public void TestMergeExon2() { string filename = "../../../data/match.tsv"; var item = new MatchedBedItemFile(filename).Next(); Assert.AreEqual(3, item.Exons.Count); item.MergeExon(); Assert.AreEqual(1, item.Exons.Count); Assert.AreEqual("ENST00000538797", item.Exons[0].TranscriptId); }
public void TestNext() { string filename = "../../../data/match.tsv"; using (MatchedBedItemFile file = new MatchedBedItemFile(filename)) { var item = file.Next(); Assert.AreEqual("2", item.Seqname); Assert.AreEqual(73470225, item.Start); Assert.AreEqual(73470251, item.End); Assert.AreEqual("2-60", item.Name); Assert.AreEqual(1064, item.Score); Assert.AreEqual('+', item.Strand); Assert.AreEqual(3, item.Exons.Count); Assert.AreEqual("ENST00000469844;ENST00000540468;ENST00000539919;ENST00000258091;ENST00000461290;ENST00000399032;ENST00000409924;ENST00000537131;ENST00000473786", item.Exons[0].TranscriptId); Assert.AreEqual("processed_transcript", item.Exons[0].TranscriptType); Assert.IsTrue(item.Exons[0].RetainedIntron); Assert.AreEqual(3, item.Exons[0].IntronSize); Assert.AreEqual(2, item.Exons[0].Count); Assert.AreEqual(73470189, ((item.Exons[0]))[0].Start); Assert.AreEqual(73470256, ((item.Exons[0]))[0].End); Assert.AreEqual(73471124, ((item.Exons[0]))[1].Start); Assert.AreEqual(73471155, ((item.Exons[0]))[1].End); Assert.AreEqual("ENST00000471927;ENST00000480489", item.Exons[1].TranscriptId); Assert.AreEqual("processed_transcript", item.Exons[1].TranscriptType); Assert.IsTrue(item.Exons[1].RetainedIntron); Assert.AreEqual(16, item.Exons[1].IntronSize); Assert.AreEqual(1, item.Exons[1].Count); Assert.AreEqual(73470189, ((item.Exons[1]))[0].Start); Assert.AreEqual(73470288, ((item.Exons[1]))[0].End); Assert.AreEqual("ENST00000538797", item.Exons[2].TranscriptId); Assert.AreEqual("protein_coding", item.Exons[2].TranscriptType); Assert.IsFalse(item.Exons[2].RetainedIntron); Assert.AreEqual(0, item.Exons[2].IntronSize); Assert.AreEqual(2, item.Exons[2].Count); Assert.AreEqual(73470189, ((item.Exons[2]))[0].Start); Assert.AreEqual(73470256, ((item.Exons[2]))[0].End); Assert.AreEqual(73471671, ((item.Exons[2]))[1].Start); Assert.AreEqual(73471702, ((item.Exons[2]))[1].End); item = file.Next(); Assert.IsNull(item); } }