/// <summary>
/// Reads gene model features into data structures contained within this library
/// </summary>
/// <param name="geneModelFile"></param>
public void ReadGeneFeatures(string geneModelFile)
{
foreach (ISequence chromFeatures in SimplerParse(geneModelFile))
{
Chromosome chrom = Genome.Chromosomes.FirstOrDefault(x => x.FriendlyName == chromFeatures.ID);
if (chrom == null)
{
continue;
}
chromFeatures.Metadata.TryGetValue("features", out object f);
List <MetadataListItem <List <string> > > features = f as List <MetadataListItem <List <string> > >;
for (int i = 0; i < features.Count; i++)
{
MetadataListItem <List <string> > feature = features[i];
long.TryParse(feature.SubItems["start"][0], out long start);
long.TryParse(feature.SubItems["end"][0], out long end);
var attributes = SplitAttributes(feature.FreeText);
if (feature.FreeText.Contains('='))
{
ProcessGff3Feature(feature, start, end, chrom, attributes);
}
else
{
ProcessGtfFeature(feature, start, end, chrom, attributes);
}
}
}
if (currentTranscript != null)
{
Transcript.SetRegions(currentTranscript);
currentTranscript.FrameCorrection();
}
CreateIntergenicRegions();
// possibly check transcript sanity here with Parallel.ForEach(Genes.SelectMany(g => g.Transcripts).ToList(), t => t.SanityCheck());
GenomeForest.Build();
}
