/// <summary>
/// loads all the genes in the specified file
/// </summary>
private List <MutableGene> LoadGenes(string genesPath, string description)
{
var genes = new List <MutableGene>();
using (var reader = new VepGeneReader(genesPath))
{
if (_header == null)
{
_header = reader.Header;
}
while (true)
{
var gene = reader.Next();
if (gene == null)
{
break;
}
genes.Add(gene);
}
}
var transcriptDataSource = genes.First().TranscriptDataSource;
int numGenesWithoutSymbol = GetNumGenesWithoutSymbol(description, genes);
if (numGenesWithoutSymbol > 0 && transcriptDataSource == TranscriptDataSource.RefSeq)
{
ResolveMissingRefSeqGeneSymbols(description, genes);
}
return(genes);
}
/// <summary>
/// constructor
/// </summary>
public TempPredictionReader(string filePath, string description, GlobalImportCommon.FileType fileType)
{
// sanity check
if (!File.Exists(filePath))
{
throw new FileNotFoundException($"The specified protein function prediction file ({filePath}) does not exist.");
}
// open the vcf file and parse the header
_reader = GZipUtilities.GetAppropriateBinaryReader(filePath);
Header = GetHeader(description, filePath, fileType, _reader);
}
/// <summary>
/// constructor
/// </summary>
public VepGeneReader(string filePath)
{
// sanity check
if (!File.Exists(filePath))
{
throw new FileNotFoundException($"The specified gene file ({filePath}) does not exist.");
}
// open the vcf file and parse the header
_reader = GZipUtilities.GetAppropriateStreamReader(filePath);
Header = VepReaderCommon.GetHeader("gene", filePath, GlobalImportCommon.FileType.Gene, _reader);
}
/// <summary>
/// constructor
/// </summary>
public VepTranscriptReader(string filePath)
{
// sanity check
if (!File.Exists(filePath))
{
throw new FileNotFoundException($"The specified transcripts file ({filePath}) does not exist.");
}
// open the vcf file and parse the header
_filePath = filePath;
_reader = GZipUtilities.GetAppropriateStreamReader(filePath);
Header = GetHeader();
}
/// <summary>
/// writes the header to our output file
/// </summary>
private static void WriteHeader(StreamWriter writer, GlobalImportHeader header)
{
writer.WriteLine("{0}\t{1}", GlobalImportCommon.Header, (byte)GlobalImportCommon.FileType.Gene);
writer.WriteLine("{0}\t{1}\t{2}\t{3}", header.VepVersion, header.VepReleaseTicks,
(byte)TranscriptDataSource.BothRefSeqAndEnsembl, (byte)header.GenomeAssembly);
}
