/// <summary>
/// Filters GTF or GFF entries that lack strand information
/// Can filter also by zero abundance stringtie estimates
/// Add CDS at the end
/// </summary>
/// <param name="gtfPath"></param>
/// <param name="gtfOutPath"></param>
public static void FilterGtfEntriesWithoutStrand(string gtfPath, string referenceGenomePath, string referenceGeneModelPath, bool filterEntriesWithZeroAbundanceStringtieEstimates = false)
{
var chromFeatures = GeneModel.SimplerParse(gtfPath);
string filteredGtfPath = Path.Combine(Path.GetDirectoryName(gtfPath), Path.GetFileNameWithoutExtension(gtfPath) + ".filtered.gtf");
using (var file = File.Create(filteredGtfPath))
{
var formatter = new GffFormatter();
foreach (var chromISeq in chromFeatures)
{
List <MetadataListItem <List <string> > > filteredFeatures = new List <MetadataListItem <List <string> > >();
bool isMetadata = chromISeq.Metadata.TryGetValue("features", out object featuresObj);
if (isMetadata)
{
bool okayTranscript = false;
var features = featuresObj as List <MetadataListItem <List <string> > >;
foreach (var feature in features)
{
if (!feature.SubItems.TryGetValue("strand", out List <string> strandish))
{
continue;
}
var attributes = GeneModel.SplitAttributes(feature.FreeText);
if (feature.Key == "transcript")
{
bool okayFpkm = !filterEntriesWithZeroAbundanceStringtieEstimates ||
attributes.TryGetValue("FPKM", out string fpkm) && double.TryParse(fpkm, out double fpkmValue) && fpkmValue > 0;
bool okayTpm = !filterEntriesWithZeroAbundanceStringtieEstimates ||
attributes.TryGetValue("TPM", out string tpm) && double.TryParse(tpm, out double tpmValue) && tpmValue > 0;
okayTranscript = okayFpkm && okayTpm;
}
if (okayTranscript)
{
filteredFeatures.Add(feature);
}
}
}
chromISeq.Metadata["features"] = filteredFeatures;
}
formatter.Format(file, chromFeatures);
}
Genome ensemblGenome = new Genome(referenceGenomePath);
GeneModel newGeneModel = new GeneModel(ensemblGenome, filteredGtfPath);
GeneModel referenceGeneModel = new GeneModel(ensemblGenome, referenceGeneModelPath);
newGeneModel.CreateCDSFromAnnotatedStartCodons(referenceGeneModel);
string filteredGtfWithCdsPath = Path.Combine(Path.GetDirectoryName(filteredGtfPath), Path.GetFileNameWithoutExtension(filteredGtfPath) + ".withcds.gtf");
newGeneModel.PrintToGTF(filteredGtfWithCdsPath);
}
/// <summary>
/// Filters GTF or GFF entries that lack strand information
/// </summary>
/// <param name="gtfPath"></param>
/// <param name="gtfOutPath"></param>
public void FilterGtfEntriesWithoutStrand(string gtfPath, string gtfOutPath, bool filterEntriesWithZeroAbundanceStringtieEstimates)
{
var chromFeatures = GeneModel.SimplerParse(gtfPath);
//if (!File.Exists(gtfOutPath))
//{
using (var file = File.Create(gtfOutPath))
{
var formatter = new GffFormatter();
foreach (var chromISeq in chromFeatures)
{
List <MetadataListItem <List <string> > > filteredFeatures = new List <MetadataListItem <List <string> > >();
bool isMetadata = chromISeq.Metadata.TryGetValue("features", out object featuresObj);
if (isMetadata)
{
bool okayTranscript = false;
var features = featuresObj as List <MetadataListItem <List <string> > >;
foreach (var feature in features)
{
if (!feature.SubItems.TryGetValue("strand", out List <string> strandish))
{
continue;
}
var attributes = GeneModel.SplitAttributes(feature.FreeText);
if (feature.Key == "transcript")
{
bool okayFpkm = !filterEntriesWithZeroAbundanceStringtieEstimates ||
attributes.TryGetValue("FPKM", out string fpkm) && double.TryParse(fpkm, out double fpkmValue) && fpkmValue > 0;
bool okayTpm = !filterEntriesWithZeroAbundanceStringtieEstimates ||
attributes.TryGetValue("TPM", out string tpm) && double.TryParse(tpm, out double tpmValue) && tpmValue > 0;
okayTranscript = okayFpkm && okayTpm;
}
if (okayTranscript)
{
filteredFeatures.Add(feature);
}
}
}
chromISeq.Metadata["features"] = filteredFeatures;
}
formatter.Format(file, chromFeatures);
}
//}
}
