public void TestMergeExon1()
{
var item = new MatchedBedItem();
MatchExon e1 = new MatchExon();
e1.TranscriptId = "E1";
e1.Add(new Location(1, 10));
e1.Add(new Location(30, 40));
MatchExon e2 = new MatchExon();
e2.TranscriptId = "E2";
e2.Add(new Location(1, 10));
e2.Add(new Location(30, 40));
MatchExon e3 = new MatchExon();
e3.TranscriptId = "E3";
e3.Add(new Location(30, 39));
item.Exons.Add(e1);
item.Exons.Add(e2);
item.Exons.Add(e3);
Assert.AreEqual(3, item.Exons.Count);
item.MergeExon();
Assert.AreEqual(1, item.Exons.Count);
Assert.AreEqual("E1;E2", item.Exons[0].TranscriptId);
}
public string GetValue(MatchedBedItem item)
{
StringBuilder sb = new StringBuilder();
bool bFirst = true;
foreach (var exon in item.Exons)
{
if (bFirst)
{
sb.Append(string.Format("{0}\t{1}", bedFile.GetValue(item), item.Exons.Count));
}
else
{
sb.Append(string.Format("{0}\t{1}", missHeader, item.Exons.Count));
}
sb.AppendLine(string.Format("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}",
exon.TranscriptId,
exon.TranscriptType,
exon.TranscriptCount,
exon.RetainedIntron ? 1 : 0,
exon.IntronSize,
exon.Count,
string.Join(";", exon.ConvertAll(m => string.Format("{0}-{1}", m.Start, m.End)))));
}
return(sb.ToString());
}
public MatchedBedItem Next()
{
string line = "";
while ((line = reader.ReadLine()) != null)
{
if (line.Length > 0 && line[0] != '\t')
{
var parts = line.Split('\t');
if (parts.Length < 14)
{
continue;
}
long chromstart;
if (!long.TryParse(parts[1], out chromstart))
{
continue;
}
var result = new MatchedBedItem();
result.Seqname = parts[0];
result.Start = chromstart;
result.End = long.Parse(parts[2]);
result.Name = parts[3];
result.Score = double.Parse(parts[4]);
result.Strand = parts[5][0];
result.Exons.Add(ParseMatchExon(parts));
int c;
while ((c = reader.Peek()) != -1)
{
if (c != '\t')
{
break;
}
line = reader.ReadLine();
parts = line.Split('\t');
result.Exons.Add(ParseMatchExon(parts));
}
return(result);
}
}
return(null);
}
public MatchedBedItem Next()
{
string line = "";
while ((line = reader.ReadLine()) != null)
{
if (line.Length > 0 && line[0] != '\t')
{
var parts = line.Split('\t');
if (parts.Length < 14)
{
continue;
}
long chromstart;
if (!long.TryParse(parts[1], out chromstart))
{
continue;
}
var result = new MatchedBedItem();
result.Seqname = parts[0];
result.Start = chromstart;
result.End = long.Parse(parts[2]);
result.Name = parts[3];
result.Score = double.Parse(parts[4]);
result.Strand = parts[5][0];
result.Exons.Add(ParseMatchExon(parts));
int c;
while ((c = reader.Peek()) != -1)
{
if (c != '\t')
{
break;
}
line = reader.ReadLine();
parts = line.Split('\t');
result.Exons.Add(ParseMatchExon(parts));
}
return result;
}
}
return null;
}
public string GetValue(MatchedBedItem item)
{
StringBuilder sb = new StringBuilder();
bool bFirst = true;
foreach (var exon in item.Exons)
{
if (bFirst)
{
sb.Append(string.Format("{0}\t{1}", bedFile.GetValue(item), item.Exons.Count));
}
else
{
sb.Append(string.Format("{0}\t{1}", missHeader, item.Exons.Count));
}
sb.AppendLine(string.Format("\t{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}",
exon.TranscriptId,
exon.TranscriptType,
exon.TranscriptCount,
exon.RetainedIntron ? 1 : 0,
exon.IntronSize,
exon.Count,
string.Join(";", exon.ConvertAll(m => string.Format("{0}-{1}", m.Start, m.End)))));
}
return sb.ToString();
}
