/// <summary>
/// Extracts transcript name and FPKM/RPM values and creates bed locations with score
/// When multiple transcripts are present, adds all transcripts
/// </summary>
/// <param name="fields">Fields.</param>
/// <param name="layout">Layout.</param>
/// <param name="data">Data.</param>
/// <param name="entryCount">Entry count.</param>
protected override void ParseFields(string[] fields, Layout layout, List <Tuple <Genomics.Location, string> > data, ref int entryCount)
{
//Console.WriteLine(EntryTypeFieldFormat [expressionType] + "\t" + expressionType + "\t" + fields [2]);
if (EntryTypeFieldFormat [expressionType] == fields [2])
{
string geneName = "";
List <string> transcriptNames = ParseNameData(fields [layout.Name], ref entryCount, out geneName);
var startSite = new Genomics.Location
{
Start = int.Parse(fields [layout.Start]),
End = int.Parse(fields [layout.End])
};
foreach (string transcriptName in transcriptNames)
{
string name = transcriptName;
var location = new Genomics.Location
{
Name = name,
Chromosome = fields [layout.Chromosome],
Start = int.Parse(fields [layout.Start]),
End = int.Parse(fields [layout.End]),
Strand = fields [layout.Strand],
Score = expressionLevel,
Data = fields,
AlternateName = geneName
};
// Short expression only measures exons, so use each exon
// start as it's own 'transcript' and 'gene'
if (expressionType == ExpressionType.Short)
{
name = transcriptName + "." + location.DirectionalStart;
location = new Genomics.Location
{
Name = name,
Chromosome = fields [layout.Chromosome],
Start = int.Parse(fields [layout.Start]),
End = int.Parse(fields [layout.End]),
Strand = fields [layout.Strand],
Score = expressionLevel,
Data = fields,
AlternateName = geneName
};
}
if (this.IsValidTranscriptName(name))
{
data.Add(new Tuple <Genomics.Location, string>(location, name));
}
}
}
}
/// <summary>
/// Parses the fields.
/// </summary>
/// <param name="fields">Fields.</param>
/// <param name="layout">Layout.</param>
/// <param name="data">Data.</param>
/// <param name="entryCount">Entry count.</param>
protected override void ParseFields(string[] fields, Layout layout, List <Tuple <Genomics.Location, string> > data, ref int entryCount)
{
if (fields[0][0] == '#')
{
return;
}
if (fields [2] != this.Feature)
{
return;
}
var nameData = ParseNameData(fields [layout.Name]);
var startSite = new Genomics.Location
{
Start = int.Parse(fields [layout.Start]),
End = int.Parse(fields [layout.End])
};
linecount++;
if (linecount % 10000 == 0)
{
Console.WriteLine(linecount);
}
var name = nameData["transcript_id"];
string geneName = nameData["gene_id"];
var location = new Genomics.Location
{
Name = nameData["transcript_id"],
Chromosome = fields [layout.Chromosome],
Start = int.Parse(fields [layout.Start]),
End = int.Parse(fields [layout.End]),
Strand = fields [layout.Strand],
Data = fields,
AdditionalFields = nameData,
AlternateName = geneName + "." + startSite.DirectionalStart
};
data.Add(new Tuple <Genomics.Location, string>(
location,
nameData["transcript_id"])
);
}
