public override string GetGtfAttributes()
{
var attributes = GeneModel.SplitAttributes(FeatureMetadata.FreeText);
List <Tuple <string, string> > attributeSubsections = new List <Tuple <string, string> >();
string exonIdLabel = "exon_id";
bool hasExonId = attributes.TryGetValue(exonIdLabel, out string exonId);
if (hasExonId)
{
attributeSubsections.Add(new Tuple <string, string>(exonIdLabel, exonId));
}
string exonVersionLabel = "exon_version";
bool hasExonVersion = attributes.TryGetValue(exonVersionLabel, out string exonVersion);
if (hasExonVersion)
{
attributeSubsections.Add(new Tuple <string, string>(exonVersionLabel, exonVersion));
}
string exonNumberLabel = "exon_number";
string exonNumber = (Parent as Transcript).Exons.Count(x => x.OneBasedStart <= OneBasedStart).ToString();
attributeSubsections.Add(new Tuple <string, string>(exonNumberLabel, exonNumber));
return(Parent.GetGtfAttributes() + " " + String.Join(" ", attributeSubsections.Select(x => x.Item1 + " \"" + x.Item2 + "\";")));
}
public override string GetGtfAttributes()
{
var attributes = GeneModel.SplitAttributes(FeatureMetadata.FreeText);
List <Tuple <string, string> > attributeSubsections = new List <Tuple <string, string> >();
string tIdLabel = "transcript_id";
bool hasTranscriptId = attributes.TryGetValue(tIdLabel, out string transcriptId);
if (hasTranscriptId)
{
attributeSubsections.Add(new Tuple <string, string>(tIdLabel, transcriptId));
}
string tVersionLabel = "transcript_version";
bool hasTranscriptVersion = attributes.TryGetValue(tVersionLabel, out string transcriptVersion);
if (hasTranscriptVersion)
{
attributeSubsections.Add(new Tuple <string, string>(tVersionLabel, transcriptVersion));
}
string tBiotypeLabel = "transcript_biotype";
bool hasTranscriptBiotype = attributes.TryGetValue(tBiotypeLabel, out string transcriptBiotype);
if (hasTranscriptVersion)
{
attributeSubsections.Add(new Tuple <string, string>(tBiotypeLabel, transcriptBiotype));
}
// Cufflinks-related, but not using Cufflinks much because stringtie is better
//bool hasNearestRef = attributes.TryGetValue("nearest_ref", out string nearestRef);
//bool hasClassCode = attributes.TryGetValue("class_code", out string classCode);
bool hasSource = FeatureMetadata.SubItems.TryGetValue("source", out List <string> sourceish);
bool hasStrand = FeatureMetadata.SubItems.TryGetValue("strand", out List <string> strandish);
bool hasFrame = FeatureMetadata.SubItems.TryGetValue("frame", out List <string> framey);
return(Parent.GetGtfAttributes() + " " + String.Join(" ", attributeSubsections.Select(x => x.Item1 + " \"" + x.Item2 + "\";")));
}
public override string GetGtfAttributes()
{
var attributes = GeneModel.SplitAttributes(FeatureMetadata.FreeText);
List <Tuple <string, string> > attributeSubsections = new List <Tuple <string, string> >();
string geneIdLabel = "gene_id";
bool hasGeneId = attributes.TryGetValue(geneIdLabel, out string geneId);
if (hasGeneId)
{
attributeSubsections.Add(new Tuple <string, string>(geneIdLabel, geneId));
}
string geneNameLabel = "gene_name";
bool hasGeneName = attributes.TryGetValue(geneNameLabel, out string geneName);
if (hasGeneName)
{
attributeSubsections.Add(new Tuple <string, string>(geneNameLabel, geneName));
}
string geneVersionLabel = "gene_version";
bool hasGeneVersion = attributes.TryGetValue(geneVersionLabel, out string geneVersion);
if (hasGeneVersion)
{
attributeSubsections.Add(new Tuple <string, string>(geneVersionLabel, geneVersion));
}
string geneBiotypeLabel = "gene_biotype";
bool hasGeneBiotype = attributes.TryGetValue(geneBiotypeLabel, out string geneBiotype);
if (hasGeneBiotype)
{
attributeSubsections.Add(new Tuple <string, string>(geneBiotypeLabel, geneBiotype));
}
return(String.Join(" ", attributeSubsections.Select(x => x.Item1 + " \"" + x.Item2 + "\";")));
}