Path.Combine(spritzDirectory, "Tools", "SnpEff", "snpEff.config")),
"echo \"\t" + snpeffReference + ".MT.codonTable : Vertebrate_Mitochondrial\" >> " + WrapperUtility.ConvertWindowsPath(Path.Combine(spritzDirectory, "Tools", "SnpEff", "snpEff.config")),
}).WaitForExit();
}
public static int InferInnerDistance(string spritzDirectory, string analysisDirectory, string bamPath, string geneModelPath, out string[] outputFiles)
{
if (Path.GetExtension(geneModelPath) != ".bed")
{
geneModelPath = BEDOPSWrapper.GffOrGtf2Bed12(spritzDirectory, analysisDirectory, geneModelPath);
}
outputFiles = new string[]
{
Path.Combine(Path.GetDirectoryName(bamPath), Path.GetFileNameWithoutExtension(bamPath)) + InnerDistanceRPlotSuffix,
Path.Combine(Path.GetDirectoryName(bamPath), Path.GetFileNameWithoutExtension(bamPath)) + InnerDistanceFrequencyTableSuffix,
Path.Combine(Path.GetDirectoryName(bamPath), Path.GetFileNameWithoutExtension(bamPath)) + InnerDistanceDistanceTableSuffix
};
WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "InferInnerDistance.bash"), new List <string>
{
WrapperUtility.ChangeToToolsDirectoryCommand(spritzDirectory),
"python RSeQC-2.6.4/scripts/inner_distance.py" +
" -i " + WrapperUtility.ConvertWindowsPath(bamPath) + // input
" -o " + WrapperUtility.ConvertWindowsPath(Path.Combine(Path.GetDirectoryName(bamPath), Path.GetFileNameWithoutExtension(bamPath))) + // out prefix
" -r " + WrapperUtility.ConvertWindowsPath(geneModelPath), // gene model in BED format
WrapperUtility.EnsureClosedFileCommands(outputFiles[0]),
WrapperUtility.EnsureClosedFileCommands(outputFiles[1]),
WrapperUtility.EnsureClosedFileCommands(outputFiles[2]),
}).WaitForExit();
string[] distance_lines = File.ReadAllLines(Path.Combine(Path.GetDirectoryName(bamPath), Path.GetFileNameWithoutExtension(bamPath)) + InnerDistanceDistanceTableSuffix);
List <int> distances = new List <int>();
foreach (string dline in distance_lines)
{
if (int.TryParse(dline.Split('\t')[1], out int distance) &&
distance <250 && distance> -250) // default settings for infer_distance
{
distances.Add(distance);
}
}
int averageDistance = (int)Math.Round(distances.Average(), 0);
return(averageDistance);
}