From c93f5c0dfd3bed41a508b69fdab695227f84fabc Mon Sep 17 00:00:00 2001
From: squinker <william.bellamy@genomicsengland.co.uk>
Date: Tue, 6 Sep 2022 17:07:12 +0100
Subject: [PATCH] chore: Add unit tests for HgvsCalculator

---
 .../variant/hgvs/HgvsCalculatorUnitTest.java  | 125 ++++++++++++++++++
 1 file changed, 125 insertions(+)
 create mode 100644 cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorUnitTest.java

diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorUnitTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorUnitTest.java
new file mode 100644
index 0000000000..d23cd3f7bd
--- /dev/null
+++ b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/variant/hgvs/HgvsCalculatorUnitTest.java
@@ -0,0 +1,125 @@
+package org.opencb.cellbase.lib.variant.hgvs;
+
+import org.junit.jupiter.api.Test;
+import org.opencb.biodata.models.core.Exon;
+import org.opencb.biodata.models.core.Gene;
+import org.opencb.biodata.models.core.Transcript;
+import org.opencb.biodata.models.variant.Variant;
+import org.opencb.biodata.models.variant.avro.VariantType;
+import org.opencb.cellbase.core.exception.CellBaseException;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+public class HgvsCalculatorUnitTest {
+
+    @Test
+    void shouldProduceOneWellFormedHgvsEntryForASNVVariant() throws CellBaseException {
+
+        HgvsCalculator hgvsCalculator = new HgvsCalculator(null, 1);
+        Gene gene = new Gene();
+        gene.setId("ENSG00000000001");
+        Transcript transcript = new Transcript();
+        transcript.setId("ENST00000000001");
+        transcript.setChromosome("1");
+        transcript.setStart(1);
+        transcript.setEnd(2);
+        transcript.setStrand("+");
+        transcript.setCdnaCodingEnd(1);
+        Exon exon = new Exon();
+        exon.setStart(1);
+        exon.setEnd(2);
+        transcript.setExons(Arrays.asList(exon));
+        gene.setTranscripts(Arrays.asList(transcript));
+        Variant variant = Variant.newBuilder("1", 1, 2, "A", "T").build();
+        variant.setType(VariantType.SNV);
+        List<String> result = hgvsCalculator.run(variant, Arrays.asList(gene), false);
+
+        assertEquals(Arrays.asList("ENST00000000001(ENSG00000000001):c.*A>T"), result);
+    }
+
+    @Test
+    void shouldHaveAPdotValueFollowingACorrespondingCdotValue() throws CellBaseException {
+
+        final String _10_GCC = String.join("", Collections.nCopies(10, "GCC"));
+        final String _9_A = String.join("", Collections.nCopies(9, "A"));
+
+        final String trans1 = "ENST00000000001";
+        final String trans2 = "ENST00000000002";
+        final String trans3 = "ENST00000000003";
+
+        final String gene1 = "ENSG00000000001";
+
+        final String protein1 = "ENSP00000000001";
+        final String protein2 = "ENSP00000000002";
+        final String protein3 = "ENSP00000000003";
+
+        HgvsCalculator hgvsCalculator = new HgvsCalculator(null, 1);
+
+        // Three transcripts whose coding sequences overlap the variant position
+        Transcript transcript1 = new Transcript()
+                .setId(trans1)
+                .setChromosome("1")
+                .setStart(15)
+                .setEnd(45)
+                .setStrand("+")
+                .setCdnaCodingEnd(30)
+                .setCdnaSequence(_10_GCC)
+                .setProteinSequence(_9_A)
+                .setGenomicCodingStart(15)
+                .setGenomicCodingEnd(45)
+                .setCdsLength(33)
+                .setProteinId(protein1)
+                .setExons(Arrays.asList(new Exon().setStart(15).setEnd(30)));
+
+        Transcript transcript2 = new Transcript()
+                .setId(trans2)
+                .setChromosome("1")
+                .setStart(18)
+                .setEnd(48)
+                .setStrand("+")
+                .setCdnaCodingEnd(30)
+                .setCdnaSequence(_10_GCC)
+                .setProteinSequence(_9_A)
+                .setGenomicCodingStart(18)
+                .setGenomicCodingEnd(48)
+                .setCdsLength(33)
+                .setProteinId(protein2)
+                .setExons(Arrays.asList(new Exon().setStart(15).setEnd(30)));
+
+        Transcript transcript3 = new Transcript()
+                .setId(trans3)
+                .setChromosome("1")
+                .setStart(21)
+                .setEnd(51)
+                .setStrand("+")
+                .setCdnaCodingEnd(30)
+                .setCdnaSequence(_10_GCC)
+                .setProteinSequence(_9_A)
+                .setGenomicCodingStart(21)
+                .setGenomicCodingEnd(51)
+                .setCdsLength(33)
+                .setProteinId(protein3)
+                .setExons(Arrays.asList(new Exon().setStart(15).setEnd(30)));
+
+
+        Gene gene = new Gene()
+                .setId(gene1)
+                .setTranscripts(Arrays.asList(transcript1, transcript2, transcript3));
+
+        Variant variant = Variant.newBuilder("1", 22, 22, "C", "G").build();
+        variant.setType(VariantType.SNV);
+
+        assertEquals(Arrays.asList(
+                trans1 + "(" + gene1 + "):c.22C>G",
+                protein1 + ":p.Arg8Gly",
+                trans2 + "(" + gene1 + "):c.22C>G",
+                protein2 + ":p.Arg8Gly",
+                trans3 + "(" + gene1 + "):c.22C>G",
+                protein3 + ":p.Arg8Gly"
+        ), hgvsCalculator.run(variant, Arrays.asList(gene), false));
+    }
+}