public void TestNextTranscriptItem()
{
GtfTranscriptItemFile file = new GtfTranscriptItemFile();
file.Open(TestGtfItemFile.filename);
GtfTranscriptItem tr = file.Next(false);
Assert.AreEqual(1, tr.Count);
Assert.AreEqual("ENST00000578976", tr[0].TranscriptId);
tr = file.Next();
Assert.AreEqual(11, tr.Count);
foreach (var tritem in tr)
{
Assert.AreEqual("ENST00000327822", tritem.TranscriptId);
}
var item = (tr)[10];
Assert.AreEqual("GL000213.1", item.Seqname);
Assert.AreEqual("protein_coding", item.Source);
Assert.AreEqual("exon", item.Feature);
Assert.AreEqual(138767, item.Start);
Assert.AreEqual(139339, item.End);
Assert.AreEqual(".", item.Score);
Assert.AreEqual('-', item.Strand);
Assert.AreEqual('.', item.Frame);
Assert.AreEqual(" gene_id \"ENSG00000237375\"; transcript_id \"ENST00000327822\"; exon_number \"1\"; gene_name \"BX072566.1\"; gene_biotype \"protein_coding\"; transcript_name \"BX072566.1-201\";", item.Attributes);
GtfTranscriptItem item2 = file.Next();
Assert.AreEqual("ENST00000459553", item2[0].TranscriptId);
}
public void TestSameTranscript()
{
GtfTranscriptItemFile file = new GtfTranscriptItemFile();
file.Open(TestGtfItemFile.filename);
GtfTranscriptItem item = file.Next();
GtfTranscriptItem next = file.Next();
for (int i = 1; i < 11; i++)
{
Assert.IsTrue(item.IsSameTranscript(item[i]));
Assert.IsFalse(next.IsSameTranscript(item[i]));
}
}
public void TestFindItemIndex()
{
GtfTranscriptItemFile file = new GtfTranscriptItemFile();
file.Open(TestGtfItemFile.filename);
GtfTranscriptItem item = file.Next();
GtfTranscriptItem next = file.Next();
int index = item.FindItemIndex(134290, 134380);
Assert.IsTrue(index >= 0);
GtfItem find = item[index];
Assert.AreEqual(2, find.ExonNumber);
Assert.AreEqual(-1, item.FindItemIndex(1342900, 1343800));
Assert.AreEqual(-1, item.FindItemIndex(134, 1343));
}