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)); }