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 void TestContainLocations()
{
MatchExon e1 = new MatchExon();
e1.Add(new Location(1, 10));
e1.Add(new Location(30, 40));
var e2 = new[] { new Location(1, 10), new Location(30, 40) };
var e3 = new[] { new Location(1, 11), new Location(30, 40) };
Assert.IsTrue(e1.EqualLocations(e2));
Assert.IsFalse(e1.EqualLocations(e3));
}
public void TestContainLocation()
{
MatchExon e1 = new MatchExon();
e1.Add(new Location(1, 10));
e1.Add(new Location(30, 40));
Location l1 = new Location(3, 6);
Assert.IsTrue(e1.ContainLocation(l1));
Location l2 = new Location(3, 11);
Assert.IsFalse(e1.ContainLocation(l2));
Location l3 = new Location(25, 35);
Assert.IsFalse(e1.ContainLocation(l3));
}
private MatchExon ParseMatchExon(string[] parts)
{
MatchExon mx = new MatchExon();
mx.TranscriptId = parts[7];
mx.TranscriptType = parts[8];
mx.TranscriptCount = int.Parse(parts[9]);
mx.RetainedIntron = parts[10] == "1";
mx.IntronSize = int.Parse(parts[11]);
var exons = parts[13].Split(';');
foreach (var exon in exons)
{
mx.Add(new Location(exon));
}
return mx;
}
public void TestEqualLocations()
{
MatchExon e1 = new MatchExon();
e1.Add(new Location(1, 10));
e1.Add(new Location(30, 40));
MatchExon e2 = new MatchExon();
e2.Add(new Location(1, 10));
e2.Add(new Location(30, 40));
MatchExon e3 = new MatchExon();
e3.Add(new Location(1, 11));
e3.Add(new Location(30, 40));
Assert.IsTrue(e1.EqualLocations(e2));
Assert.IsFalse(e1.EqualLocations(e3));
}
private MatchExon ParseMatchExon(string[] parts)
{
MatchExon mx = new MatchExon();
mx.TranscriptId = parts[7];
mx.TranscriptType = parts[8];
mx.TranscriptCount = int.Parse(parts[9]);
mx.RetainedIntron = parts[10] == "1";
mx.IntronSize = int.Parse(parts[11]);
var exons = parts[13].Split(';');
foreach (var exon in exons)
{
mx.Add(new Location(exon));
}
return(mx);
}
public void MatchGtfTranscriptItem(GtfTranscriptItem gtItem)
{
int index = gtItem.FindItemIndex(this.Start, this.End - 1);
if (-1 == index)
{
return;
}
GtfItem gitem = gtItem[index];
MatchExon exon = new MatchExon();
this.exons.Add(exon);
exon.TranscriptId = gitem.TranscriptId;
exon.TranscriptCount = 1;
exon.TranscriptType = gitem.Source;
Location ml = new Location();
exon.Add(ml);
if (gitem.Start > this.Start)
{
//if the peak range is out of the exon range, that peak range may be potential exon which
//is detected by RNASeq data, so just extend the peak range to expect length rather than
//extend by prior exon range
ml.Start = this.ExpectStart;
exon.IntronSize = gitem.Start - this.Start;
exon.RetainedIntron = true;
}
else if (gitem.Start <= this.ExpectStart)
{
//the exon has enough base pair
ml.Start = this.ExpectStart;
}
else
{
//the exon has no enough base pair
ml.Start = gitem.Start;
long expectLength = ml.Start - this.ExpectStart;
int curindex = index - 1;
while (expectLength > 0 && curindex >= 0)
{
Location lp = new Location();
exon.Insert(0, lp);
GtfItem prior = gtItem[curindex];
lp.End = prior.End;
if (prior.Length >= expectLength)
{
lp.Start = prior.End - expectLength + 1;
break;
}
else
{
lp.Start = prior.Start;
expectLength = expectLength - prior.Length;
curindex--;
}
}
}
if (gitem.End < this.End - 1)
{
ml.End = this.ExpectEnd;
exon.IntronSize = this.End - 1 - gitem.End;
exon.RetainedIntron = true;
}
else if (gitem.End >= this.ExpectEnd)
{
ml.End = this.ExpectEnd;
}
else
{
ml.End = gitem.End;
long expectLength = this.ExpectEnd - ml.End;
int curindex = index + 1;
while (expectLength > 0 && curindex < gtItem.Count)
{
Location lp = new Location();
exon.Add(lp);
GtfItem next = gtItem[curindex];
lp.Start = next.Start;
if (next.Length >= expectLength)
{
lp.End = next.Start + expectLength - 1;
break;
}
else
{
lp.End = next.End;
expectLength = expectLength - next.Length;
curindex++;
}
}
}
}
public void MatchGtfTranscriptItem(GtfTranscriptItem gtItem)
{
int index = gtItem.FindItemIndex(this.Start, this.End - 1);
if (-1 == index)
{
return;
}
GtfItem gitem = gtItem[index];
MatchExon exon = new MatchExon();
this.exons.Add(exon);
exon.TranscriptId = gitem.TranscriptId;
exon.TranscriptCount = 1;
exon.TranscriptType = gitem.Source;
Location ml = new Location();
exon.Add(ml);
if (gitem.Start > this.Start)
{
//if the peak range is out of the exon range, that peak range may be potential exon which
//is detected by RNASeq data, so just extend the peak range to expect length rather than
//extend by prior exon range
ml.Start = this.ExpectStart;
exon.IntronSize = gitem.Start - this.Start;
exon.RetainedIntron = true;
}
else if (gitem.Start <= this.ExpectStart)
{
//the exon has enough base pair
ml.Start = this.ExpectStart;
}
else
{
//the exon has no enough base pair
ml.Start = gitem.Start;
long expectLength = ml.Start - this.ExpectStart;
int curindex = index - 1;
while (expectLength > 0 && curindex >= 0)
{
Location lp = new Location();
exon.Insert(0, lp);
GtfItem prior = gtItem[curindex];
lp.End = prior.End;
if (prior.Length >= expectLength)
{
lp.Start = prior.End - expectLength + 1;
break;
}
else
{
lp.Start = prior.Start;
expectLength = expectLength - prior.Length;
curindex--;
}
}
}
if (gitem.End < this.End - 1)
{
ml.End = this.ExpectEnd;
exon.IntronSize = this.End - 1 - gitem.End;
exon.RetainedIntron = true;
}
else if (gitem.End >= this.ExpectEnd)
{
ml.End = this.ExpectEnd;
}
else
{
ml.End = gitem.End;
long expectLength = this.ExpectEnd - ml.End;
int curindex = index + 1;
while (expectLength > 0 && curindex < gtItem.Count)
{
Location lp = new Location();
exon.Add(lp);
GtfItem next = gtItem[curindex];
lp.Start = next.Start;
if (next.Length >= expectLength)
{
lp.End = next.Start + expectLength - 1;
break;
}
else
{
lp.End = next.End;
expectLength = expectLength - next.Length;
curindex++;
}
}
}
}
