/// <summary>
/// Converts a gene model file (GTF?) to a BED12 file with all 12 columns sometimes required of a BED file.
///
/// see https://gist.github.com/gireeshkbogu/f478ad8495dca56545746cd391615b93
///
/// </summary>
/// <param name="spritzDirectory"></param>
/// <param name="filteredGeneModelGtfGffPath"></param>
/// <returns></returns>
public static string Gtf2Bed12(string spritzDirectory, string analysisDirectory, string filteredGeneModelGtfGffPath, string genomeFastaPath)
{
string geneModelGtf = filteredGeneModelGtfGffPath;
if (Path.GetExtension(filteredGeneModelGtfGffPath).StartsWith(".gff"))
{
CufflinksWrapper.GffToGtf(spritzDirectory, analysisDirectory, filteredGeneModelGtfGffPath, out geneModelGtf);
}
string genePredPath = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".genePred");
string bed12Path = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".bed12");
string sortedBed12Path = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".sorted.bed12");
WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "Bed12FaidxSortConversion.bash"), new List <string>
{
"gtfToGenePred " + WrapperUtility.ConvertWindowsPath(geneModelGtf) + " " + WrapperUtility.ConvertWindowsPath(genePredPath),
"genePredToBed " + WrapperUtility.ConvertWindowsPath(genePredPath) + " " + WrapperUtility.ConvertWindowsPath(bed12Path),
"bedtools sort -faidx " + WrapperUtility.ConvertWindowsPath(genomeFastaPath + ".fai") + " -i " + WrapperUtility.ConvertWindowsPath(bed12Path) + " > " + WrapperUtility.ConvertWindowsPath(sortedBed12Path),
}).WaitForExit();
return(sortedBed12Path);
}
/// <summary>
/// Converts a gene model file (GTF?) to a BED12 file with all 12 columns sometimes required of a BED file.
///
/// see https://gist.github.com/gireeshkbogu/f478ad8495dca56545746cd391615b93
///
/// </summary>
/// <param name="spritzDirectory"></param>
/// <param name="geneModelGtfOrGff"></param>
/// <returns></returns>
public static string GffOrGtf2Bed12(string spritzDirectory, string analysisDirectory, string geneModelGtfOrGff)
{
string geneModelGtf = geneModelGtfOrGff;
if (Path.GetExtension(geneModelGtfOrGff).StartsWith(".gff"))
{
CufflinksWrapper.GffToGtf(spritzDirectory, analysisDirectory, geneModelGtfOrGff, out geneModelGtf);
}
string genePredPath = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".genePred");
string bed12Path = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".bed12");
string sortedBed12Path = Path.Combine(Path.GetDirectoryName(geneModelGtf), Path.GetFileNameWithoutExtension(geneModelGtf) + ".sorted.bed12");
WrapperUtility.GenerateAndRunScript(WrapperUtility.GetAnalysisScriptPath(analysisDirectory, "Bed12conversion.bash"), new List <string>
{
// Note, there is a gff3ToGenePred program. Could test and replace that here for gff3 files.
"gtfToGenePred " + WrapperUtility.ConvertWindowsPath(geneModelGtf) + " " + WrapperUtility.ConvertWindowsPath(genePredPath),
"genePredToBed " + WrapperUtility.ConvertWindowsPath(genePredPath) + " " + WrapperUtility.ConvertWindowsPath(bed12Path),
"sort -k1,1 -k2,2n " + WrapperUtility.ConvertWindowsPath(bed12Path) + " > " + WrapperUtility.ConvertWindowsPath(sortedBed12Path),
}).WaitForExit();
return(sortedBed12Path);
}